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.GeneticCodeI;
  28 import jalview.analysis.ParseProperties;
  29 import jalview.analysis.SequenceIdMatcher;
  30 import jalview.api.AlignExportSettingI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.SimilarityParamsI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.HiddenColumns;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.io.AlignmentProperties;
  67 import jalview.io.AnnotationFile;
  68 import jalview.io.BackupFiles;
  69 import jalview.io.BioJsHTMLOutput;
  70 import jalview.io.DataSourceType;
  71 import jalview.io.FileFormat;
  72 import jalview.io.FileFormatI;
  73 import jalview.io.FileFormats;
  74 import jalview.io.FileLoader;
  75 import jalview.io.FileParse;
  76 import jalview.io.FormatAdapter;
  77 import jalview.io.HtmlSvgOutput;
  78 import jalview.io.IdentifyFile;
  79 import jalview.io.JPredFile;
  80 import jalview.io.JalviewFileChooser;
  81 import jalview.io.JalviewFileView;
  82 import jalview.io.JnetAnnotationMaker;
  83 import jalview.io.NewickFile;
  84 import jalview.io.ScoreMatrixFile;
  85 import jalview.io.TCoffeeScoreFile;
  86 import jalview.io.vcf.VCFLoader;
  87 import jalview.jbgui.GAlignFrame;
  88 import jalview.schemes.ColourSchemeI;
  89 import jalview.schemes.ColourSchemes;
  90 import jalview.schemes.ResidueColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.util.MessageManager;
  93 import jalview.viewmodel.AlignmentViewport;
  94 import jalview.viewmodel.ViewportRanges;
  95 import jalview.ws.DBRefFetcher;
  96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Component;
 104 import java.awt.Rectangle;
 105 import java.awt.Toolkit;
 106 import java.awt.datatransfer.Clipboard;
 107 import java.awt.datatransfer.DataFlavor;
 108 import java.awt.datatransfer.StringSelection;
 109 import java.awt.datatransfer.Transferable;
 110 import java.awt.dnd.DnDConstants;
 111 import java.awt.dnd.DropTargetDragEvent;
 112 import java.awt.dnd.DropTargetDropEvent;
 113 import java.awt.dnd.DropTargetEvent;
 114 import java.awt.dnd.DropTargetListener;
 115 import java.awt.event.ActionEvent;
 116 import java.awt.event.ActionListener;
 117 import java.awt.event.FocusAdapter;
 118 import java.awt.event.FocusEvent;
 119 import java.awt.event.ItemEvent;
 120 import java.awt.event.ItemListener;
 121 import java.awt.event.KeyAdapter;
 122 import java.awt.event.KeyEvent;
 123 import java.awt.event.MouseEvent;
 124 import java.awt.print.PageFormat;
 125 import java.awt.print.PrinterJob;
 126 import java.beans.PropertyChangeEvent;
 127 import java.io.File;
 128 import java.io.FileWriter;
 129 import java.io.PrintWriter;
 130 import java.net.URL;
 131 import java.util.ArrayList;
 132 import java.util.Arrays;
 133 import java.util.Deque;
 134 import java.util.Enumeration;
 135 import java.util.Hashtable;
 136 import java.util.List;
 137 import java.util.Vector;
 138
 139 import javax.swing.JCheckBoxMenuItem;
 140 import javax.swing.JEditorPane;
 141 import javax.swing.JInternalFrame;
 142 import javax.swing.JLayeredPane;
 143 import javax.swing.JMenu;
 144 import javax.swing.JMenuItem;
 145 import javax.swing.JScrollPane;
 146 import javax.swing.SwingUtilities;
 147
 148 /**
 149  * DOCUMENT ME!
 150  *
 151  * @author $author$
 152  * @version $Revision$
 153  */
 154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 155         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 156 {
 157
 158   public static final int DEFAULT_WIDTH = 700;
 159
 160   public static final int DEFAULT_HEIGHT = 500;
 161
 162   /*
 163    * The currently displayed panel (selected tabbed view if more than one)
 164    */
 165   public AlignmentPanel alignPanel;
 166
 167   AlignViewport viewport;
 168
 169   public AlignViewControllerI avc;
 170
 171   List<AlignmentPanel> alignPanels = new ArrayList<>();
 172
 173   /**
 174    * Last format used to load or save alignments in this window
 175    */
 176   FileFormatI currentFileFormat = null;
 177
 178   /**
 179    * Current filename for this alignment
 180    */
 181   String fileName = null;
 182
 183   /**
 184    * Creates a new AlignFrame object with specific width and height.
 185    *
 186    * @param al
 187    * @param width
 188    * @param height
 189    */
 190   public AlignFrame(AlignmentI al, int width, int height)
 191   {
 192     this(al, null, width, height);
 193   }
 194
 195   /**
 196    * Creates a new AlignFrame object with specific width, height and
 197    * sequenceSetId
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    * @param sequenceSetId
 203    */
 204   public AlignFrame(AlignmentI al, int width, int height,
 205           String sequenceSetId)
 206   {
 207     this(al, null, width, height, sequenceSetId);
 208   }
 209
 210   /**
 211    * Creates a new AlignFrame object with specific width, height and
 212    * sequenceSetId
 213    *
 214    * @param al
 215    * @param width
 216    * @param height
 217    * @param sequenceSetId
 218    * @param viewId
 219    */
 220   public AlignFrame(AlignmentI al, int width, int height,
 221           String sequenceSetId, String viewId)
 222   {
 223     this(al, null, width, height, sequenceSetId, viewId);
 224   }
 225
 226   /**
 227    * new alignment window with hidden columns
 228    *
 229    * @param al
 230    *          AlignmentI
 231    * @param hiddenColumns
 232    *          ColumnSelection or null
 233    * @param width
 234    *          Width of alignment frame
 235    * @param height
 236    *          height of frame.
 237    */
 238   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 239           int height)
 240   {
 241     this(al, hiddenColumns, width, height, null);
 242   }
 243
 244   /**
 245    * Create alignment frame for al with hiddenColumns, a specific width and
 246    * height, and specific sequenceId
 247    *
 248    * @param al
 249    * @param hiddenColumns
 250    * @param width
 251    * @param height
 252    * @param sequenceSetId
 253    *          (may be null)
 254    */
 255   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 256           int height, String sequenceSetId)
 257   {
 258     this(al, hiddenColumns, width, height, sequenceSetId, null);
 259   }
 260
 261   /**
 262    * Create alignment frame for al with hiddenColumns, a specific width and
 263    * height, and specific sequenceId
 264    *
 265    * @param al
 266    * @param hiddenColumns
 267    * @param width
 268    * @param height
 269    * @param sequenceSetId
 270    *          (may be null)
 271    * @param viewId
 272    *          (may be null)
 273    */
 274   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 275           int height, String sequenceSetId, String viewId)
 276   {
 277     setSize(width, height);
 278
 279     if (al.getDataset() == null)
 280     {
 281       al.setDataset(null);
 282     }
 283
 284     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 285
 286     alignPanel = new AlignmentPanel(this, viewport);
 287
 288     addAlignmentPanel(alignPanel, true);
 289     init();
 290   }
 291
 292   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 293           HiddenColumns hiddenColumns, int width, int height)
 294   {
 295     setSize(width, height);
 296
 297     if (al.getDataset() == null)
 298     {
 299       al.setDataset(null);
 300     }
 301
 302     viewport = new AlignViewport(al, hiddenColumns);
 303
 304     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 305     {
 306       viewport.hideSequence(hiddenSeqs);
 307     }
 308     alignPanel = new AlignmentPanel(this, viewport);
 309     addAlignmentPanel(alignPanel, true);
 310     init();
 311   }
 312
 313   /**
 314    * Make a new AlignFrame from existing alignmentPanels
 315    *
 316    * @param ap
 317    *          AlignmentPanel
 318    * @param av
 319    *          AlignViewport
 320    */
 321   public AlignFrame(AlignmentPanel ap)
 322   {
 323     viewport = ap.av;
 324     alignPanel = ap;
 325     addAlignmentPanel(ap, false);
 326     init();
 327   }
 328
 329   /**
 330    * initalise the alignframe from the underlying viewport data and the
 331    * configurations
 332    */
 333   void init()
 334   {
 335     if (!Jalview.isHeadlessMode())
 336     {
 337       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 338     }
 339
 340     avc = new jalview.controller.AlignViewController(this, viewport,
 341             alignPanel);
 342     if (viewport.getAlignmentConservationAnnotation() == null)
 343     {
 344       // BLOSUM62Colour.setEnabled(false);
 345       conservationMenuItem.setEnabled(false);
 346       modifyConservation.setEnabled(false);
 347       // PIDColour.setEnabled(false);
 348       // abovePIDThreshold.setEnabled(false);
 349       // modifyPID.setEnabled(false);
 350     }
 351
 352     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 353             "No sort");
 354
 355     if (sortby.equals("Id"))
 356     {
 357       sortIDMenuItem_actionPerformed(null);
 358     }
 359     else if (sortby.equals("Pairwise Identity"))
 360     {
 361       sortPairwiseMenuItem_actionPerformed(null);
 362     }
 363
 364     this.alignPanel.av
 365             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 366
 367     setMenusFromViewport(viewport);
 368     buildSortByAnnotationScoresMenu();
 369     calculateTree.addActionListener(new ActionListener()
 370     {
 371
 372       @Override
 373       public void actionPerformed(ActionEvent e)
 374       {
 375         openTreePcaDialog();
 376       }
 377     });
 378     buildColourMenu();
 379
 380     if (Desktop.desktop != null)
 381     {
 382       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 383       addServiceListeners();
 384       setGUINucleotide();
 385     }
 386
 387     if (viewport.getWrapAlignment())
 388     {
 389       wrapMenuItem_actionPerformed(null);
 390     }
 391
 392     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 393     {
 394       this.overviewMenuItem_actionPerformed(null);
 395     }
 396
 397     addKeyListener();
 398
 399     final List<AlignmentPanel> selviews = new ArrayList<>();
 400     final List<AlignmentPanel> origview = new ArrayList<>();
 401     final String menuLabel = MessageManager
 402             .getString("label.copy_format_from");
 403     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 404             new ViewSetProvider()
 405             {
 406
 407               @Override
 408               public AlignmentPanel[] getAllAlignmentPanels()
 409               {
 410                 origview.clear();
 411                 origview.add(alignPanel);
 412                 // make an array of all alignment panels except for this one
 413                 List<AlignmentPanel> aps = new ArrayList<>(
 414                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 415                 aps.remove(AlignFrame.this.alignPanel);
 416                 return aps.toArray(new AlignmentPanel[aps.size()]);
 417               }
 418             }, selviews, new ItemListener()
 419             {
 420
 421               @Override
 422               public void itemStateChanged(ItemEvent e)
 423               {
 424                 if (origview.size() > 0)
 425                 {
 426                   final AlignmentPanel ap = origview.get(0);
 427
 428                   /*
 429                    * Copy the ViewStyle of the selected panel to 'this one'.
 430                    * Don't change value of 'scaleProteinAsCdna' unless copying
 431                    * from a SplitFrame.
 432                    */
 433                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 434                           .getViewStyle();
 435                   boolean fromSplitFrame = selviews.get(0)
 436                           .getAlignViewport().getCodingComplement() != null;
 437                   if (!fromSplitFrame)
 438                   {
 439                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 440                             .getViewStyle().isScaleProteinAsCdna());
 441                   }
 442                   ap.getAlignViewport().setViewStyle(vs);
 443
 444                   /*
 445                    * Also rescale ViewStyle of SplitFrame complement if there is
 446                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 447                    * the whole ViewStyle (allow cDNA protein to have different
 448                    * fonts)
 449                    */
 450                   AlignViewportI complement = ap.getAlignViewport()
 451                           .getCodingComplement();
 452                   if (complement != null && vs.isScaleProteinAsCdna())
 453                   {
 454                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 455                     ((SplitFrame) af.getSplitViewContainer())
 456                             .adjustLayout();
 457                     af.setMenusForViewport();
 458                   }
 459
 460                   ap.updateLayout();
 461                   ap.setSelected(true);
 462                   ap.alignFrame.setMenusForViewport();
 463
 464                 }
 465               }
 466             });
 467     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 468             .indexOf("devel") > -1
 469             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 470                     .indexOf("test") > -1)
 471     {
 472       formatMenu.add(vsel);
 473     }
 474     addFocusListener(new FocusAdapter()
 475     {
 476       @Override
 477       public void focusGained(FocusEvent e)
 478       {
 479         Jalview.setCurrentAlignFrame(AlignFrame.this);
 480       }
 481     });
 482
 483   }
 484
 485   /**
 486    * Change the filename and format for the alignment, and enable the 'reload'
 487    * button functionality.
 488    *
 489    * @param file
 490    *          valid filename
 491    * @param format
 492    *          format of file
 493    */
 494   public void setFileName(String file, FileFormatI format)
 495   {
 496     fileName = file;
 497     setFileFormat(format);
 498     reload.setEnabled(true);
 499   }
 500
 501   /**
 502    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 503    * events
 504    */
 505   void addKeyListener()
 506   {
 507     addKeyListener(new KeyAdapter()
 508     {
 509       @Override
 510       public void keyPressed(KeyEvent evt)
 511       {
 512         if (viewport.cursorMode
 513                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 514                         && evt.getKeyCode() <= KeyEvent.VK_9)
 515                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 516                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 517                 && Character.isDigit(evt.getKeyChar()))
 518         {
 519           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 520         }
 521
 522         switch (evt.getKeyCode())
 523         {
 524
 525         case 27: // escape key
 526           deselectAllSequenceMenuItem_actionPerformed(null);
 527
 528           break;
 529
 530         case KeyEvent.VK_DOWN:
 531           if (evt.isAltDown() || !viewport.cursorMode)
 532           {
 533             moveSelectedSequences(false);
 534           }
 535           if (viewport.cursorMode)
 536           {
 537             alignPanel.getSeqPanel().moveCursor(0, 1);
 538           }
 539           break;
 540
 541         case KeyEvent.VK_UP:
 542           if (evt.isAltDown() || !viewport.cursorMode)
 543           {
 544             moveSelectedSequences(true);
 545           }
 546           if (viewport.cursorMode)
 547           {
 548             alignPanel.getSeqPanel().moveCursor(0, -1);
 549           }
 550
 551           break;
 552
 553         case KeyEvent.VK_LEFT:
 554           if (evt.isAltDown() || !viewport.cursorMode)
 555           {
 556             slideSequences(false,
 557                     alignPanel.getSeqPanel().getKeyboardNo1());
 558           }
 559           else
 560           {
 561             alignPanel.getSeqPanel().moveCursor(-1, 0);
 562           }
 563
 564           break;
 565
 566         case KeyEvent.VK_RIGHT:
 567           if (evt.isAltDown() || !viewport.cursorMode)
 568           {
 569             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 570           }
 571           else
 572           {
 573             alignPanel.getSeqPanel().moveCursor(1, 0);
 574           }
 575           break;
 576
 577         case KeyEvent.VK_SPACE:
 578           if (viewport.cursorMode)
 579           {
 580             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 581                     || evt.isShiftDown() || evt.isAltDown());
 582           }
 583           break;
 584
 585         // case KeyEvent.VK_A:
 586         // if (viewport.cursorMode)
 587         // {
 588         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 589         // //System.out.println("A");
 590         // }
 591         // break;
 592         /*
 593          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 594          * System.out.println("closing bracket"); } break;
 595          */
 596         case KeyEvent.VK_DELETE:
 597         case KeyEvent.VK_BACK_SPACE:
 598           if (!viewport.cursorMode)
 599           {
 600             cut_actionPerformed(null);
 601           }
 602           else
 603           {
 604             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 605                     || evt.isShiftDown() || evt.isAltDown());
 606           }
 607
 608           break;
 609
 610         case KeyEvent.VK_S:
 611           if (viewport.cursorMode)
 612           {
 613             alignPanel.getSeqPanel().setCursorRow();
 614           }
 615           break;
 616         case KeyEvent.VK_C:
 617           if (viewport.cursorMode && !evt.isControlDown())
 618           {
 619             alignPanel.getSeqPanel().setCursorColumn();
 620           }
 621           break;
 622         case KeyEvent.VK_P:
 623           if (viewport.cursorMode)
 624           {
 625             alignPanel.getSeqPanel().setCursorPosition();
 626           }
 627           break;
 628
 629         case KeyEvent.VK_ENTER:
 630         case KeyEvent.VK_COMMA:
 631           if (viewport.cursorMode)
 632           {
 633             alignPanel.getSeqPanel().setCursorRowAndColumn();
 634           }
 635           break;
 636
 637         case KeyEvent.VK_Q:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 641           }
 642           break;
 643         case KeyEvent.VK_M:
 644           if (viewport.cursorMode)
 645           {
 646             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 647           }
 648           break;
 649
 650         case KeyEvent.VK_F2:
 651           viewport.cursorMode = !viewport.cursorMode;
 652           statusBar.setText(MessageManager
 653                   .formatMessage("label.keyboard_editing_mode", new String[]
 654                   { (viewport.cursorMode ? "on" : "off") }));
 655           if (viewport.cursorMode)
 656           {
 657             ViewportRanges ranges = viewport.getRanges();
 658             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 659                     .getStartRes();
 660             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 661                     .getStartSeq();
 662           }
 663           alignPanel.getSeqPanel().seqCanvas.repaint();
 664           break;
 665
 666         case KeyEvent.VK_F1:
 667           try
 668           {
 669             Help.showHelpWindow();
 670           } catch (Exception ex)
 671           {
 672             ex.printStackTrace();
 673           }
 674           break;
 675         case KeyEvent.VK_H:
 676         {
 677           boolean toggleSeqs = !evt.isControlDown();
 678           boolean toggleCols = !evt.isShiftDown();
 679           toggleHiddenRegions(toggleSeqs, toggleCols);
 680           break;
 681         }
 682         case KeyEvent.VK_B:
 683         {
 684           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 685           boolean modifyExisting = true; // always modify, don't clear
 686                                          // evt.isShiftDown();
 687           boolean invertHighlighted = evt.isAltDown();
 688           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 689                   toggleSel);
 690           break;
 691         }
 692         case KeyEvent.VK_PAGE_UP:
 693           viewport.getRanges().pageUp();
 694           break;
 695         case KeyEvent.VK_PAGE_DOWN:
 696           viewport.getRanges().pageDown();
 697           break;
 698         }
 699       }
 700
 701       @Override
 702       public void keyReleased(KeyEvent evt)
 703       {
 704         switch (evt.getKeyCode())
 705         {
 706         case KeyEvent.VK_LEFT:
 707           if (evt.isAltDown() || !viewport.cursorMode)
 708           {
 709             viewport.firePropertyChange("alignment", null,
 710                     viewport.getAlignment().getSequences());
 711           }
 712           break;
 713
 714         case KeyEvent.VK_RIGHT:
 715           if (evt.isAltDown() || !viewport.cursorMode)
 716           {
 717             viewport.firePropertyChange("alignment", null,
 718                     viewport.getAlignment().getSequences());
 719           }
 720           break;
 721         }
 722       }
 723     });
 724   }
 725
 726   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 727   {
 728     ap.alignFrame = this;
 729     avc = new jalview.controller.AlignViewController(this, viewport,
 730             alignPanel);
 731
 732     alignPanels.add(ap);
 733
 734     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 735
 736     int aSize = alignPanels.size();
 737
 738     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 739
 740     if (aSize == 1 && ap.av.getViewName() == null)
 741     {
 742       this.getContentPane().add(ap, BorderLayout.CENTER);
 743     }
 744     else
 745     {
 746       if (aSize == 2)
 747       {
 748         setInitialTabVisible();
 749       }
 750
 751       expandViews.setEnabled(true);
 752       gatherViews.setEnabled(true);
 753       tabbedPane.addTab(ap.av.getViewName(), ap);
 754
 755       ap.setVisible(false);
 756     }
 757
 758     if (newPanel)
 759     {
 760       if (ap.av.isPadGaps())
 761       {
 762         ap.av.getAlignment().padGaps();
 763       }
 764       ap.av.updateConservation(ap);
 765       ap.av.updateConsensus(ap);
 766       ap.av.updateStrucConsensus(ap);
 767     }
 768   }
 769
 770   public void setInitialTabVisible()
 771   {
 772     expandViews.setEnabled(true);
 773     gatherViews.setEnabled(true);
 774     tabbedPane.setVisible(true);
 775     AlignmentPanel first = alignPanels.get(0);
 776     tabbedPane.addTab(first.av.getViewName(), first);
 777     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 778   }
 779
 780   public AlignViewport getViewport()
 781   {
 782     return viewport;
 783   }
 784
 785   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 786   private void addServiceListeners()
 787   {
 788     final java.beans.PropertyChangeListener thisListener;
 789     Desktop.instance.addJalviewPropertyChangeListener("services",
 790             thisListener = new java.beans.PropertyChangeListener()
 791             {
 792               @Override
 793               public void propertyChange(PropertyChangeEvent evt)
 794               {
 795                 // // System.out.println("Discoverer property change.");
 796                 // if (evt.getPropertyName().equals("services"))
 797                 {
 798                   SwingUtilities.invokeLater(new Runnable()
 799                   {
 800
 801                     @Override
 802                     public void run()
 803                     {
 804                       System.err.println(
 805                               "Rebuild WS Menu for service change");
 806                       BuildWebServiceMenu();
 807                     }
 808
 809                   });
 810                 }
 811               }
 812             });
 813     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 814     {
 815       @Override
 816       public void internalFrameClosed(
 817               javax.swing.event.InternalFrameEvent evt)
 818       {
 819         // System.out.println("deregistering discoverer listener");
 820         Desktop.instance.removeJalviewPropertyChangeListener("services",
 821                 thisListener);
 822         closeMenuItem_actionPerformed(true);
 823       };
 824     });
 825     // Finally, build the menu once to get current service state
 826     new Thread(new Runnable()
 827     {
 828       @Override
 829       public void run()
 830       {
 831         BuildWebServiceMenu();
 832       }
 833     }).start();
 834   }
 835
 836   /**
 837    * Configure menu items that vary according to whether the alignment is
 838    * nucleotide or protein
 839    */
 840   public void setGUINucleotide()
 841   {
 842     AlignmentI al = getViewport().getAlignment();
 843     boolean nucleotide = al.isNucleotide();
 844
 845     loadVcf.setVisible(nucleotide);
 846     showTranslation.setVisible(nucleotide);
 847     showReverse.setVisible(nucleotide);
 848     showReverseComplement.setVisible(nucleotide);
 849     conservationMenuItem.setEnabled(!nucleotide);
 850     modifyConservation
 851             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 852     showGroupConservation.setEnabled(!nucleotide);
 853
 854     showComplementMenuItem
 855             .setText(nucleotide ? MessageManager.getString("label.protein")
 856                     : MessageManager.getString("label.nucleotide"));
 857   }
 858
 859   /**
 860    * set up menus for the current viewport. This may be called after any
 861    * operation that affects the data in the current view (selection changed,
 862    * etc) to update the menus to reflect the new state.
 863    */
 864   @Override
 865   public void setMenusForViewport()
 866   {
 867     setMenusFromViewport(viewport);
 868   }
 869
 870   /**
 871    * Need to call this method when tabs are selected for multiple views, or when
 872    * loading from Jalview2XML.java
 873    *
 874    * @param av
 875    *          AlignViewport
 876    */
 877   public void setMenusFromViewport(AlignViewport av)
 878   {
 879     padGapsMenuitem.setSelected(av.isPadGaps());
 880     colourTextMenuItem.setSelected(av.isShowColourText());
 881     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 882     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 883     conservationMenuItem.setSelected(av.getConservationSelected());
 884     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 885     seqLimits.setSelected(av.getShowJVSuffix());
 886     idRightAlign.setSelected(av.isRightAlignIds());
 887     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 888     renderGapsMenuItem.setSelected(av.isRenderGaps());
 889     wrapMenuItem.setSelected(av.getWrapAlignment());
 890     scaleAbove.setVisible(av.getWrapAlignment());
 891     scaleLeft.setVisible(av.getWrapAlignment());
 892     scaleRight.setVisible(av.getWrapAlignment());
 893     annotationPanelMenuItem.setState(av.isShowAnnotation());
 894     /*
 895      * Show/hide annotations only enabled if annotation panel is shown
 896      */
 897     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 901     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 902     viewTextMenuItem.setSelected(av.getShowText());
 903     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 904     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 905     showGroupConservation.setSelected(av.isShowGroupConservation());
 906     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 907     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 908     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 909
 910     ColourMenuHelper.setColourSelected(colourMenu,
 911             av.getGlobalColourScheme());
 912
 913     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 914     hiddenMarkers.setState(av.getShowHiddenMarkers());
 915     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 916     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 917     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 918     autoCalculate.setSelected(av.autoCalculateConsensus);
 919     sortByTree.setSelected(av.sortByTree);
 920     listenToViewSelections.setSelected(av.followSelection);
 921
 922     showProducts.setEnabled(canShowProducts());
 923     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 924
 925     updateEditMenuBar();
 926   }
 927
 928   /**
 929    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 930    *
 931    * @param b
 932    */
 933   public void setGroovyEnabled(boolean b)
 934   {
 935     runGroovy.setEnabled(b);
 936   }
 937
 938   private IProgressIndicator progressBar;
 939
 940   /*
 941    * (non-Javadoc)
 942    *
 943    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 944    */
 945   @Override
 946   public void setProgressBar(String message, long id)
 947   {
 948     progressBar.setProgressBar(message, id);
 949   }
 950
 951   @Override
 952   public void registerHandler(final long id,
 953           final IProgressIndicatorHandler handler)
 954   {
 955     progressBar.registerHandler(id, handler);
 956   }
 957
 958   /**
 959    *
 960    * @return true if any progress bars are still active
 961    */
 962   @Override
 963   public boolean operationInProgress()
 964   {
 965     return progressBar.operationInProgress();
 966   }
 967
 968   /**
 969    * Sets the text of the status bar. Note that setting a null or empty value
 970    * will cause the status bar to be hidden, with possibly undesirable flicker
 971    * of the screen layout.
 972    */
 973   @Override
 974   public void setStatus(String text)
 975   {
 976     statusBar.setText(text);
 977   }
 978
 979   /*
 980    * Added so Castor Mapping file can obtain Jalview Version
 981    */
 982   public String getVersion()
 983   {
 984     return jalview.bin.Cache.getProperty("VERSION");
 985   }
 986
 987   public FeatureRenderer getFeatureRenderer()
 988   {
 989     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 990   }
 991
 992   @Override
 993   public void fetchSequence_actionPerformed(ActionEvent e)
 994   {
 995     new jalview.gui.SequenceFetcher(this);
 996   }
 997
 998   @Override
 999   public void addFromFile_actionPerformed(ActionEvent e)
1000   {
1001     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1002   }
1003
1004   @Override
1005   public void reload_actionPerformed(ActionEvent e)
1006   {
1007     if (fileName != null)
1008     {
1009       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1010       // originating file's format
1011       // TODO: work out how to recover feature settings for correct view(s) when
1012       // file is reloaded.
1013       if (FileFormat.Jalview.equals(currentFileFormat))
1014       {
1015         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1016         for (int i = 0; i < frames.length; i++)
1017         {
1018           if (frames[i] instanceof AlignFrame && frames[i] != this
1019                   && ((AlignFrame) frames[i]).fileName != null
1020                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1021           {
1022             try
1023             {
1024               frames[i].setSelected(true);
1025               Desktop.instance.closeAssociatedWindows();
1026             } catch (java.beans.PropertyVetoException ex)
1027             {
1028             }
1029           }
1030
1031         }
1032         Desktop.instance.closeAssociatedWindows();
1033
1034         FileLoader loader = new FileLoader();
1035         DataSourceType protocol = fileName.startsWith("http:")
1036                 ? DataSourceType.URL
1037                 : DataSourceType.FILE;
1038         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1039       }
1040       else
1041       {
1042         Rectangle bounds = this.getBounds();
1043
1044         FileLoader loader = new FileLoader();
1045         DataSourceType protocol = fileName.startsWith("http:")
1046                 ? DataSourceType.URL
1047                 : DataSourceType.FILE;
1048         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1049                 protocol, currentFileFormat);
1050
1051         newframe.setBounds(bounds);
1052         if (featureSettings != null && featureSettings.isShowing())
1053         {
1054           final Rectangle fspos = featureSettings.frame.getBounds();
1055           // TODO: need a 'show feature settings' function that takes bounds -
1056           // need to refactor Desktop.addFrame
1057           newframe.featureSettings_actionPerformed(null);
1058           final FeatureSettings nfs = newframe.featureSettings;
1059           SwingUtilities.invokeLater(new Runnable()
1060           {
1061             @Override
1062             public void run()
1063             {
1064               nfs.frame.setBounds(fspos);
1065             }
1066           });
1067           this.featureSettings.close();
1068           this.featureSettings = null;
1069         }
1070         this.closeMenuItem_actionPerformed(true);
1071       }
1072     }
1073   }
1074
1075   @Override
1076   public void addFromText_actionPerformed(ActionEvent e)
1077   {
1078     Desktop.instance
1079             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1080   }
1081
1082   @Override
1083   public void addFromURL_actionPerformed(ActionEvent e)
1084   {
1085     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1086   }
1087
1088   @Override
1089   public void save_actionPerformed(ActionEvent e)
1090   {
1091     if (fileName == null || (currentFileFormat == null)
1092             || fileName.startsWith("http"))
1093     {
1094       saveAs_actionPerformed(null);
1095     }
1096     else
1097     {
1098       saveAlignment(fileName, currentFileFormat);
1099     }
1100   }
1101
1102   /**
1103    * DOCUMENT ME!
1104    *
1105    * @param e
1106    *          DOCUMENT ME!
1107    */
1108   @Override
1109   public void saveAs_actionPerformed(ActionEvent e)
1110   {
1111     String format = currentFileFormat == null ? null
1112             : currentFileFormat.getName();
1113     JalviewFileChooser chooser = JalviewFileChooser
1114             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1115
1116     chooser.setFileView(new JalviewFileView());
1117     chooser.setDialogTitle(
1118             MessageManager.getString("label.save_alignment_to_file"));
1119     chooser.setToolTipText(MessageManager.getString("action.save"));
1120
1121     int value = chooser.showSaveDialog(this);
1122
1123     if (value == JalviewFileChooser.APPROVE_OPTION)
1124     {
1125       currentFileFormat = chooser.getSelectedFormat();
1126       while (currentFileFormat == null)
1127       {
1128         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1129                 MessageManager.getString(
1130                         "label.select_file_format_before_saving"),
1131                 MessageManager.getString("label.file_format_not_specified"),
1132                 JvOptionPane.WARNING_MESSAGE);
1133         currentFileFormat = chooser.getSelectedFormat();
1134         value = chooser.showSaveDialog(this);
1135         if (value != JalviewFileChooser.APPROVE_OPTION)
1136         {
1137           return;
1138         }
1139       }
1140
1141       fileName = chooser.getSelectedFile().getPath();
1142
1143       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1144
1145       Cache.setProperty("LAST_DIRECTORY", fileName);
1146       saveAlignment(fileName, currentFileFormat);
1147     }
1148   }
1149
1150   public boolean saveAlignment(String file, FileFormatI format)
1151   {
1152     boolean success = true;
1153
1154     if (FileFormat.Jalview.equals(format))
1155     {
1156       String shortName = title;
1157
1158       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1159       {
1160         shortName = shortName.substring(
1161                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1162       }
1163
1164       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1165               shortName);
1166
1167       statusBar.setText(MessageManager.formatMessage(
1168               "label.successfully_saved_to_file_in_format", new Object[]
1169               { fileName, format }));
1170
1171     }
1172     else
1173     {
1174       AlignmentExportData exportData = getAlignmentForExport(format,
1175               viewport, null);
1176       if (exportData.getSettings().isCancelled())
1177       {
1178         return false;
1179       }
1180       FormatAdapter f = new FormatAdapter(alignPanel,
1181               exportData.getSettings());
1182       String output = f.formatSequences(format, exportData.getAlignment(), // class
1183                                                                            // cast
1184                                                                            // exceptions
1185                                                                            // will
1186               // occur in the distant future
1187               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1188               f.getCacheSuffixDefault(format),
1189               viewport.getAlignment().getHiddenColumns());
1190
1191       if (output == null)
1192       {
1193         success = false;
1194       }
1195       else
1196       {
1197         // create backupfiles object and get new temp filename destination
1198         BackupFiles backupfiles = new BackupFiles(file);
1199
1200         try
1201         {
1202           PrintWriter out = new PrintWriter(
1203                   new FileWriter(backupfiles.getTempFilePath()));
1204
1205           out.print(output);
1206           out.close();
1207           this.setTitle(file);
1208           statusBar.setText(MessageManager.formatMessage(
1209                   "label.successfully_saved_to_file_in_format", new Object[]
1210                   { fileName, format.getName() }));
1211         } catch (Exception ex)
1212         {
1213           success = false;
1214           ex.printStackTrace();
1215         }
1216
1217         backupfiles.setWriteSuccess(success);
1218         // do the backup file roll and rename the temp file to actual file
1219         success = backupfiles.rollBackupsAndRenameTempFile();
1220
1221       }
1222     }
1223
1224     if (!success)
1225     {
1226       JvOptionPane.showInternalMessageDialog(this, MessageManager
1227               .formatMessage("label.couldnt_save_file", new Object[]
1228               { fileName }),
1229               MessageManager.getString("label.error_saving_file"),
1230               JvOptionPane.WARNING_MESSAGE);
1231     }
1232
1233     return success;
1234   }
1235
1236   private void warningMessage(String warning, String title)
1237   {
1238     if (new jalview.util.Platform().isHeadless())
1239     {
1240       System.err.println("Warning: " + title + "\nWarning: " + warning);
1241
1242     }
1243     else
1244     {
1245       JvOptionPane.showInternalMessageDialog(this, warning, title,
1246               JvOptionPane.WARNING_MESSAGE);
1247     }
1248     return;
1249   }
1250
1251   /**
1252    * DOCUMENT ME!
1253    *
1254    * @param e
1255    *          DOCUMENT ME!
1256    */
1257   @Override
1258   protected void outputText_actionPerformed(ActionEvent e)
1259   {
1260     FileFormatI fileFormat = FileFormats.getInstance()
1261             .forName(e.getActionCommand());
1262     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1263             viewport, null);
1264     if (exportData.getSettings().isCancelled())
1265     {
1266       return;
1267     }
1268     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1269     cap.setForInput(null);
1270     try
1271     {
1272       FileFormatI format = fileFormat;
1273       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1274               .formatSequences(format, exportData.getAlignment(),
1275                       exportData.getOmitHidden(),
1276                       exportData.getStartEndPostions(),
1277                       viewport.getAlignment().getHiddenColumns()));
1278       Desktop.addInternalFrame(cap, MessageManager
1279               .formatMessage("label.alignment_output_command", new Object[]
1280               { e.getActionCommand() }), 600, 500);
1281     } catch (OutOfMemoryError oom)
1282     {
1283       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1284               oom);
1285       cap.dispose();
1286     }
1287
1288   }
1289
1290   public static AlignmentExportData getAlignmentForExport(
1291           FileFormatI format, AlignViewportI viewport,
1292           AlignExportSettingI exportSettings)
1293   {
1294     AlignmentI alignmentToExport = null;
1295     AlignExportSettingI settings = exportSettings;
1296     String[] omitHidden = null;
1297
1298     HiddenSequences hiddenSeqs = viewport.getAlignment()
1299             .getHiddenSequences();
1300
1301     alignmentToExport = viewport.getAlignment();
1302
1303     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1304     if (settings == null)
1305     {
1306       settings = new AlignExportSettings(hasHiddenSeqs,
1307               viewport.hasHiddenColumns(), format);
1308     }
1309     // settings.isExportAnnotations();
1310
1311     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1312     {
1313       omitHidden = viewport.getViewAsString(false,
1314               settings.isExportHiddenSequences());
1315     }
1316
1317     int[] alignmentStartEnd = new int[2];
1318     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1319     {
1320       alignmentToExport = hiddenSeqs.getFullAlignment();
1321     }
1322     else
1323     {
1324       alignmentToExport = viewport.getAlignment();
1325     }
1326     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1327             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1328     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1329             omitHidden, alignmentStartEnd, settings);
1330     return ed;
1331   }
1332
1333   /**
1334    * DOCUMENT ME!
1335    *
1336    * @param e
1337    *          DOCUMENT ME!
1338    */
1339   @Override
1340   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1341   {
1342     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1343     htmlSVG.exportHTML(null);
1344   }
1345
1346   @Override
1347   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348   {
1349     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1350     bjs.exportHTML(null);
1351   }
1352
1353   public void createImageMap(File file, String image)
1354   {
1355     alignPanel.makePNGImageMap(file, image);
1356   }
1357
1358   /**
1359    * DOCUMENT ME!
1360    *
1361    * @param e
1362    *          DOCUMENT ME!
1363    */
1364   @Override
1365   public void createPNG(File f)
1366   {
1367     alignPanel.makePNG(f);
1368   }
1369
1370   /**
1371    * DOCUMENT ME!
1372    *
1373    * @param e
1374    *          DOCUMENT ME!
1375    */
1376   @Override
1377   public void createEPS(File f)
1378   {
1379     alignPanel.makeEPS(f);
1380   }
1381
1382   @Override
1383   public void createSVG(File f)
1384   {
1385     alignPanel.makeSVG(f);
1386   }
1387
1388   @Override
1389   public void pageSetup_actionPerformed(ActionEvent e)
1390   {
1391     PrinterJob printJob = PrinterJob.getPrinterJob();
1392     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1393   }
1394
1395   /**
1396    * DOCUMENT ME!
1397    *
1398    * @param e
1399    *          DOCUMENT ME!
1400    */
1401   @Override
1402   public void printMenuItem_actionPerformed(ActionEvent e)
1403   {
1404     // Putting in a thread avoids Swing painting problems
1405     PrintThread thread = new PrintThread(alignPanel);
1406     thread.start();
1407   }
1408
1409   @Override
1410   public void exportFeatures_actionPerformed(ActionEvent e)
1411   {
1412     new AnnotationExporter(alignPanel).exportFeatures();
1413   }
1414
1415   @Override
1416   public void exportAnnotations_actionPerformed(ActionEvent e)
1417   {
1418     new AnnotationExporter(alignPanel).exportAnnotations();
1419   }
1420
1421   @Override
1422   public void associatedData_actionPerformed(ActionEvent e)
1423   {
1424     // Pick the tree file
1425     JalviewFileChooser chooser = new JalviewFileChooser(
1426             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1427     chooser.setFileView(new JalviewFileView());
1428     chooser.setDialogTitle(
1429             MessageManager.getString("label.load_jalview_annotations"));
1430     chooser.setToolTipText(
1431             MessageManager.getString("label.load_jalview_annotations"));
1432
1433     int value = chooser.showOpenDialog(null);
1434
1435     if (value == JalviewFileChooser.APPROVE_OPTION)
1436     {
1437       String choice = chooser.getSelectedFile().getPath();
1438       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1439       loadJalviewDataFile(choice, null, null, null);
1440     }
1441
1442   }
1443
1444   /**
1445    * Close the current view or all views in the alignment frame. If the frame
1446    * only contains one view then the alignment will be removed from memory.
1447    *
1448    * @param closeAllTabs
1449    */
1450   @Override
1451   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452   {
1453     if (alignPanels != null && alignPanels.size() < 2)
1454     {
1455       closeAllTabs = true;
1456     }
1457
1458     try
1459     {
1460       if (alignPanels != null)
1461       {
1462         if (closeAllTabs)
1463         {
1464           if (this.isClosed())
1465           {
1466             // really close all the windows - otherwise wait till
1467             // setClosed(true) is called
1468             for (int i = 0; i < alignPanels.size(); i++)
1469             {
1470               AlignmentPanel ap = alignPanels.get(i);
1471               ap.closePanel();
1472             }
1473           }
1474         }
1475         else
1476         {
1477           closeView(alignPanel);
1478         }
1479       }
1480
1481       if (closeAllTabs)
1482       {
1483         /*
1484          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1485          * be called recursively, with the frame now in 'closed' state
1486          */
1487         this.setClosed(true);
1488       }
1489     } catch (Exception ex)
1490     {
1491       ex.printStackTrace();
1492     }
1493   }
1494
1495   /**
1496    * Close the specified panel and close up tabs appropriately.
1497    *
1498    * @param panelToClose
1499    */
1500   public void closeView(AlignmentPanel panelToClose)
1501   {
1502     int index = tabbedPane.getSelectedIndex();
1503     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1504     alignPanels.remove(panelToClose);
1505     panelToClose.closePanel();
1506     panelToClose = null;
1507
1508     tabbedPane.removeTabAt(closedindex);
1509     tabbedPane.validate();
1510
1511     if (index > closedindex || index == tabbedPane.getTabCount())
1512     {
1513       // modify currently selected tab index if necessary.
1514       index--;
1515     }
1516
1517     this.tabSelectionChanged(index);
1518   }
1519
1520   /**
1521    * DOCUMENT ME!
1522    */
1523   void updateEditMenuBar()
1524   {
1525
1526     if (viewport.getHistoryList().size() > 0)
1527     {
1528       undoMenuItem.setEnabled(true);
1529       CommandI command = viewport.getHistoryList().peek();
1530       undoMenuItem.setText(MessageManager
1531               .formatMessage("label.undo_command", new Object[]
1532               { command.getDescription() }));
1533     }
1534     else
1535     {
1536       undoMenuItem.setEnabled(false);
1537       undoMenuItem.setText(MessageManager.getString("action.undo"));
1538     }
1539
1540     if (viewport.getRedoList().size() > 0)
1541     {
1542       redoMenuItem.setEnabled(true);
1543
1544       CommandI command = viewport.getRedoList().peek();
1545       redoMenuItem.setText(MessageManager
1546               .formatMessage("label.redo_command", new Object[]
1547               { command.getDescription() }));
1548     }
1549     else
1550     {
1551       redoMenuItem.setEnabled(false);
1552       redoMenuItem.setText(MessageManager.getString("action.redo"));
1553     }
1554   }
1555
1556   @Override
1557   public void addHistoryItem(CommandI command)
1558   {
1559     if (command.getSize() > 0)
1560     {
1561       viewport.addToHistoryList(command);
1562       viewport.clearRedoList();
1563       updateEditMenuBar();
1564       viewport.updateHiddenColumns();
1565       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1566       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1567       // viewport.getColumnSelection()
1568       // .getHiddenColumns().size() > 0);
1569     }
1570   }
1571
1572   /**
1573    *
1574    * @return alignment objects for all views
1575    */
1576   AlignmentI[] getViewAlignments()
1577   {
1578     if (alignPanels != null)
1579     {
1580       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581       int i = 0;
1582       for (AlignmentPanel ap : alignPanels)
1583       {
1584         als[i++] = ap.av.getAlignment();
1585       }
1586       return als;
1587     }
1588     if (viewport != null)
1589     {
1590       return new AlignmentI[] { viewport.getAlignment() };
1591     }
1592     return null;
1593   }
1594
1595   /**
1596    * DOCUMENT ME!
1597    *
1598    * @param e
1599    *          DOCUMENT ME!
1600    */
1601   @Override
1602   protected void undoMenuItem_actionPerformed(ActionEvent e)
1603   {
1604     if (viewport.getHistoryList().isEmpty())
1605     {
1606       return;
1607     }
1608     CommandI command = viewport.getHistoryList().pop();
1609     viewport.addToRedoList(command);
1610     command.undoCommand(getViewAlignments());
1611
1612     AlignmentViewport originalSource = getOriginatingSource(command);
1613     updateEditMenuBar();
1614
1615     if (originalSource != null)
1616     {
1617       if (originalSource != viewport)
1618       {
1619         Cache.log.warn(
1620                 "Implementation worry: mismatch of viewport origin for undo");
1621       }
1622       originalSource.updateHiddenColumns();
1623       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624       // null
1625       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1626       // viewport.getColumnSelection()
1627       // .getHiddenColumns().size() > 0);
1628       originalSource.firePropertyChange("alignment", null,
1629               originalSource.getAlignment().getSequences());
1630     }
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   @Override
1640   protected void redoMenuItem_actionPerformed(ActionEvent e)
1641   {
1642     if (viewport.getRedoList().size() < 1)
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getRedoList().pop();
1648     viewport.addToHistoryList(command);
1649     command.doCommand(getViewAlignments());
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     updateEditMenuBar();
1653
1654     if (originalSource != null)
1655     {
1656
1657       if (originalSource != viewport)
1658       {
1659         Cache.log.warn(
1660                 "Implementation worry: mismatch of viewport origin for redo");
1661       }
1662       originalSource.updateHiddenColumns();
1663       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664       // null
1665       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1666       // viewport.getColumnSelection()
1667       // .getHiddenColumns().size() > 0);
1668       originalSource.firePropertyChange("alignment", null,
1669               originalSource.getAlignment().getSequences());
1670     }
1671   }
1672
1673   AlignmentViewport getOriginatingSource(CommandI command)
1674   {
1675     AlignmentViewport originalSource = null;
1676     // For sequence removal and addition, we need to fire
1677     // the property change event FROM the viewport where the
1678     // original alignment was altered
1679     AlignmentI al = null;
1680     if (command instanceof EditCommand)
1681     {
1682       EditCommand editCommand = (EditCommand) command;
1683       al = editCommand.getAlignment();
1684       List<Component> comps = PaintRefresher.components
1685               .get(viewport.getSequenceSetId());
1686
1687       for (Component comp : comps)
1688       {
1689         if (comp instanceof AlignmentPanel)
1690         {
1691           if (al == ((AlignmentPanel) comp).av.getAlignment())
1692           {
1693             originalSource = ((AlignmentPanel) comp).av;
1694             break;
1695           }
1696         }
1697       }
1698     }
1699
1700     if (originalSource == null)
1701     {
1702       // The original view is closed, we must validate
1703       // the current view against the closed view first
1704       if (al != null)
1705       {
1706         PaintRefresher.validateSequences(al, viewport.getAlignment());
1707       }
1708
1709       originalSource = viewport;
1710     }
1711
1712     return originalSource;
1713   }
1714
1715   /**
1716    * DOCUMENT ME!
1717    *
1718    * @param up
1719    *          DOCUMENT ME!
1720    */
1721   public void moveSelectedSequences(boolean up)
1722   {
1723     SequenceGroup sg = viewport.getSelectionGroup();
1724
1725     if (sg == null)
1726     {
1727       return;
1728     }
1729     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730             viewport.getHiddenRepSequences(), up);
1731     alignPanel.paintAlignment(true, false);
1732   }
1733
1734   synchronized void slideSequences(boolean right, int size)
1735   {
1736     List<SequenceI> sg = new ArrayList<>();
1737     if (viewport.cursorMode)
1738     {
1739       sg.add(viewport.getAlignment()
1740               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1741     }
1742     else if (viewport.getSelectionGroup() != null
1743             && viewport.getSelectionGroup().getSize() != viewport
1744                     .getAlignment().getHeight())
1745     {
1746       sg = viewport.getSelectionGroup()
1747               .getSequences(viewport.getHiddenRepSequences());
1748     }
1749
1750     if (sg.size() < 1)
1751     {
1752       return;
1753     }
1754
1755     List<SequenceI> invertGroup = new ArrayList<>();
1756
1757     for (SequenceI seq : viewport.getAlignment().getSequences())
1758     {
1759       if (!sg.contains(seq))
1760       {
1761         invertGroup.add(seq);
1762       }
1763     }
1764
1765     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766
1767     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1768     for (int i = 0; i < invertGroup.size(); i++)
1769     {
1770       seqs2[i] = invertGroup.get(i);
1771     }
1772
1773     SlideSequencesCommand ssc;
1774     if (right)
1775     {
1776       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1777               viewport.getGapCharacter());
1778     }
1779     else
1780     {
1781       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1782               viewport.getGapCharacter());
1783     }
1784
1785     int groupAdjustment = 0;
1786     if (ssc.getGapsInsertedBegin() && right)
1787     {
1788       if (viewport.cursorMode)
1789       {
1790         alignPanel.getSeqPanel().moveCursor(size, 0);
1791       }
1792       else
1793       {
1794         groupAdjustment = size;
1795       }
1796     }
1797     else if (!ssc.getGapsInsertedBegin() && !right)
1798     {
1799       if (viewport.cursorMode)
1800       {
1801         alignPanel.getSeqPanel().moveCursor(-size, 0);
1802       }
1803       else
1804       {
1805         groupAdjustment = -size;
1806       }
1807     }
1808
1809     if (groupAdjustment != 0)
1810     {
1811       viewport.getSelectionGroup().setStartRes(
1812               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1813       viewport.getSelectionGroup().setEndRes(
1814               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1815     }
1816
1817     /*
1818      * just extend the last slide command if compatible; but not if in
1819      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820      */
1821     boolean appendHistoryItem = false;
1822     Deque<CommandI> historyList = viewport.getHistoryList();
1823     boolean inSplitFrame = getSplitViewContainer() != null;
1824     if (!inSplitFrame && historyList != null && historyList.size() > 0
1825             && historyList.peek() instanceof SlideSequencesCommand)
1826     {
1827       appendHistoryItem = ssc.appendSlideCommand(
1828               (SlideSequencesCommand) historyList.peek());
1829     }
1830
1831     if (!appendHistoryItem)
1832     {
1833       addHistoryItem(ssc);
1834     }
1835
1836     repaint();
1837   }
1838
1839   /**
1840    * DOCUMENT ME!
1841    *
1842    * @param e
1843    *          DOCUMENT ME!
1844    */
1845   @Override
1846   protected void copy_actionPerformed(ActionEvent e)
1847   {
1848     if (viewport.getSelectionGroup() == null)
1849     {
1850       return;
1851     }
1852     // TODO: preserve the ordering of displayed alignment annotation in any
1853     // internal paste (particularly sequence associated annotation)
1854     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1855     String[] omitHidden = null;
1856
1857     if (viewport.hasHiddenColumns())
1858     {
1859       omitHidden = viewport.getViewAsString(true);
1860     }
1861
1862     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1863             seqs, omitHidden, null);
1864
1865     StringSelection ss = new StringSelection(output);
1866
1867     try
1868     {
1869       jalview.gui.Desktop.internalCopy = true;
1870       // Its really worth setting the clipboard contents
1871       // to empty before setting the large StringSelection!!
1872       Toolkit.getDefaultToolkit().getSystemClipboard()
1873               .setContents(new StringSelection(""), null);
1874
1875       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1876               Desktop.instance);
1877     } catch (OutOfMemoryError er)
1878     {
1879       new OOMWarning("copying region", er);
1880       return;
1881     }
1882
1883     HiddenColumns hiddenColumns = null;
1884     if (viewport.hasHiddenColumns())
1885     {
1886       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1887       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1888
1889       // create new HiddenColumns object with copy of hidden regions
1890       // between startRes and endRes, offset by startRes
1891       hiddenColumns = new HiddenColumns(
1892               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1893               hiddenCutoff, hiddenOffset);
1894     }
1895
1896     Desktop.jalviewClipboard = new Object[] { seqs,
1897         viewport.getAlignment().getDataset(), hiddenColumns };
1898     statusBar.setText(MessageManager.formatMessage(
1899             "label.copied_sequences_to_clipboard", new Object[]
1900             { Integer.valueOf(seqs.length).toString() }));
1901   }
1902
1903   /**
1904    * DOCUMENT ME!
1905    *
1906    * @param e
1907    *          DOCUMENT ME!
1908    */
1909   @Override
1910   protected void pasteNew_actionPerformed(ActionEvent e)
1911   {
1912     paste(true);
1913   }
1914
1915   /**
1916    * DOCUMENT ME!
1917    *
1918    * @param e
1919    *          DOCUMENT ME!
1920    */
1921   @Override
1922   protected void pasteThis_actionPerformed(ActionEvent e)
1923   {
1924     paste(false);
1925   }
1926
1927   /**
1928    * Paste contents of Jalview clipboard
1929    *
1930    * @param newAlignment
1931    *          true to paste to a new alignment, otherwise add to this.
1932    */
1933   void paste(boolean newAlignment)
1934   {
1935     boolean externalPaste = true;
1936     try
1937     {
1938       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1939       Transferable contents = c.getContents(this);
1940
1941       if (contents == null)
1942       {
1943         return;
1944       }
1945
1946       String str;
1947       FileFormatI format;
1948       try
1949       {
1950         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1951         if (str.length() < 1)
1952         {
1953           return;
1954         }
1955
1956         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1957
1958       } catch (OutOfMemoryError er)
1959       {
1960         new OOMWarning("Out of memory pasting sequences!!", er);
1961         return;
1962       }
1963
1964       SequenceI[] sequences;
1965       boolean annotationAdded = false;
1966       AlignmentI alignment = null;
1967
1968       if (Desktop.jalviewClipboard != null)
1969       {
1970         // The clipboard was filled from within Jalview, we must use the
1971         // sequences
1972         // And dataset from the copied alignment
1973         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1974         // be doubly sure that we create *new* sequence objects.
1975         sequences = new SequenceI[newseq.length];
1976         for (int i = 0; i < newseq.length; i++)
1977         {
1978           sequences[i] = new Sequence(newseq[i]);
1979         }
1980         alignment = new Alignment(sequences);
1981         externalPaste = false;
1982       }
1983       else
1984       {
1985         // parse the clipboard as an alignment.
1986         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1987                 format);
1988         sequences = alignment.getSequencesArray();
1989       }
1990
1991       int alwidth = 0;
1992       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1993       int fgroup = -1;
1994
1995       if (newAlignment)
1996       {
1997
1998         if (Desktop.jalviewClipboard != null)
1999         {
2000           // dataset is inherited
2001           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2002         }
2003         else
2004         {
2005           // new dataset is constructed
2006           alignment.setDataset(null);
2007         }
2008         alwidth = alignment.getWidth() + 1;
2009       }
2010       else
2011       {
2012         AlignmentI pastedal = alignment; // preserve pasted alignment object
2013         // Add pasted sequences and dataset into existing alignment.
2014         alignment = viewport.getAlignment();
2015         alwidth = alignment.getWidth() + 1;
2016         // decide if we need to import sequences from an existing dataset
2017         boolean importDs = Desktop.jalviewClipboard != null
2018                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2019         // importDs==true instructs us to copy over new dataset sequences from
2020         // an existing alignment
2021         Vector newDs = (importDs) ? new Vector() : null; // used to create
2022         // minimum dataset set
2023
2024         for (int i = 0; i < sequences.length; i++)
2025         {
2026           if (importDs)
2027           {
2028             newDs.addElement(null);
2029           }
2030           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2031           // paste
2032           if (importDs && ds != null)
2033           {
2034             if (!newDs.contains(ds))
2035             {
2036               newDs.setElementAt(ds, i);
2037               ds = new Sequence(ds);
2038               // update with new dataset sequence
2039               sequences[i].setDatasetSequence(ds);
2040             }
2041             else
2042             {
2043               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2044             }
2045           }
2046           else
2047           {
2048             // copy and derive new dataset sequence
2049             sequences[i] = sequences[i].deriveSequence();
2050             alignment.getDataset()
2051                     .addSequence(sequences[i].getDatasetSequence());
2052             // TODO: avoid creation of duplicate dataset sequences with a
2053             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2054           }
2055           alignment.addSequence(sequences[i]); // merges dataset
2056         }
2057         if (newDs != null)
2058         {
2059           newDs.clear(); // tidy up
2060         }
2061         if (alignment.getAlignmentAnnotation() != null)
2062         {
2063           for (AlignmentAnnotation alan : alignment
2064                   .getAlignmentAnnotation())
2065           {
2066             if (alan.graphGroup > fgroup)
2067             {
2068               fgroup = alan.graphGroup;
2069             }
2070           }
2071         }
2072         if (pastedal.getAlignmentAnnotation() != null)
2073         {
2074           // Add any annotation attached to alignment.
2075           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2076           for (int i = 0; i < alann.length; i++)
2077           {
2078             annotationAdded = true;
2079             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2080             {
2081               AlignmentAnnotation newann = new AlignmentAnnotation(
2082                       alann[i]);
2083               if (newann.graphGroup > -1)
2084               {
2085                 if (newGraphGroups.size() <= newann.graphGroup
2086                         || newGraphGroups.get(newann.graphGroup) == null)
2087                 {
2088                   for (int q = newGraphGroups
2089                           .size(); q <= newann.graphGroup; q++)
2090                   {
2091                     newGraphGroups.add(q, null);
2092                   }
2093                   newGraphGroups.set(newann.graphGroup,
2094                           new Integer(++fgroup));
2095                 }
2096                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2097                         .intValue();
2098               }
2099
2100               newann.padAnnotation(alwidth);
2101               alignment.addAnnotation(newann);
2102             }
2103           }
2104         }
2105       }
2106       if (!newAlignment)
2107       {
2108         // /////
2109         // ADD HISTORY ITEM
2110         //
2111         addHistoryItem(new EditCommand(
2112                 MessageManager.getString("label.add_sequences"),
2113                 Action.PASTE, sequences, 0, alignment.getWidth(),
2114                 alignment));
2115       }
2116       // Add any annotations attached to sequences
2117       for (int i = 0; i < sequences.length; i++)
2118       {
2119         if (sequences[i].getAnnotation() != null)
2120         {
2121           AlignmentAnnotation newann;
2122           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2123           {
2124             annotationAdded = true;
2125             newann = sequences[i].getAnnotation()[a];
2126             newann.adjustForAlignment();
2127             newann.padAnnotation(alwidth);
2128             if (newann.graphGroup > -1)
2129             {
2130               if (newann.graphGroup > -1)
2131               {
2132                 if (newGraphGroups.size() <= newann.graphGroup
2133                         || newGraphGroups.get(newann.graphGroup) == null)
2134                 {
2135                   for (int q = newGraphGroups
2136                           .size(); q <= newann.graphGroup; q++)
2137                   {
2138                     newGraphGroups.add(q, null);
2139                   }
2140                   newGraphGroups.set(newann.graphGroup,
2141                           new Integer(++fgroup));
2142                 }
2143                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2144                         .intValue();
2145               }
2146             }
2147             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2148             // was
2149             // duplicated
2150             // earlier
2151             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2152                     a);
2153           }
2154         }
2155       }
2156       if (!newAlignment)
2157       {
2158
2159         // propagate alignment changed.
2160         viewport.getRanges().setEndSeq(alignment.getHeight());
2161         if (annotationAdded)
2162         {
2163           // Duplicate sequence annotation in all views.
2164           AlignmentI[] alview = this.getViewAlignments();
2165           for (int i = 0; i < sequences.length; i++)
2166           {
2167             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2168             if (sann == null)
2169             {
2170               continue;
2171             }
2172             for (int avnum = 0; avnum < alview.length; avnum++)
2173             {
2174               if (alview[avnum] != alignment)
2175               {
2176                 // duplicate in a view other than the one with input focus
2177                 int avwidth = alview[avnum].getWidth() + 1;
2178                 // this relies on sann being preserved after we
2179                 // modify the sequence's annotation array for each duplication
2180                 for (int a = 0; a < sann.length; a++)
2181                 {
2182                   AlignmentAnnotation newann = new AlignmentAnnotation(
2183                           sann[a]);
2184                   sequences[i].addAlignmentAnnotation(newann);
2185                   newann.padAnnotation(avwidth);
2186                   alview[avnum].addAnnotation(newann); // annotation was
2187                   // duplicated earlier
2188                   // TODO JAL-1145 graphGroups are not updated for sequence
2189                   // annotation added to several views. This may cause
2190                   // strangeness
2191                   alview[avnum].setAnnotationIndex(newann, a);
2192                 }
2193               }
2194             }
2195           }
2196           buildSortByAnnotationScoresMenu();
2197         }
2198         viewport.firePropertyChange("alignment", null,
2199                 alignment.getSequences());
2200         if (alignPanels != null)
2201         {
2202           for (AlignmentPanel ap : alignPanels)
2203           {
2204             ap.validateAnnotationDimensions(false);
2205           }
2206         }
2207         else
2208         {
2209           alignPanel.validateAnnotationDimensions(false);
2210         }
2211
2212       }
2213       else
2214       {
2215         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2216                 DEFAULT_HEIGHT);
2217         String newtitle = new String("Copied sequences");
2218
2219         if (Desktop.jalviewClipboard != null
2220                 && Desktop.jalviewClipboard[2] != null)
2221         {
2222           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2223           af.viewport.setHiddenColumns(hc);
2224         }
2225
2226         // >>>This is a fix for the moment, until a better solution is
2227         // found!!<<<
2228         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2229                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2230                         .getFeatureRenderer());
2231
2232         // TODO: maintain provenance of an alignment, rather than just make the
2233         // title a concatenation of operations.
2234         if (!externalPaste)
2235         {
2236           if (title.startsWith("Copied sequences"))
2237           {
2238             newtitle = title;
2239           }
2240           else
2241           {
2242             newtitle = newtitle.concat("- from " + title);
2243           }
2244         }
2245         else
2246         {
2247           newtitle = new String("Pasted sequences");
2248         }
2249
2250         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2251                 DEFAULT_HEIGHT);
2252
2253       }
2254
2255     } catch (Exception ex)
2256     {
2257       ex.printStackTrace();
2258       System.out.println("Exception whilst pasting: " + ex);
2259       // could be anything being pasted in here
2260     }
2261
2262   }
2263
2264   @Override
2265   protected void expand_newalign(ActionEvent e)
2266   {
2267     try
2268     {
2269       AlignmentI alignment = AlignmentUtils
2270               .expandContext(getViewport().getAlignment(), -1);
2271       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2272               DEFAULT_HEIGHT);
2273       String newtitle = new String("Flanking alignment");
2274
2275       if (Desktop.jalviewClipboard != null
2276               && Desktop.jalviewClipboard[2] != null)
2277       {
2278         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2279         af.viewport.setHiddenColumns(hc);
2280       }
2281
2282       // >>>This is a fix for the moment, until a better solution is
2283       // found!!<<<
2284       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2285               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2286                       .getFeatureRenderer());
2287
2288       // TODO: maintain provenance of an alignment, rather than just make the
2289       // title a concatenation of operations.
2290       {
2291         if (title.startsWith("Copied sequences"))
2292         {
2293           newtitle = title;
2294         }
2295         else
2296         {
2297           newtitle = newtitle.concat("- from " + title);
2298         }
2299       }
2300
2301       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2302
2303     } catch (Exception ex)
2304     {
2305       ex.printStackTrace();
2306       System.out.println("Exception whilst pasting: " + ex);
2307       // could be anything being pasted in here
2308     } catch (OutOfMemoryError oom)
2309     {
2310       new OOMWarning("Viewing flanking region of alignment", oom);
2311     }
2312   }
2313
2314   /**
2315    * DOCUMENT ME!
2316    *
2317    * @param e
2318    *          DOCUMENT ME!
2319    */
2320   @Override
2321   protected void cut_actionPerformed(ActionEvent e)
2322   {
2323     copy_actionPerformed(null);
2324     delete_actionPerformed(null);
2325   }
2326
2327   /**
2328    * DOCUMENT ME!
2329    *
2330    * @param e
2331    *          DOCUMENT ME!
2332    */
2333   @Override
2334   protected void delete_actionPerformed(ActionEvent evt)
2335   {
2336
2337     SequenceGroup sg = viewport.getSelectionGroup();
2338     if (sg == null)
2339     {
2340       return;
2341     }
2342
2343     /*
2344      * If the cut affects all sequences, warn, remove highlighted columns
2345      */
2346     if (sg.getSize() == viewport.getAlignment().getHeight())
2347     {
2348       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2349               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2350       if (isEntireAlignWidth)
2351       {
2352         int confirm = JvOptionPane.showConfirmDialog(this,
2353                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2354                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2355                 JvOptionPane.OK_CANCEL_OPTION);
2356
2357         if (confirm == JvOptionPane.CANCEL_OPTION
2358                 || confirm == JvOptionPane.CLOSED_OPTION)
2359         {
2360           return;
2361         }
2362       }
2363       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2364               sg.getEndRes() + 1);
2365     }
2366     SequenceI[] cut = sg.getSequences()
2367             .toArray(new SequenceI[sg.getSize()]);
2368
2369     addHistoryItem(new EditCommand(
2370             MessageManager.getString("label.cut_sequences"), Action.CUT,
2371             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2372             viewport.getAlignment()));
2373
2374     viewport.setSelectionGroup(null);
2375     viewport.sendSelection();
2376     viewport.getAlignment().deleteGroup(sg);
2377
2378     viewport.firePropertyChange("alignment", null,
2379             viewport.getAlignment().getSequences());
2380     if (viewport.getAlignment().getHeight() < 1)
2381     {
2382       try
2383       {
2384         this.setClosed(true);
2385       } catch (Exception ex)
2386       {
2387       }
2388     }
2389   }
2390
2391   /**
2392    * DOCUMENT ME!
2393    *
2394    * @param e
2395    *          DOCUMENT ME!
2396    */
2397   @Override
2398   protected void deleteGroups_actionPerformed(ActionEvent e)
2399   {
2400     if (avc.deleteGroups())
2401     {
2402       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2403       alignPanel.updateAnnotation();
2404       alignPanel.paintAlignment(true, true);
2405     }
2406   }
2407
2408   /**
2409    * DOCUMENT ME!
2410    *
2411    * @param e
2412    *          DOCUMENT ME!
2413    */
2414   @Override
2415   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2416   {
2417     SequenceGroup sg = new SequenceGroup(
2418             viewport.getAlignment().getSequences());
2419
2420     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2421     viewport.setSelectionGroup(sg);
2422     viewport.isSelectionGroupChanged(true);
2423     viewport.sendSelection();
2424     // JAL-2034 - should delegate to
2425     // alignPanel to decide if overview needs
2426     // updating.
2427     alignPanel.paintAlignment(false, false);
2428     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2429   }
2430
2431   /**
2432    * DOCUMENT ME!
2433    *
2434    * @param e
2435    *          DOCUMENT ME!
2436    */
2437   @Override
2438   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2439   {
2440     if (viewport.cursorMode)
2441     {
2442       alignPanel.getSeqPanel().keyboardNo1 = null;
2443       alignPanel.getSeqPanel().keyboardNo2 = null;
2444     }
2445     viewport.setSelectionGroup(null);
2446     viewport.getColumnSelection().clear();
2447     viewport.setSelectionGroup(null);
2448     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2449     // JAL-2034 - should delegate to
2450     // alignPanel to decide if overview needs
2451     // updating.
2452     alignPanel.paintAlignment(false, false);
2453     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2454     viewport.sendSelection();
2455   }
2456
2457   /**
2458    * DOCUMENT ME!
2459    *
2460    * @param e
2461    *          DOCUMENT ME!
2462    */
2463   @Override
2464   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2465   {
2466     SequenceGroup sg = viewport.getSelectionGroup();
2467
2468     if (sg == null)
2469     {
2470       selectAllSequenceMenuItem_actionPerformed(null);
2471
2472       return;
2473     }
2474
2475     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2476     {
2477       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2478     }
2479     // JAL-2034 - should delegate to
2480     // alignPanel to decide if overview needs
2481     // updating.
2482
2483     alignPanel.paintAlignment(true, false);
2484     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2485     viewport.sendSelection();
2486   }
2487
2488   @Override
2489   public void invertColSel_actionPerformed(ActionEvent e)
2490   {
2491     viewport.invertColumnSelection();
2492     alignPanel.paintAlignment(true, false);
2493     viewport.sendSelection();
2494   }
2495
2496   /**
2497    * DOCUMENT ME!
2498    *
2499    * @param e
2500    *          DOCUMENT ME!
2501    */
2502   @Override
2503   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2504   {
2505     trimAlignment(true);
2506   }
2507
2508   /**
2509    * DOCUMENT ME!
2510    *
2511    * @param e
2512    *          DOCUMENT ME!
2513    */
2514   @Override
2515   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2516   {
2517     trimAlignment(false);
2518   }
2519
2520   void trimAlignment(boolean trimLeft)
2521   {
2522     ColumnSelection colSel = viewport.getColumnSelection();
2523     int column;
2524
2525     if (!colSel.isEmpty())
2526     {
2527       if (trimLeft)
2528       {
2529         column = colSel.getMin();
2530       }
2531       else
2532       {
2533         column = colSel.getMax();
2534       }
2535
2536       SequenceI[] seqs;
2537       if (viewport.getSelectionGroup() != null)
2538       {
2539         seqs = viewport.getSelectionGroup()
2540                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2541       }
2542       else
2543       {
2544         seqs = viewport.getAlignment().getSequencesArray();
2545       }
2546
2547       TrimRegionCommand trimRegion;
2548       if (trimLeft)
2549       {
2550         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2551                 column, viewport.getAlignment());
2552         viewport.getRanges().setStartRes(0);
2553       }
2554       else
2555       {
2556         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2557                 column, viewport.getAlignment());
2558       }
2559
2560       statusBar.setText(MessageManager
2561               .formatMessage("label.removed_columns", new String[]
2562               { Integer.valueOf(trimRegion.getSize()).toString() }));
2563
2564       addHistoryItem(trimRegion);
2565
2566       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2567       {
2568         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2569                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2570         {
2571           viewport.getAlignment().deleteGroup(sg);
2572         }
2573       }
2574
2575       viewport.firePropertyChange("alignment", null,
2576               viewport.getAlignment().getSequences());
2577     }
2578   }
2579
2580   /**
2581    * DOCUMENT ME!
2582    *
2583    * @param e
2584    *          DOCUMENT ME!
2585    */
2586   @Override
2587   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2588   {
2589     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2590
2591     SequenceI[] seqs;
2592     if (viewport.getSelectionGroup() != null)
2593     {
2594       seqs = viewport.getSelectionGroup()
2595               .getSequencesAsArray(viewport.getHiddenRepSequences());
2596       start = viewport.getSelectionGroup().getStartRes();
2597       end = viewport.getSelectionGroup().getEndRes();
2598     }
2599     else
2600     {
2601       seqs = viewport.getAlignment().getSequencesArray();
2602     }
2603
2604     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2605             "Remove Gapped Columns", seqs, start, end,
2606             viewport.getAlignment());
2607
2608     addHistoryItem(removeGapCols);
2609
2610     statusBar.setText(MessageManager
2611             .formatMessage("label.removed_empty_columns", new Object[]
2612             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2613
2614     // This is to maintain viewport position on first residue
2615     // of first sequence
2616     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2617     ViewportRanges ranges = viewport.getRanges();
2618     int startRes = seq.findPosition(ranges.getStartRes());
2619     // ShiftList shifts;
2620     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2621     // edit.alColumnChanges=shifts.getInverse();
2622     // if (viewport.hasHiddenColumns)
2623     // viewport.getColumnSelection().compensateForEdits(shifts);
2624     ranges.setStartRes(seq.findIndex(startRes) - 1);
2625     viewport.firePropertyChange("alignment", null,
2626             viewport.getAlignment().getSequences());
2627
2628   }
2629
2630   /**
2631    * DOCUMENT ME!
2632    *
2633    * @param e
2634    *          DOCUMENT ME!
2635    */
2636   @Override
2637   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2638   {
2639     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2640
2641     SequenceI[] seqs;
2642     if (viewport.getSelectionGroup() != null)
2643     {
2644       seqs = viewport.getSelectionGroup()
2645               .getSequencesAsArray(viewport.getHiddenRepSequences());
2646       start = viewport.getSelectionGroup().getStartRes();
2647       end = viewport.getSelectionGroup().getEndRes();
2648     }
2649     else
2650     {
2651       seqs = viewport.getAlignment().getSequencesArray();
2652     }
2653
2654     // This is to maintain viewport position on first residue
2655     // of first sequence
2656     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2657     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2658
2659     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2660             viewport.getAlignment()));
2661
2662     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2663
2664     viewport.firePropertyChange("alignment", null,
2665             viewport.getAlignment().getSequences());
2666
2667   }
2668
2669   /**
2670    * DOCUMENT ME!
2671    *
2672    * @param e
2673    *          DOCUMENT ME!
2674    */
2675   @Override
2676   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2677   {
2678     viewport.setPadGaps(padGapsMenuitem.isSelected());
2679     viewport.firePropertyChange("alignment", null,
2680             viewport.getAlignment().getSequences());
2681   }
2682
2683   /**
2684    * DOCUMENT ME!
2685    *
2686    * @param e
2687    *          DOCUMENT ME!
2688    */
2689   @Override
2690   public void findMenuItem_actionPerformed(ActionEvent e)
2691   {
2692     new Finder();
2693   }
2694
2695   /**
2696    * Create a new view of the current alignment.
2697    */
2698   @Override
2699   public void newView_actionPerformed(ActionEvent e)
2700   {
2701     newView(null, true);
2702   }
2703
2704   /**
2705    * Creates and shows a new view of the current alignment.
2706    *
2707    * @param viewTitle
2708    *          title of newly created view; if null, one will be generated
2709    * @param copyAnnotation
2710    *          if true then duplicate all annnotation, groups and settings
2711    * @return new alignment panel, already displayed.
2712    */
2713   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2714   {
2715     /*
2716      * Create a new AlignmentPanel (with its own, new Viewport)
2717      */
2718     AlignmentPanel newap = new jalview.project.Jalview2XML()
2719             .copyAlignPanel(alignPanel);
2720     if (!copyAnnotation)
2721     {
2722       /*
2723        * remove all groups and annotation except for the automatic stuff
2724        */
2725       newap.av.getAlignment().deleteAllGroups();
2726       newap.av.getAlignment().deleteAllAnnotations(false);
2727     }
2728
2729     newap.av.setGatherViewsHere(false);
2730
2731     if (viewport.getViewName() == null)
2732     {
2733       viewport.setViewName(MessageManager
2734               .getString("label.view_name_original"));
2735     }
2736
2737     /*
2738      * Views share the same edits undo and redo stacks
2739      */
2740     newap.av.setHistoryList(viewport.getHistoryList());
2741     newap.av.setRedoList(viewport.getRedoList());
2742
2743     /*
2744      * Views share the same mappings; need to deregister any new mappings
2745      * created by copyAlignPanel, and register the new reference to the shared
2746      * mappings
2747      */
2748     newap.av.replaceMappings(viewport.getAlignment());
2749
2750     /*
2751      * start up cDNA consensus (if applicable) now mappings are in place
2752      */
2753     if (newap.av.initComplementConsensus())
2754     {
2755       newap.refresh(true); // adjust layout of annotations
2756     }
2757
2758     newap.av.setViewName(getNewViewName(viewTitle));
2759
2760     addAlignmentPanel(newap, true);
2761     newap.alignmentChanged();
2762
2763     if (alignPanels.size() == 2)
2764     {
2765       viewport.setGatherViewsHere(true);
2766     }
2767     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2768     return newap;
2769   }
2770
2771   /**
2772    * Make a new name for the view, ensuring it is unique within the current
2773    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2774    * these now use viewId. Unique view names are still desirable for usability.)
2775    *
2776    * @param viewTitle
2777    * @return
2778    */
2779   protected String getNewViewName(String viewTitle)
2780   {
2781     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2782     boolean addFirstIndex = false;
2783     if (viewTitle == null || viewTitle.trim().length() == 0)
2784     {
2785       viewTitle = MessageManager.getString("action.view");
2786       addFirstIndex = true;
2787     }
2788     else
2789     {
2790       index = 1;// we count from 1 if given a specific name
2791     }
2792     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2793
2794     List<Component> comps = PaintRefresher.components
2795             .get(viewport.getSequenceSetId());
2796
2797     List<String> existingNames = getExistingViewNames(comps);
2798
2799     while (existingNames.contains(newViewName))
2800     {
2801       newViewName = viewTitle + " " + (++index);
2802     }
2803     return newViewName;
2804   }
2805
2806   /**
2807    * Returns a list of distinct view names found in the given list of
2808    * components. View names are held on the viewport of an AlignmentPanel.
2809    *
2810    * @param comps
2811    * @return
2812    */
2813   protected List<String> getExistingViewNames(List<Component> comps)
2814   {
2815     List<String> existingNames = new ArrayList<>();
2816     for (Component comp : comps)
2817     {
2818       if (comp instanceof AlignmentPanel)
2819       {
2820         AlignmentPanel ap = (AlignmentPanel) comp;
2821         if (!existingNames.contains(ap.av.getViewName()))
2822         {
2823           existingNames.add(ap.av.getViewName());
2824         }
2825       }
2826     }
2827     return existingNames;
2828   }
2829
2830   /**
2831    * Explode tabbed views into separate windows.
2832    */
2833   @Override
2834   public void expandViews_actionPerformed(ActionEvent e)
2835   {
2836     Desktop.explodeViews(this);
2837   }
2838
2839   /**
2840    * Gather views in separate windows back into a tabbed presentation.
2841    */
2842   @Override
2843   public void gatherViews_actionPerformed(ActionEvent e)
2844   {
2845     Desktop.instance.gatherViews(this);
2846   }
2847
2848   /**
2849    * DOCUMENT ME!
2850    *
2851    * @param e
2852    *          DOCUMENT ME!
2853    */
2854   @Override
2855   public void font_actionPerformed(ActionEvent e)
2856   {
2857     new FontChooser(alignPanel);
2858   }
2859
2860   /**
2861    * DOCUMENT ME!
2862    *
2863    * @param e
2864    *          DOCUMENT ME!
2865    */
2866   @Override
2867   protected void seqLimit_actionPerformed(ActionEvent e)
2868   {
2869     viewport.setShowJVSuffix(seqLimits.isSelected());
2870
2871     alignPanel.getIdPanel().getIdCanvas()
2872             .setPreferredSize(alignPanel.calculateIdWidth());
2873     alignPanel.paintAlignment(true, false);
2874   }
2875
2876   @Override
2877   public void idRightAlign_actionPerformed(ActionEvent e)
2878   {
2879     viewport.setRightAlignIds(idRightAlign.isSelected());
2880     alignPanel.paintAlignment(false, false);
2881   }
2882
2883   @Override
2884   public void centreColumnLabels_actionPerformed(ActionEvent e)
2885   {
2886     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2887     alignPanel.paintAlignment(false, false);
2888   }
2889
2890   /*
2891    * (non-Javadoc)
2892    *
2893    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2894    */
2895   @Override
2896   protected void followHighlight_actionPerformed()
2897   {
2898     /*
2899      * Set the 'follow' flag on the Viewport (and scroll to position if now
2900      * true).
2901      */
2902     final boolean state = this.followHighlightMenuItem.getState();
2903     viewport.setFollowHighlight(state);
2904     if (state)
2905     {
2906       alignPanel.scrollToPosition(viewport.getSearchResults());
2907     }
2908   }
2909
2910   /**
2911    * DOCUMENT ME!
2912    *
2913    * @param e
2914    *          DOCUMENT ME!
2915    */
2916   @Override
2917   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2918   {
2919     viewport.setColourText(colourTextMenuItem.isSelected());
2920     alignPanel.paintAlignment(false, false);
2921   }
2922
2923   /**
2924    * DOCUMENT ME!
2925    *
2926    * @param e
2927    *          DOCUMENT ME!
2928    */
2929   @Override
2930   public void wrapMenuItem_actionPerformed(ActionEvent e)
2931   {
2932     scaleAbove.setVisible(wrapMenuItem.isSelected());
2933     scaleLeft.setVisible(wrapMenuItem.isSelected());
2934     scaleRight.setVisible(wrapMenuItem.isSelected());
2935     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2936     alignPanel.updateLayout();
2937   }
2938
2939   @Override
2940   public void showAllSeqs_actionPerformed(ActionEvent e)
2941   {
2942     viewport.showAllHiddenSeqs();
2943   }
2944
2945   @Override
2946   public void showAllColumns_actionPerformed(ActionEvent e)
2947   {
2948     viewport.showAllHiddenColumns();
2949     alignPanel.paintAlignment(true, true);
2950     viewport.sendSelection();
2951   }
2952
2953   @Override
2954   public void hideSelSequences_actionPerformed(ActionEvent e)
2955   {
2956     viewport.hideAllSelectedSeqs();
2957   }
2958
2959   /**
2960    * called by key handler and the hide all/show all menu items
2961    *
2962    * @param toggleSeqs
2963    * @param toggleCols
2964    */
2965   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2966   {
2967
2968     boolean hide = false;
2969     SequenceGroup sg = viewport.getSelectionGroup();
2970     if (!toggleSeqs && !toggleCols)
2971     {
2972       // Hide everything by the current selection - this is a hack - we do the
2973       // invert and then hide
2974       // first check that there will be visible columns after the invert.
2975       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2976               && sg.getStartRes() <= sg.getEndRes()))
2977       {
2978         // now invert the sequence set, if required - empty selection implies
2979         // that no hiding is required.
2980         if (sg != null)
2981         {
2982           invertSequenceMenuItem_actionPerformed(null);
2983           sg = viewport.getSelectionGroup();
2984           toggleSeqs = true;
2985
2986         }
2987         viewport.expandColSelection(sg, true);
2988         // finally invert the column selection and get the new sequence
2989         // selection.
2990         invertColSel_actionPerformed(null);
2991         toggleCols = true;
2992       }
2993     }
2994
2995     if (toggleSeqs)
2996     {
2997       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2998       {
2999         hideSelSequences_actionPerformed(null);
3000         hide = true;
3001       }
3002       else if (!(toggleCols && viewport.hasSelectedColumns()))
3003       {
3004         showAllSeqs_actionPerformed(null);
3005       }
3006     }
3007
3008     if (toggleCols)
3009     {
3010       if (viewport.hasSelectedColumns())
3011       {
3012         hideSelColumns_actionPerformed(null);
3013         if (!toggleSeqs)
3014         {
3015           viewport.setSelectionGroup(sg);
3016         }
3017       }
3018       else if (!hide)
3019       {
3020         showAllColumns_actionPerformed(null);
3021       }
3022     }
3023   }
3024
3025   /*
3026    * (non-Javadoc)
3027    *
3028    * @see
3029    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3030    * event.ActionEvent)
3031    */
3032   @Override
3033   public void hideAllButSelection_actionPerformed(ActionEvent e)
3034   {
3035     toggleHiddenRegions(false, false);
3036     viewport.sendSelection();
3037   }
3038
3039   /*
3040    * (non-Javadoc)
3041    *
3042    * @see
3043    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3044    * .ActionEvent)
3045    */
3046   @Override
3047   public void hideAllSelection_actionPerformed(ActionEvent e)
3048   {
3049     SequenceGroup sg = viewport.getSelectionGroup();
3050     viewport.expandColSelection(sg, false);
3051     viewport.hideAllSelectedSeqs();
3052     viewport.hideSelectedColumns();
3053     alignPanel.updateLayout();
3054     alignPanel.paintAlignment(true, true);
3055     viewport.sendSelection();
3056   }
3057
3058   /*
3059    * (non-Javadoc)
3060    *
3061    * @see
3062    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3063    * ActionEvent)
3064    */
3065   @Override
3066   public void showAllhidden_actionPerformed(ActionEvent e)
3067   {
3068     viewport.showAllHiddenColumns();
3069     viewport.showAllHiddenSeqs();
3070     alignPanel.paintAlignment(true, true);
3071     viewport.sendSelection();
3072   }
3073
3074   @Override
3075   public void hideSelColumns_actionPerformed(ActionEvent e)
3076   {
3077     viewport.hideSelectedColumns();
3078     alignPanel.updateLayout();
3079     alignPanel.paintAlignment(true, true);
3080     viewport.sendSelection();
3081   }
3082
3083   @Override
3084   public void hiddenMarkers_actionPerformed(ActionEvent e)
3085   {
3086     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3087     repaint();
3088   }
3089
3090   /**
3091    * DOCUMENT ME!
3092    *
3093    * @param e
3094    *          DOCUMENT ME!
3095    */
3096   @Override
3097   protected void scaleAbove_actionPerformed(ActionEvent e)
3098   {
3099     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3100     // TODO: do we actually need to update overview for scale above change ?
3101     alignPanel.paintAlignment(true, false);
3102   }
3103
3104   /**
3105    * DOCUMENT ME!
3106    *
3107    * @param e
3108    *          DOCUMENT ME!
3109    */
3110   @Override
3111   protected void scaleLeft_actionPerformed(ActionEvent e)
3112   {
3113     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3114     alignPanel.paintAlignment(true, false);
3115   }
3116
3117   /**
3118    * DOCUMENT ME!
3119    *
3120    * @param e
3121    *          DOCUMENT ME!
3122    */
3123   @Override
3124   protected void scaleRight_actionPerformed(ActionEvent e)
3125   {
3126     viewport.setScaleRightWrapped(scaleRight.isSelected());
3127     alignPanel.paintAlignment(true, false);
3128   }
3129
3130   /**
3131    * DOCUMENT ME!
3132    *
3133    * @param e
3134    *          DOCUMENT ME!
3135    */
3136   @Override
3137   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3138   {
3139     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3140     alignPanel.paintAlignment(false, false);
3141   }
3142
3143   /**
3144    * DOCUMENT ME!
3145    *
3146    * @param e
3147    *          DOCUMENT ME!
3148    */
3149   @Override
3150   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3151   {
3152     viewport.setShowText(viewTextMenuItem.isSelected());
3153     alignPanel.paintAlignment(false, false);
3154   }
3155
3156   /**
3157    * DOCUMENT ME!
3158    *
3159    * @param e
3160    *          DOCUMENT ME!
3161    */
3162   @Override
3163   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3164   {
3165     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3166     alignPanel.paintAlignment(false, false);
3167   }
3168
3169   public FeatureSettings featureSettings;
3170
3171   @Override
3172   public FeatureSettingsControllerI getFeatureSettingsUI()
3173   {
3174     return featureSettings;
3175   }
3176
3177   @Override
3178   public void featureSettings_actionPerformed(ActionEvent e)
3179   {
3180     if (featureSettings != null)
3181     {
3182       featureSettings.close();
3183       featureSettings = null;
3184     }
3185     if (!showSeqFeatures.isSelected())
3186     {
3187       // make sure features are actually displayed
3188       showSeqFeatures.setSelected(true);
3189       showSeqFeatures_actionPerformed(null);
3190     }
3191     featureSettings = new FeatureSettings(this);
3192   }
3193
3194   /**
3195    * Set or clear 'Show Sequence Features'
3196    *
3197    * @param evt
3198    *          DOCUMENT ME!
3199    */
3200   @Override
3201   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3202   {
3203     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3204     alignPanel.paintAlignment(true, true);
3205   }
3206
3207   /**
3208    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3209    * the annotations panel as a whole.
3210    *
3211    * The options to show/hide all annotations should be enabled when the panel
3212    * is shown, and disabled when the panel is hidden.
3213    *
3214    * @param e
3215    */
3216   @Override
3217   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3218   {
3219     final boolean setVisible = annotationPanelMenuItem.isSelected();
3220     viewport.setShowAnnotation(setVisible);
3221     this.showAllSeqAnnotations.setEnabled(setVisible);
3222     this.hideAllSeqAnnotations.setEnabled(setVisible);
3223     this.showAllAlAnnotations.setEnabled(setVisible);
3224     this.hideAllAlAnnotations.setEnabled(setVisible);
3225     alignPanel.updateLayout();
3226   }
3227
3228   @Override
3229   public void alignmentProperties()
3230   {
3231     JEditorPane editPane = new JEditorPane("text/html", "");
3232     editPane.setEditable(false);
3233     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3234             .formatAsHtml();
3235     editPane.setText(
3236             MessageManager.formatMessage("label.html_content", new Object[]
3237             { contents.toString() }));
3238     JInternalFrame frame = new JInternalFrame();
3239     frame.getContentPane().add(new JScrollPane(editPane));
3240
3241     Desktop.addInternalFrame(frame, MessageManager
3242             .formatMessage("label.alignment_properties", new Object[]
3243             { getTitle() }), 500, 400);
3244   }
3245
3246   /**
3247    * DOCUMENT ME!
3248    *
3249    * @param e
3250    *          DOCUMENT ME!
3251    */
3252   @Override
3253   public void overviewMenuItem_actionPerformed(ActionEvent e)
3254   {
3255     if (alignPanel.overviewPanel != null)
3256     {
3257       return;
3258     }
3259
3260     JInternalFrame frame = new JInternalFrame();
3261     final OverviewPanel overview = new OverviewPanel(alignPanel);
3262     frame.setContentPane(overview);
3263     Desktop.addInternalFrame(frame, MessageManager
3264             .formatMessage("label.overview_params", new Object[]
3265             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3266             true, true);
3267     frame.pack();
3268     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3269     frame.addInternalFrameListener(
3270             new javax.swing.event.InternalFrameAdapter()
3271             {
3272               @Override
3273               public void internalFrameClosed(
3274                       javax.swing.event.InternalFrameEvent evt)
3275               {
3276                 overview.dispose();
3277                 alignPanel.setOverviewPanel(null);
3278               };
3279             });
3280     if (getKeyListeners().length > 0)
3281     {
3282       frame.addKeyListener(getKeyListeners()[0]);
3283     }
3284
3285     alignPanel.setOverviewPanel(overview);
3286   }
3287
3288   @Override
3289   public void textColour_actionPerformed()
3290   {
3291     new TextColourChooser().chooseColour(alignPanel, null);
3292   }
3293
3294   /*
3295    * public void covariationColour_actionPerformed() {
3296    * changeColour(new
3297    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3298    * ()[0])); }
3299    */
3300   @Override
3301   public void annotationColour_actionPerformed()
3302   {
3303     new AnnotationColourChooser(viewport, alignPanel);
3304   }
3305
3306   @Override
3307   public void annotationColumn_actionPerformed(ActionEvent e)
3308   {
3309     new AnnotationColumnChooser(viewport, alignPanel);
3310   }
3311
3312   /**
3313    * Action on the user checking or unchecking the option to apply the selected
3314    * colour scheme to all groups. If unchecked, groups may have their own
3315    * independent colour schemes.
3316    *
3317    * @param selected
3318    */
3319   @Override
3320   public void applyToAllGroups_actionPerformed(boolean selected)
3321   {
3322     viewport.setColourAppliesToAllGroups(selected);
3323   }
3324
3325   /**
3326    * Action on user selecting a colour from the colour menu
3327    *
3328    * @param name
3329    *          the name (not the menu item label!) of the colour scheme
3330    */
3331   @Override
3332   public void changeColour_actionPerformed(String name)
3333   {
3334     /*
3335      * 'User Defined' opens a panel to configure or load a
3336      * user-defined colour scheme
3337      */
3338     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3339     {
3340       new UserDefinedColours(alignPanel);
3341       return;
3342     }
3343
3344     /*
3345      * otherwise set the chosen colour scheme (or null for 'None')
3346      */
3347     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3348             viewport.getAlignment(), viewport.getHiddenRepSequences());
3349     changeColour(cs);
3350   }
3351
3352   /**
3353    * Actions on setting or changing the alignment colour scheme
3354    *
3355    * @param cs
3356    */
3357   @Override
3358   public void changeColour(ColourSchemeI cs)
3359   {
3360     // TODO: pull up to controller method
3361     ColourMenuHelper.setColourSelected(colourMenu, cs);
3362
3363     viewport.setGlobalColourScheme(cs);
3364
3365     alignPanel.paintAlignment(true, true);
3366   }
3367
3368   /**
3369    * Show the PID threshold slider panel
3370    */
3371   @Override
3372   protected void modifyPID_actionPerformed()
3373   {
3374     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3375             alignPanel.getViewName());
3376     SliderPanel.showPIDSlider();
3377   }
3378
3379   /**
3380    * Show the Conservation slider panel
3381    */
3382   @Override
3383   protected void modifyConservation_actionPerformed()
3384   {
3385     SliderPanel.setConservationSlider(alignPanel,
3386             viewport.getResidueShading(), alignPanel.getViewName());
3387     SliderPanel.showConservationSlider();
3388   }
3389
3390   /**
3391    * Action on selecting or deselecting (Colour) By Conservation
3392    */
3393   @Override
3394   public void conservationMenuItem_actionPerformed(boolean selected)
3395   {
3396     modifyConservation.setEnabled(selected);
3397     viewport.setConservationSelected(selected);
3398     viewport.getResidueShading().setConservationApplied(selected);
3399
3400     changeColour(viewport.getGlobalColourScheme());
3401     if (selected)
3402     {
3403       modifyConservation_actionPerformed();
3404     }
3405     else
3406     {
3407       SliderPanel.hideConservationSlider();
3408     }
3409   }
3410
3411   /**
3412    * Action on selecting or deselecting (Colour) Above PID Threshold
3413    */
3414   @Override
3415   public void abovePIDThreshold_actionPerformed(boolean selected)
3416   {
3417     modifyPID.setEnabled(selected);
3418     viewport.setAbovePIDThreshold(selected);
3419     if (!selected)
3420     {
3421       viewport.getResidueShading().setThreshold(0,
3422               viewport.isIgnoreGapsConsensus());
3423     }
3424
3425     changeColour(viewport.getGlobalColourScheme());
3426     if (selected)
3427     {
3428       modifyPID_actionPerformed();
3429     }
3430     else
3431     {
3432       SliderPanel.hidePIDSlider();
3433     }
3434   }
3435
3436   /**
3437    * DOCUMENT ME!
3438    *
3439    * @param e
3440    *          DOCUMENT ME!
3441    */
3442   @Override
3443   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3444   {
3445     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3446     AlignmentSorter.sortByPID(viewport.getAlignment(),
3447             viewport.getAlignment().getSequenceAt(0));
3448     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3449             viewport.getAlignment()));
3450     alignPanel.paintAlignment(true, false);
3451   }
3452
3453   /**
3454    * DOCUMENT ME!
3455    *
3456    * @param e
3457    *          DOCUMENT ME!
3458    */
3459   @Override
3460   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3461   {
3462     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3463     AlignmentSorter.sortByID(viewport.getAlignment());
3464     addHistoryItem(
3465             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3466     alignPanel.paintAlignment(true, false);
3467   }
3468
3469   /**
3470    * DOCUMENT ME!
3471    *
3472    * @param e
3473    *          DOCUMENT ME!
3474    */
3475   @Override
3476   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3477   {
3478     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3479     AlignmentSorter.sortByLength(viewport.getAlignment());
3480     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3481             viewport.getAlignment()));
3482     alignPanel.paintAlignment(true, false);
3483   }
3484
3485   /**
3486    * DOCUMENT ME!
3487    *
3488    * @param e
3489    *          DOCUMENT ME!
3490    */
3491   @Override
3492   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3493   {
3494     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3495     AlignmentSorter.sortByGroup(viewport.getAlignment());
3496     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3497             viewport.getAlignment()));
3498
3499     alignPanel.paintAlignment(true, false);
3500   }
3501
3502   /**
3503    * DOCUMENT ME!
3504    *
3505    * @param e
3506    *          DOCUMENT ME!
3507    */
3508   @Override
3509   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3510   {
3511     new RedundancyPanel(alignPanel, this);
3512   }
3513
3514   /**
3515    * DOCUMENT ME!
3516    *
3517    * @param e
3518    *          DOCUMENT ME!
3519    */
3520   @Override
3521   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3522   {
3523     if ((viewport.getSelectionGroup() == null)
3524             || (viewport.getSelectionGroup().getSize() < 2))
3525     {
3526       JvOptionPane.showInternalMessageDialog(this,
3527               MessageManager.getString(
3528                       "label.you_must_select_least_two_sequences"),
3529               MessageManager.getString("label.invalid_selection"),
3530               JvOptionPane.WARNING_MESSAGE);
3531     }
3532     else
3533     {
3534       JInternalFrame frame = new JInternalFrame();
3535       frame.setContentPane(new PairwiseAlignPanel(viewport));
3536       Desktop.addInternalFrame(frame,
3537               MessageManager.getString("action.pairwise_alignment"), 600,
3538               500);
3539     }
3540   }
3541
3542   @Override
3543   public void autoCalculate_actionPerformed(ActionEvent e)
3544   {
3545     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3546     if (viewport.autoCalculateConsensus)
3547     {
3548       viewport.firePropertyChange("alignment", null,
3549               viewport.getAlignment().getSequences());
3550     }
3551   }
3552
3553   @Override
3554   public void sortByTreeOption_actionPerformed(ActionEvent e)
3555   {
3556     viewport.sortByTree = sortByTree.isSelected();
3557   }
3558
3559   @Override
3560   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3561   {
3562     viewport.followSelection = listenToViewSelections.isSelected();
3563   }
3564
3565   /**
3566    * Constructs a tree panel and adds it to the desktop
3567    *
3568    * @param type
3569    *          tree type (NJ or AV)
3570    * @param modelName
3571    *          name of score model used to compute the tree
3572    * @param options
3573    *          parameters for the distance or similarity calculation
3574    */
3575   void newTreePanel(String type, String modelName,
3576           SimilarityParamsI options)
3577   {
3578     String frameTitle = "";
3579     TreePanel tp;
3580
3581     boolean onSelection = false;
3582     if (viewport.getSelectionGroup() != null
3583             && viewport.getSelectionGroup().getSize() > 0)
3584     {
3585       SequenceGroup sg = viewport.getSelectionGroup();
3586
3587       /* Decide if the selection is a column region */
3588       for (SequenceI _s : sg.getSequences())
3589       {
3590         if (_s.getLength() < sg.getEndRes())
3591         {
3592           JvOptionPane.showMessageDialog(Desktop.desktop,
3593                   MessageManager.getString(
3594                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3595                   MessageManager.getString(
3596                           "label.sequences_selection_not_aligned"),
3597                   JvOptionPane.WARNING_MESSAGE);
3598
3599           return;
3600         }
3601       }
3602       onSelection = true;
3603     }
3604     else
3605     {
3606       if (viewport.getAlignment().getHeight() < 2)
3607       {
3608         return;
3609       }
3610     }
3611
3612     tp = new TreePanel(alignPanel, type, modelName, options);
3613     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3614
3615     frameTitle += " from ";
3616
3617     if (viewport.getViewName() != null)
3618     {
3619       frameTitle += viewport.getViewName() + " of ";
3620     }
3621
3622     frameTitle += this.title;
3623
3624     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3625   }
3626
3627   /**
3628    * DOCUMENT ME!
3629    *
3630    * @param title
3631    *          DOCUMENT ME!
3632    * @param order
3633    *          DOCUMENT ME!
3634    */
3635   public void addSortByOrderMenuItem(String title,
3636           final AlignmentOrder order)
3637   {
3638     final JMenuItem item = new JMenuItem(MessageManager
3639             .formatMessage("action.by_title_param", new Object[]
3640             { title }));
3641     sort.add(item);
3642     item.addActionListener(new java.awt.event.ActionListener()
3643     {
3644       @Override
3645       public void actionPerformed(ActionEvent e)
3646       {
3647         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3648
3649         // TODO: JBPNote - have to map order entries to curent SequenceI
3650         // pointers
3651         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3652
3653         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3654                 viewport.getAlignment()));
3655
3656         alignPanel.paintAlignment(true, false);
3657       }
3658     });
3659   }
3660
3661   /**
3662    * Add a new sort by annotation score menu item
3663    *
3664    * @param sort
3665    *          the menu to add the option to
3666    * @param scoreLabel
3667    *          the label used to retrieve scores for each sequence on the
3668    *          alignment
3669    */
3670   public void addSortByAnnotScoreMenuItem(JMenu sort,
3671           final String scoreLabel)
3672   {
3673     final JMenuItem item = new JMenuItem(scoreLabel);
3674     sort.add(item);
3675     item.addActionListener(new java.awt.event.ActionListener()
3676     {
3677       @Override
3678       public void actionPerformed(ActionEvent e)
3679       {
3680         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3681         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3682                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3683         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3684                 viewport.getAlignment()));
3685         alignPanel.paintAlignment(true, false);
3686       }
3687     });
3688   }
3689
3690   /**
3691    * last hash for alignment's annotation array - used to minimise cost of
3692    * rebuild.
3693    */
3694   protected int _annotationScoreVectorHash;
3695
3696   /**
3697    * search the alignment and rebuild the sort by annotation score submenu the
3698    * last alignment annotation vector hash is stored to minimize cost of
3699    * rebuilding in subsequence calls.
3700    *
3701    */
3702   @Override
3703   public void buildSortByAnnotationScoresMenu()
3704   {
3705     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3706     {
3707       return;
3708     }
3709
3710     if (viewport.getAlignment().getAlignmentAnnotation()
3711             .hashCode() != _annotationScoreVectorHash)
3712     {
3713       sortByAnnotScore.removeAll();
3714       // almost certainly a quicker way to do this - but we keep it simple
3715       Hashtable scoreSorts = new Hashtable();
3716       AlignmentAnnotation aann[];
3717       for (SequenceI sqa : viewport.getAlignment().getSequences())
3718       {
3719         aann = sqa.getAnnotation();
3720         for (int i = 0; aann != null && i < aann.length; i++)
3721         {
3722           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3723           {
3724             scoreSorts.put(aann[i].label, aann[i].label);
3725           }
3726         }
3727       }
3728       Enumeration labels = scoreSorts.keys();
3729       while (labels.hasMoreElements())
3730       {
3731         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3732                 (String) labels.nextElement());
3733       }
3734       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3735       scoreSorts.clear();
3736
3737       _annotationScoreVectorHash = viewport.getAlignment()
3738               .getAlignmentAnnotation().hashCode();
3739     }
3740   }
3741
3742   /**
3743    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3744    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3745    * call. Listeners are added to remove the menu item when the treePanel is
3746    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3747    * modified.
3748    */
3749   @Override
3750   public void buildTreeSortMenu()
3751   {
3752     sortByTreeMenu.removeAll();
3753
3754     List<Component> comps = PaintRefresher.components
3755             .get(viewport.getSequenceSetId());
3756     List<TreePanel> treePanels = new ArrayList<>();
3757     for (Component comp : comps)
3758     {
3759       if (comp instanceof TreePanel)
3760       {
3761         treePanels.add((TreePanel) comp);
3762       }
3763     }
3764
3765     if (treePanels.size() < 1)
3766     {
3767       sortByTreeMenu.setVisible(false);
3768       return;
3769     }
3770
3771     sortByTreeMenu.setVisible(true);
3772
3773     for (final TreePanel tp : treePanels)
3774     {
3775       final JMenuItem item = new JMenuItem(tp.getTitle());
3776       item.addActionListener(new java.awt.event.ActionListener()
3777       {
3778         @Override
3779         public void actionPerformed(ActionEvent e)
3780         {
3781           tp.sortByTree_actionPerformed();
3782           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3783
3784         }
3785       });
3786
3787       sortByTreeMenu.add(item);
3788     }
3789   }
3790
3791   public boolean sortBy(AlignmentOrder alorder, String undoname)
3792   {
3793     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3794     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3795     if (undoname != null)
3796     {
3797       addHistoryItem(new OrderCommand(undoname, oldOrder,
3798               viewport.getAlignment()));
3799     }
3800     alignPanel.paintAlignment(true, false);
3801     return true;
3802   }
3803
3804   /**
3805    * Work out whether the whole set of sequences or just the selected set will
3806    * be submitted for multiple alignment.
3807    *
3808    */
3809   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3810   {
3811     // Now, check we have enough sequences
3812     AlignmentView msa = null;
3813
3814     if ((viewport.getSelectionGroup() != null)
3815             && (viewport.getSelectionGroup().getSize() > 1))
3816     {
3817       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3818       // some common interface!
3819       /*
3820        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3821        * SequenceI[sz = seqs.getSize(false)];
3822        *
3823        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3824        * seqs.getSequenceAt(i); }
3825        */
3826       msa = viewport.getAlignmentView(true);
3827     }
3828     else if (viewport.getSelectionGroup() != null
3829             && viewport.getSelectionGroup().getSize() == 1)
3830     {
3831       int option = JvOptionPane.showConfirmDialog(this,
3832               MessageManager.getString("warn.oneseq_msainput_selection"),
3833               MessageManager.getString("label.invalid_selection"),
3834               JvOptionPane.OK_CANCEL_OPTION);
3835       if (option == JvOptionPane.OK_OPTION)
3836       {
3837         msa = viewport.getAlignmentView(false);
3838       }
3839     }
3840     else
3841     {
3842       msa = viewport.getAlignmentView(false);
3843     }
3844     return msa;
3845   }
3846
3847   /**
3848    * Decides what is submitted to a secondary structure prediction service: the
3849    * first sequence in the alignment, or in the current selection, or, if the
3850    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3851    * region or the whole alignment. (where the first sequence in the set is the
3852    * one that the prediction will be for).
3853    */
3854   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3855   {
3856     AlignmentView seqs = null;
3857
3858     if ((viewport.getSelectionGroup() != null)
3859             && (viewport.getSelectionGroup().getSize() > 0))
3860     {
3861       seqs = viewport.getAlignmentView(true);
3862     }
3863     else
3864     {
3865       seqs = viewport.getAlignmentView(false);
3866     }
3867     // limit sequences - JBPNote in future - could spawn multiple prediction
3868     // jobs
3869     // TODO: viewport.getAlignment().isAligned is a global state - the local
3870     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3871     if (!viewport.getAlignment().isAligned(false))
3872     {
3873       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3874       // TODO: if seqs.getSequences().length>1 then should really have warned
3875       // user!
3876
3877     }
3878     return seqs;
3879   }
3880
3881   /**
3882    * DOCUMENT ME!
3883    *
3884    * @param e
3885    *          DOCUMENT ME!
3886    */
3887   @Override
3888   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3889   {
3890     // Pick the tree file
3891     JalviewFileChooser chooser = new JalviewFileChooser(
3892             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3893     chooser.setFileView(new JalviewFileView());
3894     chooser.setDialogTitle(
3895             MessageManager.getString("label.select_newick_like_tree_file"));
3896     chooser.setToolTipText(
3897             MessageManager.getString("label.load_tree_file"));
3898
3899     int value = chooser.showOpenDialog(null);
3900
3901     if (value == JalviewFileChooser.APPROVE_OPTION)
3902     {
3903       String filePath = chooser.getSelectedFile().getPath();
3904       Cache.setProperty("LAST_DIRECTORY", filePath);
3905       NewickFile fin = null;
3906       try
3907       {
3908         fin = new NewickFile(filePath, DataSourceType.FILE);
3909         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3910       } catch (Exception ex)
3911       {
3912         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3913                 MessageManager.getString("label.problem_reading_tree_file"),
3914                 JvOptionPane.WARNING_MESSAGE);
3915         ex.printStackTrace();
3916       }
3917       if (fin != null && fin.hasWarningMessage())
3918       {
3919         JvOptionPane.showMessageDialog(Desktop.desktop,
3920                 fin.getWarningMessage(),
3921                 MessageManager
3922                         .getString("label.possible_problem_with_tree_file"),
3923                 JvOptionPane.WARNING_MESSAGE);
3924       }
3925     }
3926   }
3927
3928   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3929   {
3930     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3931   }
3932
3933   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3934           int h, int x, int y)
3935   {
3936     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3937   }
3938
3939   /**
3940    * Add a treeviewer for the tree extracted from a Newick file object to the
3941    * current alignment view
3942    *
3943    * @param nf
3944    *          the tree
3945    * @param title
3946    *          tree viewer title
3947    * @param input
3948    *          Associated alignment input data (or null)
3949    * @param w
3950    *          width
3951    * @param h
3952    *          height
3953    * @param x
3954    *          position
3955    * @param y
3956    *          position
3957    * @return TreePanel handle
3958    */
3959   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3960           AlignmentView input, int w, int h, int x, int y)
3961   {
3962     TreePanel tp = null;
3963
3964     try
3965     {
3966       nf.parse();
3967
3968       if (nf.getTree() != null)
3969       {
3970         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3971
3972         tp.setSize(w, h);
3973
3974         if (x > 0 && y > 0)
3975         {
3976           tp.setLocation(x, y);
3977         }
3978
3979         Desktop.addInternalFrame(tp, treeTitle, w, h);
3980       }
3981     } catch (Exception ex)
3982     {
3983       ex.printStackTrace();
3984     }
3985
3986     return tp;
3987   }
3988
3989   private boolean buildingMenu = false;
3990
3991   /**
3992    * Generates menu items and listener event actions for web service clients
3993    *
3994    */
3995   public void BuildWebServiceMenu()
3996   {
3997     while (buildingMenu)
3998     {
3999       try
4000       {
4001         System.err.println("Waiting for building menu to finish.");
4002         Thread.sleep(10);
4003       } catch (Exception e)
4004       {
4005       }
4006     }
4007     final AlignFrame me = this;
4008     buildingMenu = true;
4009     new Thread(new Runnable()
4010     {
4011       @Override
4012       public void run()
4013       {
4014         final List<JMenuItem> legacyItems = new ArrayList<>();
4015         try
4016         {
4017           // System.err.println("Building ws menu again "
4018           // + Thread.currentThread());
4019           // TODO: add support for context dependent disabling of services based
4020           // on
4021           // alignment and current selection
4022           // TODO: add additional serviceHandle parameter to specify abstract
4023           // handler
4024           // class independently of AbstractName
4025           // TODO: add in rediscovery GUI function to restart discoverer
4026           // TODO: group services by location as well as function and/or
4027           // introduce
4028           // object broker mechanism.
4029           final Vector<JMenu> wsmenu = new Vector<>();
4030           final IProgressIndicator af = me;
4031
4032           /*
4033            * do not i18n these strings - they are hard-coded in class
4034            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4035            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4036            */
4037           final JMenu msawsmenu = new JMenu("Alignment");
4038           final JMenu secstrmenu = new JMenu(
4039                   "Secondary Structure Prediction");
4040           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4041           final JMenu analymenu = new JMenu("Analysis");
4042           final JMenu dismenu = new JMenu("Protein Disorder");
4043           // JAL-940 - only show secondary structure prediction services from
4044           // the legacy server
4045           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4046               // &&
4047           Discoverer.services != null && (Discoverer.services.size() > 0))
4048           {
4049             // TODO: refactor to allow list of AbstractName/Handler bindings to
4050             // be
4051             // stored or retrieved from elsewhere
4052             // No MSAWS used any more:
4053             // Vector msaws = null; // (Vector)
4054             // Discoverer.services.get("MsaWS");
4055             Vector secstrpr = (Vector) Discoverer.services
4056                     .get("SecStrPred");
4057             if (secstrpr != null)
4058             {
4059               // Add any secondary structure prediction services
4060               for (int i = 0, j = secstrpr.size(); i < j; i++)
4061               {
4062                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4063                         .get(i);
4064                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4065                         .getServiceClient(sh);
4066                 int p = secstrmenu.getItemCount();
4067                 impl.attachWSMenuEntry(secstrmenu, me);
4068                 int q = secstrmenu.getItemCount();
4069                 for (int litm = p; litm < q; litm++)
4070                 {
4071                   legacyItems.add(secstrmenu.getItem(litm));
4072                 }
4073               }
4074             }
4075           }
4076
4077           // Add all submenus in the order they should appear on the web
4078           // services menu
4079           wsmenu.add(msawsmenu);
4080           wsmenu.add(secstrmenu);
4081           wsmenu.add(dismenu);
4082           wsmenu.add(analymenu);
4083           // No search services yet
4084           // wsmenu.add(seqsrchmenu);
4085
4086           javax.swing.SwingUtilities.invokeLater(new Runnable()
4087           {
4088             @Override
4089             public void run()
4090             {
4091               try
4092               {
4093                 webService.removeAll();
4094                 // first, add discovered services onto the webservices menu
4095                 if (wsmenu.size() > 0)
4096                 {
4097                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4098                   {
4099                     webService.add(wsmenu.get(i));
4100                   }
4101                 }
4102                 else
4103                 {
4104                   webService.add(me.webServiceNoServices);
4105                 }
4106                 // TODO: move into separate menu builder class.
4107                 boolean new_sspred = false;
4108                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4109                 {
4110                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4111                   if (jws2servs != null)
4112                   {
4113                     if (jws2servs.hasServices())
4114                     {
4115                       jws2servs.attachWSMenuEntry(webService, me);
4116                       for (Jws2Instance sv : jws2servs.getServices())
4117                       {
4118                         if (sv.description.toLowerCase().contains("jpred"))
4119                         {
4120                           for (JMenuItem jmi : legacyItems)
4121                           {
4122                             jmi.setVisible(false);
4123                           }
4124                         }
4125                       }
4126
4127                     }
4128                     if (jws2servs.isRunning())
4129                     {
4130                       JMenuItem tm = new JMenuItem(
4131                               "Still discovering JABA Services");
4132                       tm.setEnabled(false);
4133                       webService.add(tm);
4134                     }
4135                   }
4136                 }
4137                 build_urlServiceMenu(me.webService);
4138                 build_fetchdbmenu(webService);
4139                 for (JMenu item : wsmenu)
4140                 {
4141                   if (item.getItemCount() == 0)
4142                   {
4143                     item.setEnabled(false);
4144                   }
4145                   else
4146                   {
4147                     item.setEnabled(true);
4148                   }
4149                 }
4150               } catch (Exception e)
4151               {
4152                 Cache.log.debug(
4153                         "Exception during web service menu building process.",
4154                         e);
4155               }
4156             }
4157           });
4158         } catch (Exception e)
4159         {
4160         }
4161         buildingMenu = false;
4162       }
4163     }).start();
4164
4165   }
4166
4167   /**
4168    * construct any groupURL type service menu entries.
4169    *
4170    * @param webService
4171    */
4172   private void build_urlServiceMenu(JMenu webService)
4173   {
4174     // TODO: remove this code when 2.7 is released
4175     // DEBUG - alignmentView
4176     /*
4177      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4178      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4179      *
4180      * @Override public void actionPerformed(ActionEvent e) {
4181      * jalview.datamodel.AlignmentView
4182      * .testSelectionViews(af.viewport.getAlignment(),
4183      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4184      *
4185      * }); webService.add(testAlView);
4186      */
4187     // TODO: refactor to RestClient discoverer and merge menu entries for
4188     // rest-style services with other types of analysis/calculation service
4189     // SHmmr test client - still being implemented.
4190     // DEBUG - alignmentView
4191
4192     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4193             .getRestClients())
4194     {
4195       client.attachWSMenuEntry(
4196               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4197               this);
4198     }
4199   }
4200
4201   /**
4202    * Searches the alignment sequences for xRefs and builds the Show
4203    * Cross-References menu (formerly called Show Products), with database
4204    * sources for which cross-references are found (protein sources for a
4205    * nucleotide alignment and vice versa)
4206    *
4207    * @return true if Show Cross-references menu should be enabled
4208    */
4209   public boolean canShowProducts()
4210   {
4211     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4212     AlignmentI dataset = viewport.getAlignment().getDataset();
4213
4214     showProducts.removeAll();
4215     final boolean dna = viewport.getAlignment().isNucleotide();
4216
4217     if (seqs == null || seqs.length == 0)
4218     {
4219       // nothing to see here.
4220       return false;
4221     }
4222
4223     boolean showp = false;
4224     try
4225     {
4226       List<String> ptypes = new CrossRef(seqs, dataset)
4227               .findXrefSourcesForSequences(dna);
4228
4229       for (final String source : ptypes)
4230       {
4231         showp = true;
4232         final AlignFrame af = this;
4233         JMenuItem xtype = new JMenuItem(source);
4234         xtype.addActionListener(new ActionListener()
4235         {
4236           @Override
4237           public void actionPerformed(ActionEvent e)
4238           {
4239             showProductsFor(af.viewport.getSequenceSelection(), dna,
4240                     source);
4241           }
4242         });
4243         showProducts.add(xtype);
4244       }
4245       showProducts.setVisible(showp);
4246       showProducts.setEnabled(showp);
4247     } catch (Exception e)
4248     {
4249       Cache.log.warn(
4250               "canShowProducts threw an exception - please report to help@jalview.org",
4251               e);
4252       return false;
4253     }
4254     return showp;
4255   }
4256
4257   /**
4258    * Finds and displays cross-references for the selected sequences (protein
4259    * products for nucleotide sequences, dna coding sequences for peptides).
4260    *
4261    * @param sel
4262    *          the sequences to show cross-references for
4263    * @param dna
4264    *          true if from a nucleotide alignment (so showing proteins)
4265    * @param source
4266    *          the database to show cross-references for
4267    */
4268   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4269           final String source)
4270   {
4271     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4272             .start();
4273   }
4274
4275   /**
4276    * Construct and display a new frame containing the translation of this
4277    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4278    */
4279   @Override
4280   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4281   {
4282     AlignmentI al = null;
4283     try
4284     {
4285       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4286
4287       al = dna.translateCdna(codeTable);
4288     } catch (Exception ex)
4289     {
4290       jalview.bin.Cache.log.error(
4291               "Exception during translation. Please report this !", ex);
4292       final String msg = MessageManager.getString(
4293               "label.error_when_translating_sequences_submit_bug_report");
4294       final String errorTitle = MessageManager
4295               .getString("label.implementation_error")
4296               + MessageManager.getString("label.translation_failed");
4297       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4298               JvOptionPane.ERROR_MESSAGE);
4299       return;
4300     }
4301     if (al == null || al.getHeight() == 0)
4302     {
4303       final String msg = MessageManager.getString(
4304               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4305       final String errorTitle = MessageManager
4306               .getString("label.translation_failed");
4307       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4308               JvOptionPane.WARNING_MESSAGE);
4309     }
4310     else
4311     {
4312       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4313       af.setFileFormat(this.currentFileFormat);
4314       final String newTitle = MessageManager
4315               .formatMessage("label.translation_of_params", new Object[]
4316               { this.getTitle(), codeTable.getId() });
4317       af.setTitle(newTitle);
4318       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4319       {
4320         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4321         viewport.openSplitFrame(af, new Alignment(seqs));
4322       }
4323       else
4324       {
4325         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4326                 DEFAULT_HEIGHT);
4327       }
4328     }
4329   }
4330
4331   /**
4332    * Set the file format
4333    *
4334    * @param format
4335    */
4336   public void setFileFormat(FileFormatI format)
4337   {
4338     this.currentFileFormat = format;
4339   }
4340
4341   /**
4342    * Try to load a features file onto the alignment.
4343    *
4344    * @param file
4345    *          contents or path to retrieve file
4346    * @param sourceType
4347    *          access mode of file (see jalview.io.AlignFile)
4348    * @return true if features file was parsed correctly.
4349    */
4350   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4351   {
4352     return avc.parseFeaturesFile(file, sourceType,
4353             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4354
4355   }
4356
4357   @Override
4358   public void refreshFeatureUI(boolean enableIfNecessary)
4359   {
4360     // note - currently this is only still here rather than in the controller
4361     // because of the featureSettings hard reference that is yet to be
4362     // abstracted
4363     if (enableIfNecessary)
4364     {
4365       viewport.setShowSequenceFeatures(true);
4366       showSeqFeatures.setSelected(true);
4367     }
4368
4369   }
4370
4371   @Override
4372   public void dragEnter(DropTargetDragEvent evt)
4373   {
4374   }
4375
4376   @Override
4377   public void dragExit(DropTargetEvent evt)
4378   {
4379   }
4380
4381   @Override
4382   public void dragOver(DropTargetDragEvent evt)
4383   {
4384   }
4385
4386   @Override
4387   public void dropActionChanged(DropTargetDragEvent evt)
4388   {
4389   }
4390
4391   @Override
4392   public void drop(DropTargetDropEvent evt)
4393   {
4394     // JAL-1552 - acceptDrop required before getTransferable call for
4395     // Java's Transferable for native dnd
4396     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4397     Transferable t = evt.getTransferable();
4398     final AlignFrame thisaf = this;
4399     final List<String> files = new ArrayList<>();
4400     List<DataSourceType> protocols = new ArrayList<>();
4401
4402     try
4403     {
4404       Desktop.transferFromDropTarget(files, protocols, evt, t);
4405     } catch (Exception e)
4406     {
4407       e.printStackTrace();
4408     }
4409     if (files != null)
4410     {
4411       new Thread(new Runnable()
4412       {
4413         @Override
4414         public void run()
4415         {
4416           try
4417           {
4418             // check to see if any of these files have names matching sequences
4419             // in
4420             // the alignment
4421             SequenceIdMatcher idm = new SequenceIdMatcher(
4422                     viewport.getAlignment().getSequencesArray());
4423             /**
4424              * Object[] { String,SequenceI}
4425              */
4426             ArrayList<Object[]> filesmatched = new ArrayList<>();
4427             ArrayList<String> filesnotmatched = new ArrayList<>();
4428             for (int i = 0; i < files.size(); i++)
4429             {
4430               String file = files.get(i).toString();
4431               String pdbfn = "";
4432               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4433               if (protocol == DataSourceType.FILE)
4434               {
4435                 File fl = new File(file);
4436                 pdbfn = fl.getName();
4437               }
4438               else if (protocol == DataSourceType.URL)
4439               {
4440                 URL url = new URL(file);
4441                 pdbfn = url.getFile();
4442               }
4443               if (pdbfn.length() > 0)
4444               {
4445                 // attempt to find a match in the alignment
4446                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4447                 int l = 0, c = pdbfn.indexOf(".");
4448                 while (mtch == null && c != -1)
4449                 {
4450                   do
4451                   {
4452                     l = c;
4453                   } while ((c = pdbfn.indexOf(".", l)) > l);
4454                   if (l > -1)
4455                   {
4456                     pdbfn = pdbfn.substring(0, l);
4457                   }
4458                   mtch = idm.findAllIdMatches(pdbfn);
4459                 }
4460                 if (mtch != null)
4461                 {
4462                   FileFormatI type = null;
4463                   try
4464                   {
4465                     type = new IdentifyFile().identify(file, protocol);
4466                   } catch (Exception ex)
4467                   {
4468                     type = null;
4469                   }
4470                   if (type != null && type.isStructureFile())
4471                   {
4472                     filesmatched.add(new Object[] { file, protocol, mtch });
4473                     continue;
4474                   }
4475                 }
4476                 // File wasn't named like one of the sequences or wasn't a PDB
4477                 // file.
4478                 filesnotmatched.add(file);
4479               }
4480             }
4481             int assocfiles = 0;
4482             if (filesmatched.size() > 0)
4483             {
4484               boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4485               if (!autoAssociate)
4486               {
4487                 String msg = MessageManager.formatMessage(
4488                         "label.automatically_associate_structure_files_with_sequences_same_name",
4489                         new Object[]
4490                         { Integer.valueOf(filesmatched.size())
4491                                 .toString() });
4492                 String ttl = MessageManager.getString(
4493                         "label.automatically_associate_structure_files_by_name");
4494                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4495                         ttl, JvOptionPane.YES_NO_OPTION);
4496                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4497               }
4498               if (autoAssociate)
4499               {
4500                 for (Object[] fm : filesmatched)
4501                 {
4502                   // try and associate
4503                   // TODO: may want to set a standard ID naming formalism for
4504                   // associating PDB files which have no IDs.
4505                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4506                   {
4507                     PDBEntry pe = new AssociatePdbFileWithSeq()
4508                             .associatePdbWithSeq((String) fm[0],
4509                                     (DataSourceType) fm[1], toassoc, false,
4510                                     Desktop.instance);
4511                     if (pe != null)
4512                     {
4513                       System.err.println("Associated file : "
4514                               + ((String) fm[0]) + " with "
4515                               + toassoc.getDisplayId(true));
4516                       assocfiles++;
4517                     }
4518                   }
4519                   // TODO: do we need to update overview ? only if features are
4520                   // shown I guess
4521                   alignPanel.paintAlignment(true, false);
4522                 }
4523               }
4524               else
4525               {
4526                 /*
4527                  * add declined structures as sequences
4528                  */
4529                 for (Object[] o : filesmatched)
4530                 {
4531                   filesnotmatched.add((String) o[0]);
4532                 }
4533               }
4534             }
4535             if (filesnotmatched.size() > 0)
4536             {
4537               if (assocfiles > 0 && (Cache.getDefault(
4538                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4539                       || JvOptionPane.showConfirmDialog(thisaf,
4540                               "<html>" + MessageManager.formatMessage(
4541                                       "label.ignore_unmatched_dropped_files_info",
4542                                       new Object[]
4543                                       { Integer.valueOf(
4544                                               filesnotmatched.size())
4545                                               .toString() })
4546                                       + "</html>",
4547                               MessageManager.getString(
4548                                       "label.ignore_unmatched_dropped_files"),
4549                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4550               {
4551                 return;
4552               }
4553               for (String fn : filesnotmatched)
4554               {
4555                 loadJalviewDataFile(fn, null, null, null);
4556               }
4557
4558             }
4559           } catch (Exception ex)
4560           {
4561             ex.printStackTrace();
4562           }
4563         }
4564       }).start();
4565     }
4566   }
4567
4568   /**
4569    * Attempt to load a "dropped" file or URL string, by testing in turn for
4570    * <ul>
4571    * <li>an Annotation file</li>
4572    * <li>a JNet file</li>
4573    * <li>a features file</li>
4574    * <li>else try to interpret as an alignment file</li>
4575    * </ul>
4576    *
4577    * @param file
4578    *          either a filename or a URL string.
4579    */
4580   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4581           FileFormatI format, SequenceI assocSeq)
4582   {
4583     try
4584     {
4585       if (sourceType == null)
4586       {
4587         sourceType = FormatAdapter.checkProtocol(file);
4588       }
4589       // if the file isn't identified, or not positively identified as some
4590       // other filetype (PFAM is default unidentified alignment file type) then
4591       // try to parse as annotation.
4592       boolean isAnnotation = (format == null
4593               || FileFormat.Pfam.equals(format))
4594                       ? new AnnotationFile().annotateAlignmentView(viewport,
4595                               file, sourceType)
4596                       : false;
4597
4598       if (!isAnnotation)
4599       {
4600         // first see if its a T-COFFEE score file
4601         TCoffeeScoreFile tcf = null;
4602         try
4603         {
4604           tcf = new TCoffeeScoreFile(file, sourceType);
4605           if (tcf.isValid())
4606           {
4607             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4608             {
4609               buildColourMenu();
4610               changeColour(
4611                       new TCoffeeColourScheme(viewport.getAlignment()));
4612               isAnnotation = true;
4613               statusBar.setText(MessageManager.getString(
4614                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4615             }
4616             else
4617             {
4618               // some problem - if no warning its probable that the ID matching
4619               // process didn't work
4620               JvOptionPane.showMessageDialog(Desktop.desktop,
4621                       tcf.getWarningMessage() == null
4622                               ? MessageManager.getString(
4623                                       "label.check_file_matches_sequence_ids_alignment")
4624                               : tcf.getWarningMessage(),
4625                       MessageManager.getString(
4626                               "label.problem_reading_tcoffee_score_file"),
4627                       JvOptionPane.WARNING_MESSAGE);
4628             }
4629           }
4630           else
4631           {
4632             tcf = null;
4633           }
4634         } catch (Exception x)
4635         {
4636           Cache.log.debug(
4637                   "Exception when processing data source as T-COFFEE score file",
4638                   x);
4639           tcf = null;
4640         }
4641         if (tcf == null)
4642         {
4643           // try to see if its a JNet 'concise' style annotation file *before*
4644           // we
4645           // try to parse it as a features file
4646           if (format == null)
4647           {
4648             format = new IdentifyFile().identify(file, sourceType);
4649           }
4650           if (FileFormat.ScoreMatrix == format)
4651           {
4652             ScoreMatrixFile sm = new ScoreMatrixFile(
4653                     new FileParse(file, sourceType));
4654             sm.parse();
4655             // todo: i18n this message
4656             statusBar.setText(MessageManager.formatMessage(
4657                     "label.successfully_loaded_matrix",
4658                     sm.getMatrixName()));
4659           }
4660           else if (FileFormat.Jnet.equals(format))
4661           {
4662             JPredFile predictions = new JPredFile(file, sourceType);
4663             new JnetAnnotationMaker();
4664             JnetAnnotationMaker.add_annotation(predictions,
4665                     viewport.getAlignment(), 0, false);
4666             viewport.getAlignment().setupJPredAlignment();
4667             isAnnotation = true;
4668           }
4669           // else if (IdentifyFile.FeaturesFile.equals(format))
4670           else if (FileFormat.Features.equals(format))
4671           {
4672             if (parseFeaturesFile(file, sourceType))
4673             {
4674               alignPanel.paintAlignment(true, true);
4675             }
4676           }
4677           else
4678           {
4679             new FileLoader().LoadFile(viewport, file, sourceType, format);
4680           }
4681         }
4682       }
4683       if (isAnnotation)
4684       {
4685
4686         alignPanel.adjustAnnotationHeight();
4687         viewport.updateSequenceIdColours();
4688         buildSortByAnnotationScoresMenu();
4689         alignPanel.paintAlignment(true, true);
4690       }
4691     } catch (Exception ex)
4692     {
4693       ex.printStackTrace();
4694     } catch (OutOfMemoryError oom)
4695     {
4696       try
4697       {
4698         System.gc();
4699       } catch (Exception x)
4700       {
4701       }
4702       new OOMWarning(
4703               "loading data "
4704                       + (sourceType != null
4705                               ? (sourceType == DataSourceType.PASTE
4706                                       ? "from clipboard."
4707                                       : "using " + sourceType + " from "
4708                                               + file)
4709                               : ".")
4710                       + (format != null
4711                               ? "(parsing as '" + format + "' file)"
4712                               : ""),
4713               oom, Desktop.desktop);
4714     }
4715   }
4716
4717   /**
4718    * Method invoked by the ChangeListener on the tabbed pane, in other words
4719    * when a different tabbed pane is selected by the user or programmatically.
4720    */
4721   @Override
4722   public void tabSelectionChanged(int index)
4723   {
4724     if (index > -1)
4725     {
4726       alignPanel = alignPanels.get(index);
4727       viewport = alignPanel.av;
4728       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4729       setMenusFromViewport(viewport);
4730     }
4731
4732     /*
4733      * 'focus' any colour slider that is open to the selected viewport
4734      */
4735     if (viewport.getConservationSelected())
4736     {
4737       SliderPanel.setConservationSlider(alignPanel,
4738               viewport.getResidueShading(), alignPanel.getViewName());
4739     }
4740     else
4741     {
4742       SliderPanel.hideConservationSlider();
4743     }
4744     if (viewport.getAbovePIDThreshold())
4745     {
4746       SliderPanel.setPIDSliderSource(alignPanel,
4747               viewport.getResidueShading(), alignPanel.getViewName());
4748     }
4749     else
4750     {
4751       SliderPanel.hidePIDSlider();
4752     }
4753
4754     /*
4755      * If there is a frame linked to this one in a SplitPane, switch it to the
4756      * same view tab index. No infinite recursion of calls should happen, since
4757      * tabSelectionChanged() should not get invoked on setting the selected
4758      * index to an unchanged value. Guard against setting an invalid index
4759      * before the new view peer tab has been created.
4760      */
4761     final AlignViewportI peer = viewport.getCodingComplement();
4762     if (peer != null)
4763     {
4764       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4765               .getAlignPanel().alignFrame;
4766       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4767       {
4768         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4769       }
4770     }
4771   }
4772
4773   /**
4774    * On right mouse click on view tab, prompt for and set new view name.
4775    */
4776   @Override
4777   public void tabbedPane_mousePressed(MouseEvent e)
4778   {
4779     if (e.isPopupTrigger())
4780     {
4781       String msg = MessageManager.getString("label.enter_view_name");
4782       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4783               JvOptionPane.QUESTION_MESSAGE);
4784
4785       if (reply != null)
4786       {
4787         viewport.setViewName(reply);
4788         // TODO warn if reply is in getExistingViewNames()?
4789         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4790       }
4791     }
4792   }
4793
4794   public AlignViewport getCurrentView()
4795   {
4796     return viewport;
4797   }
4798
4799   /**
4800    * Open the dialog for regex description parsing.
4801    */
4802   @Override
4803   protected void extractScores_actionPerformed(ActionEvent e)
4804   {
4805     ParseProperties pp = new jalview.analysis.ParseProperties(
4806             viewport.getAlignment());
4807     // TODO: verify regex and introduce GUI dialog for version 2.5
4808     // if (pp.getScoresFromDescription("col", "score column ",
4809     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4810     // true)>0)
4811     if (pp.getScoresFromDescription("description column",
4812             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4813     {
4814       buildSortByAnnotationScoresMenu();
4815     }
4816   }
4817
4818   /*
4819    * (non-Javadoc)
4820    *
4821    * @see
4822    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4823    * )
4824    */
4825   @Override
4826   protected void showDbRefs_actionPerformed(ActionEvent e)
4827   {
4828     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4829   }
4830
4831   /*
4832    * (non-Javadoc)
4833    *
4834    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4835    * ActionEvent)
4836    */
4837   @Override
4838   protected void showNpFeats_actionPerformed(ActionEvent e)
4839   {
4840     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4841   }
4842
4843   /**
4844    * find the viewport amongst the tabs in this alignment frame and close that
4845    * tab
4846    *
4847    * @param av
4848    */
4849   public boolean closeView(AlignViewportI av)
4850   {
4851     if (viewport == av)
4852     {
4853       this.closeMenuItem_actionPerformed(false);
4854       return true;
4855     }
4856     Component[] comp = tabbedPane.getComponents();
4857     for (int i = 0; comp != null && i < comp.length; i++)
4858     {
4859       if (comp[i] instanceof AlignmentPanel)
4860       {
4861         if (((AlignmentPanel) comp[i]).av == av)
4862         {
4863           // close the view.
4864           closeView((AlignmentPanel) comp[i]);
4865           return true;
4866         }
4867       }
4868     }
4869     return false;
4870   }
4871
4872   protected void build_fetchdbmenu(JMenu webService)
4873   {
4874     // Temporary hack - DBRef Fetcher always top level ws entry.
4875     // TODO We probably want to store a sequence database checklist in
4876     // preferences and have checkboxes.. rather than individual sources selected
4877     // here
4878     final JMenu rfetch = new JMenu(
4879             MessageManager.getString("action.fetch_db_references"));
4880     rfetch.setToolTipText(MessageManager.getString(
4881             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4882     webService.add(rfetch);
4883
4884     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4885             MessageManager.getString("option.trim_retrieved_seqs"));
4886     trimrs.setToolTipText(
4887             MessageManager.getString("label.trim_retrieved_sequences"));
4888     trimrs.setSelected(
4889             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4890     trimrs.addActionListener(new ActionListener()
4891     {
4892       @Override
4893       public void actionPerformed(ActionEvent e)
4894       {
4895         trimrs.setSelected(trimrs.isSelected());
4896         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4897                 Boolean.valueOf(trimrs.isSelected()).toString());
4898       };
4899     });
4900     rfetch.add(trimrs);
4901     JMenuItem fetchr = new JMenuItem(
4902             MessageManager.getString("label.standard_databases"));
4903     fetchr.setToolTipText(
4904             MessageManager.getString("label.fetch_embl_uniprot"));
4905     fetchr.addActionListener(new ActionListener()
4906     {
4907
4908       @Override
4909       public void actionPerformed(ActionEvent e)
4910       {
4911         new Thread(new Runnable()
4912         {
4913           @Override
4914           public void run()
4915           {
4916             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4917                     .getAlignment().isNucleotide();
4918             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4919                     alignPanel.av.getSequenceSelection(),
4920                     alignPanel.alignFrame, null,
4921                     alignPanel.alignFrame.featureSettings, isNucleotide);
4922             dbRefFetcher.addListener(new FetchFinishedListenerI()
4923             {
4924               @Override
4925               public void finished()
4926               {
4927                 AlignFrame.this.setMenusForViewport();
4928               }
4929             });
4930             dbRefFetcher.fetchDBRefs(false);
4931           }
4932         }).start();
4933
4934       }
4935
4936     });
4937     rfetch.add(fetchr);
4938     final AlignFrame me = this;
4939     new Thread(new Runnable()
4940     {
4941       @Override
4942       public void run()
4943       {
4944         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4945                 .getSequenceFetcherSingleton(me);
4946         javax.swing.SwingUtilities.invokeLater(new Runnable()
4947         {
4948           @Override
4949           public void run()
4950           {
4951             String[] dbclasses = sf.getOrderedSupportedSources();
4952             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4953             // jalview.util.QuickSort.sort(otherdb, otherdb);
4954             List<DbSourceProxy> otherdb;
4955             JMenu dfetch = new JMenu();
4956             JMenu ifetch = new JMenu();
4957             JMenuItem fetchr = null;
4958             int comp = 0, icomp = 0, mcomp = 15;
4959             String mname = null;
4960             int dbi = 0;
4961             for (String dbclass : dbclasses)
4962             {
4963               otherdb = sf.getSourceProxy(dbclass);
4964               // add a single entry for this class, or submenu allowing 'fetch
4965               // all' or pick one
4966               if (otherdb == null || otherdb.size() < 1)
4967               {
4968                 continue;
4969               }
4970               // List<DbSourceProxy> dbs=otherdb;
4971               // otherdb=new ArrayList<DbSourceProxy>();
4972               // for (DbSourceProxy db:dbs)
4973               // {
4974               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4975               // }
4976               if (mname == null)
4977               {
4978                 mname = "From " + dbclass;
4979               }
4980               if (otherdb.size() == 1)
4981               {
4982                 final DbSourceProxy[] dassource = otherdb
4983                         .toArray(new DbSourceProxy[0]);
4984                 DbSourceProxy src = otherdb.get(0);
4985                 fetchr = new JMenuItem(src.getDbSource());
4986                 fetchr.addActionListener(new ActionListener()
4987                 {
4988
4989                   @Override
4990                   public void actionPerformed(ActionEvent e)
4991                   {
4992                     new Thread(new Runnable()
4993                     {
4994
4995                       @Override
4996                       public void run()
4997                       {
4998                         boolean isNucleotide = alignPanel.alignFrame
4999                                 .getViewport().getAlignment()
5000                                 .isNucleotide();
5001                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5002                                 alignPanel.av.getSequenceSelection(),
5003                                 alignPanel.alignFrame, dassource,
5004                                 alignPanel.alignFrame.featureSettings,
5005                                 isNucleotide);
5006                         dbRefFetcher
5007                                 .addListener(new FetchFinishedListenerI()
5008                                 {
5009                                   @Override
5010                                   public void finished()
5011                                   {
5012                                     AlignFrame.this.setMenusForViewport();
5013                                   }
5014                                 });
5015                         dbRefFetcher.fetchDBRefs(false);
5016                       }
5017                     }).start();
5018                   }
5019
5020                 });
5021                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5022                         MessageManager.formatMessage(
5023                                 "label.fetch_retrieve_from", new Object[]
5024                                 { src.getDbName() })));
5025                 dfetch.add(fetchr);
5026                 comp++;
5027               }
5028               else
5029               {
5030                 final DbSourceProxy[] dassource = otherdb
5031                         .toArray(new DbSourceProxy[0]);
5032                 // fetch all entry
5033                 DbSourceProxy src = otherdb.get(0);
5034                 fetchr = new JMenuItem(MessageManager
5035                         .formatMessage("label.fetch_all_param", new Object[]
5036                         { src.getDbSource() }));
5037                 fetchr.addActionListener(new ActionListener()
5038                 {
5039                   @Override
5040                   public void actionPerformed(ActionEvent e)
5041                   {
5042                     new Thread(new Runnable()
5043                     {
5044
5045                       @Override
5046                       public void run()
5047                       {
5048                         boolean isNucleotide = alignPanel.alignFrame
5049                                 .getViewport().getAlignment()
5050                                 .isNucleotide();
5051                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5052                                 alignPanel.av.getSequenceSelection(),
5053                                 alignPanel.alignFrame, dassource,
5054                                 alignPanel.alignFrame.featureSettings,
5055                                 isNucleotide);
5056                         dbRefFetcher
5057                                 .addListener(new FetchFinishedListenerI()
5058                                 {
5059                                   @Override
5060                                   public void finished()
5061                                   {
5062                                     AlignFrame.this.setMenusForViewport();
5063                                   }
5064                                 });
5065                         dbRefFetcher.fetchDBRefs(false);
5066                       }
5067                     }).start();
5068                   }
5069                 });
5070
5071                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5072                         MessageManager.formatMessage(
5073                                 "label.fetch_retrieve_from_all_sources",
5074                                 new Object[]
5075                                 { Integer.valueOf(otherdb.size())
5076                                         .toString(),
5077                                     src.getDbSource(), src.getDbName() })));
5078                 dfetch.add(fetchr);
5079                 comp++;
5080                 // and then build the rest of the individual menus
5081                 ifetch = new JMenu(MessageManager.formatMessage(
5082                         "label.source_from_db_source", new Object[]
5083                         { src.getDbSource() }));
5084                 icomp = 0;
5085                 String imname = null;
5086                 int i = 0;
5087                 for (DbSourceProxy sproxy : otherdb)
5088                 {
5089                   String dbname = sproxy.getDbName();
5090                   String sname = dbname.length() > 5
5091                           ? dbname.substring(0, 5) + "..."
5092                           : dbname;
5093                   String msname = dbname.length() > 10
5094                           ? dbname.substring(0, 10) + "..."
5095                           : dbname;
5096                   if (imname == null)
5097                   {
5098                     imname = MessageManager
5099                             .formatMessage("label.from_msname", new Object[]
5100                             { sname });
5101                   }
5102                   fetchr = new JMenuItem(msname);
5103                   final DbSourceProxy[] dassrc = { sproxy };
5104                   fetchr.addActionListener(new ActionListener()
5105                   {
5106
5107                     @Override
5108                     public void actionPerformed(ActionEvent e)
5109                     {
5110                       new Thread(new Runnable()
5111                       {
5112
5113                         @Override
5114                         public void run()
5115                         {
5116                           boolean isNucleotide = alignPanel.alignFrame
5117                                   .getViewport().getAlignment()
5118                                   .isNucleotide();
5119                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5120                                   alignPanel.av.getSequenceSelection(),
5121                                   alignPanel.alignFrame, dassrc,
5122                                   alignPanel.alignFrame.featureSettings,
5123                                   isNucleotide);
5124                           dbRefFetcher
5125                                   .addListener(new FetchFinishedListenerI()
5126                                   {
5127                                     @Override
5128                                     public void finished()
5129                                     {
5130                                       AlignFrame.this.setMenusForViewport();
5131                                     }
5132                                   });
5133                           dbRefFetcher.fetchDBRefs(false);
5134                         }
5135                       }).start();
5136                     }
5137
5138                   });
5139                   fetchr.setToolTipText(
5140                           "<html>" + MessageManager.formatMessage(
5141                                   "label.fetch_retrieve_from", new Object[]
5142                                   { dbname }));
5143                   ifetch.add(fetchr);
5144                   ++i;
5145                   if (++icomp >= mcomp || i == (otherdb.size()))
5146                   {
5147                     ifetch.setText(MessageManager.formatMessage(
5148                             "label.source_to_target", imname, sname));
5149                     dfetch.add(ifetch);
5150                     ifetch = new JMenu();
5151                     imname = null;
5152                     icomp = 0;
5153                     comp++;
5154                   }
5155                 }
5156               }
5157               ++dbi;
5158               if (comp >= mcomp || dbi >= (dbclasses.length))
5159               {
5160                 dfetch.setText(MessageManager.formatMessage(
5161                         "label.source_to_target", mname, dbclass));
5162                 rfetch.add(dfetch);
5163                 dfetch = new JMenu();
5164                 mname = null;
5165                 comp = 0;
5166               }
5167             }
5168           }
5169         });
5170       }
5171     }).start();
5172
5173   }
5174
5175   /**
5176    * Left justify the whole alignment.
5177    */
5178   @Override
5179   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5180   {
5181     AlignmentI al = viewport.getAlignment();
5182     al.justify(false);
5183     viewport.firePropertyChange("alignment", null, al);
5184   }
5185
5186   /**
5187    * Right justify the whole alignment.
5188    */
5189   @Override
5190   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5191   {
5192     AlignmentI al = viewport.getAlignment();
5193     al.justify(true);
5194     viewport.firePropertyChange("alignment", null, al);
5195   }
5196
5197   @Override
5198   public void setShowSeqFeatures(boolean b)
5199   {
5200     showSeqFeatures.setSelected(b);
5201     viewport.setShowSequenceFeatures(b);
5202   }
5203
5204   /*
5205    * (non-Javadoc)
5206    *
5207    * @see
5208    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5209    * awt.event.ActionEvent)
5210    */
5211   @Override
5212   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5213   {
5214     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5215     alignPanel.paintAlignment(false, false);
5216   }
5217
5218   /*
5219    * (non-Javadoc)
5220    *
5221    * @see
5222    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5223    * .ActionEvent)
5224    */
5225   @Override
5226   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5227   {
5228     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5229     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5230
5231   }
5232
5233   /*
5234    * (non-Javadoc)
5235    *
5236    * @see
5237    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5238    * .event.ActionEvent)
5239    */
5240   @Override
5241   protected void showGroupConservation_actionPerformed(ActionEvent e)
5242   {
5243     viewport.setShowGroupConservation(showGroupConservation.getState());
5244     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5245   }
5246
5247   /*
5248    * (non-Javadoc)
5249    *
5250    * @see
5251    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5252    * .event.ActionEvent)
5253    */
5254   @Override
5255   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5256   {
5257     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5258     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5259   }
5260
5261   /*
5262    * (non-Javadoc)
5263    *
5264    * @see
5265    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5266    * .event.ActionEvent)
5267    */
5268   @Override
5269   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5270   {
5271     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5272     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5273   }
5274
5275   @Override
5276   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5277   {
5278     showSequenceLogo.setState(true);
5279     viewport.setShowSequenceLogo(true);
5280     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5281     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5282   }
5283
5284   @Override
5285   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5286   {
5287     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5288   }
5289
5290   /*
5291    * (non-Javadoc)
5292    *
5293    * @see
5294    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5295    * .event.ActionEvent)
5296    */
5297   @Override
5298   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5299   {
5300     if (avc.makeGroupsFromSelection())
5301     {
5302       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5303       alignPanel.updateAnnotation();
5304       alignPanel.paintAlignment(true, true);
5305     }
5306   }
5307
5308   public void clearAlignmentSeqRep()
5309   {
5310     // TODO refactor alignmentseqrep to controller
5311     if (viewport.getAlignment().hasSeqrep())
5312     {
5313       viewport.getAlignment().setSeqrep(null);
5314       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5315       alignPanel.updateAnnotation();
5316       alignPanel.paintAlignment(true, true);
5317     }
5318   }
5319
5320   @Override
5321   protected void createGroup_actionPerformed(ActionEvent e)
5322   {
5323     if (avc.createGroup())
5324     {
5325       if (applyAutoAnnotationSettings.isSelected())
5326       {
5327         alignPanel.updateAnnotation(true, false);
5328       }
5329       alignPanel.alignmentChanged();
5330     }
5331   }
5332
5333   @Override
5334   protected void unGroup_actionPerformed(ActionEvent e)
5335   {
5336     if (avc.unGroup())
5337     {
5338       alignPanel.alignmentChanged();
5339     }
5340   }
5341
5342   /**
5343    * make the given alignmentPanel the currently selected tab
5344    *
5345    * @param alignmentPanel
5346    */
5347   public void setDisplayedView(AlignmentPanel alignmentPanel)
5348   {
5349     if (!viewport.getSequenceSetId()
5350             .equals(alignmentPanel.av.getSequenceSetId()))
5351     {
5352       throw new Error(MessageManager.getString(
5353               "error.implementation_error_cannot_show_view_alignment_frame"));
5354     }
5355     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5356             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5357     {
5358       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5359     }
5360   }
5361
5362   /**
5363    * Action on selection of menu options to Show or Hide annotations.
5364    *
5365    * @param visible
5366    * @param forSequences
5367    *          update sequence-related annotations
5368    * @param forAlignment
5369    *          update non-sequence-related annotations
5370    */
5371   @Override
5372   protected void setAnnotationsVisibility(boolean visible,
5373           boolean forSequences, boolean forAlignment)
5374   {
5375     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5376             .getAlignmentAnnotation();
5377     if (anns == null)
5378     {
5379       return;
5380     }
5381     for (AlignmentAnnotation aa : anns)
5382     {
5383       /*
5384        * don't display non-positional annotations on an alignment
5385        */
5386       if (aa.annotations == null)
5387       {
5388         continue;
5389       }
5390       boolean apply = (aa.sequenceRef == null && forAlignment)
5391               || (aa.sequenceRef != null && forSequences);
5392       if (apply)
5393       {
5394         aa.visible = visible;
5395       }
5396     }
5397     alignPanel.validateAnnotationDimensions(true);
5398     alignPanel.alignmentChanged();
5399   }
5400
5401   /**
5402    * Store selected annotation sort order for the view and repaint.
5403    */
5404   @Override
5405   protected void sortAnnotations_actionPerformed()
5406   {
5407     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5408     this.alignPanel.av
5409             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5410     alignPanel.paintAlignment(false, false);
5411   }
5412
5413   /**
5414    *
5415    * @return alignment panels in this alignment frame
5416    */
5417   public List<? extends AlignmentViewPanel> getAlignPanels()
5418   {
5419     // alignPanels is never null
5420     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5421     return alignPanels;
5422   }
5423
5424   /**
5425    * Open a new alignment window, with the cDNA associated with this (protein)
5426    * alignment, aligned as is the protein.
5427    */
5428   protected void viewAsCdna_actionPerformed()
5429   {
5430     // TODO no longer a menu action - refactor as required
5431     final AlignmentI alignment = getViewport().getAlignment();
5432     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5433     if (mappings == null)
5434     {
5435       return;
5436     }
5437     List<SequenceI> cdnaSeqs = new ArrayList<>();
5438     for (SequenceI aaSeq : alignment.getSequences())
5439     {
5440       for (AlignedCodonFrame acf : mappings)
5441       {
5442         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5443         if (dnaSeq != null)
5444         {
5445           /*
5446            * There is a cDNA mapping for this protein sequence - add to new
5447            * alignment. It will share the same dataset sequence as other mapped
5448            * cDNA (no new mappings need to be created).
5449            */
5450           final Sequence newSeq = new Sequence(dnaSeq);
5451           newSeq.setDatasetSequence(dnaSeq);
5452           cdnaSeqs.add(newSeq);
5453         }
5454       }
5455     }
5456     if (cdnaSeqs.size() == 0)
5457     {
5458       // show a warning dialog no mapped cDNA
5459       return;
5460     }
5461     AlignmentI cdna = new Alignment(
5462             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5463     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5464             AlignFrame.DEFAULT_HEIGHT);
5465     cdna.alignAs(alignment);
5466     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5467             + this.title;
5468     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5469             AlignFrame.DEFAULT_HEIGHT);
5470   }
5471
5472   /**
5473    * Set visibility of dna/protein complement view (available when shown in a
5474    * split frame).
5475    *
5476    * @param show
5477    */
5478   @Override
5479   protected void showComplement_actionPerformed(boolean show)
5480   {
5481     SplitContainerI sf = getSplitViewContainer();
5482     if (sf != null)
5483     {
5484       sf.setComplementVisible(this, show);
5485     }
5486   }
5487
5488   /**
5489    * Generate the reverse (optionally complemented) of the selected sequences,
5490    * and add them to the alignment
5491    */
5492   @Override
5493   protected void showReverse_actionPerformed(boolean complement)
5494   {
5495     AlignmentI al = null;
5496     try
5497     {
5498       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5499       al = dna.reverseCdna(complement);
5500       viewport.addAlignment(al, "");
5501       addHistoryItem(new EditCommand(
5502               MessageManager.getString("label.add_sequences"), Action.PASTE,
5503               al.getSequencesArray(), 0, al.getWidth(),
5504               viewport.getAlignment()));
5505     } catch (Exception ex)
5506     {
5507       System.err.println(ex.getMessage());
5508       return;
5509     }
5510   }
5511
5512   /**
5513    * Try to run a script in the Groovy console, having first ensured that this
5514    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5515    * be targeted at this alignment.
5516    */
5517   @Override
5518   protected void runGroovy_actionPerformed()
5519   {
5520     Jalview.setCurrentAlignFrame(this);
5521     groovy.ui.Console console = Desktop.getGroovyConsole();
5522     if (console != null)
5523     {
5524       try
5525       {
5526         console.runScript();
5527       } catch (Exception ex)
5528       {
5529         System.err.println((ex.toString()));
5530         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5531                 MessageManager.getString("label.couldnt_run_groovy_script"),
5532                 MessageManager.getString("label.groovy_support_failed"),
5533                 JvOptionPane.ERROR_MESSAGE);
5534       }
5535     }
5536     else
5537     {
5538       System.err.println("Can't run Groovy script as console not found");
5539     }
5540   }
5541
5542   /**
5543    * Hides columns containing (or not containing) a specified feature, provided
5544    * that would not leave all columns hidden
5545    *
5546    * @param featureType
5547    * @param columnsContaining
5548    * @return
5549    */
5550   public boolean hideFeatureColumns(String featureType,
5551           boolean columnsContaining)
5552   {
5553     boolean notForHiding = avc.markColumnsContainingFeatures(
5554             columnsContaining, false, false, featureType);
5555     if (notForHiding)
5556     {
5557       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5558               false, featureType))
5559       {
5560         getViewport().hideSelectedColumns();
5561         return true;
5562       }
5563     }
5564     return false;
5565   }
5566
5567   @Override
5568   protected void selectHighlightedColumns_actionPerformed(
5569           ActionEvent actionEvent)
5570   {
5571     // include key modifier check in case user selects from menu
5572     avc.markHighlightedColumns(
5573             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5574             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5575                     | ActionEvent.CTRL_MASK)) != 0);
5576   }
5577
5578   /**
5579    * Rebuilds the Colour menu, including any user-defined colours which have
5580    * been loaded either on startup or during the session
5581    */
5582   public void buildColourMenu()
5583   {
5584     colourMenu.removeAll();
5585
5586     colourMenu.add(applyToAllGroups);
5587     colourMenu.add(textColour);
5588     colourMenu.addSeparator();
5589
5590     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5591             false);
5592
5593     colourMenu.addSeparator();
5594     colourMenu.add(conservationMenuItem);
5595     colourMenu.add(modifyConservation);
5596     colourMenu.add(abovePIDThreshold);
5597     colourMenu.add(modifyPID);
5598     colourMenu.add(annotationColour);
5599
5600     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5601     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5602   }
5603
5604   /**
5605    * Open a dialog (if not already open) that allows the user to select and
5606    * calculate PCA or Tree analysis
5607    */
5608   protected void openTreePcaDialog()
5609   {
5610     if (alignPanel.getCalculationDialog() == null)
5611     {
5612       new CalculationChooser(AlignFrame.this);
5613     }
5614   }
5615
5616   @Override
5617   protected void loadVcf_actionPerformed()
5618   {
5619     JalviewFileChooser chooser = new JalviewFileChooser(
5620             Cache.getProperty("LAST_DIRECTORY"));
5621     chooser.setFileView(new JalviewFileView());
5622     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5623     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5624
5625     int value = chooser.showOpenDialog(null);
5626
5627     if (value == JalviewFileChooser.APPROVE_OPTION)
5628     {
5629       String choice = chooser.getSelectedFile().getPath();
5630       Cache.setProperty("LAST_DIRECTORY", choice);
5631       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5632       new VCFLoader(choice).loadVCF(seqs, this);
5633     }
5634
5635   }
5636 }
5637
5638 class PrintThread extends Thread
5639 {
5640   AlignmentPanel ap;
5641
5642   public PrintThread(AlignmentPanel ap)
5643   {
5644     this.ap = ap;
5645   }
5646
5647   static PageFormat pf;
5648
5649   @Override
5650   public void run()
5651   {
5652     PrinterJob printJob = PrinterJob.getPrinterJob();
5653
5654     if (pf != null)
5655     {
5656       printJob.setPrintable(ap, pf);
5657     }
5658     else
5659     {
5660       printJob.setPrintable(ap);
5661     }
5662
5663     if (printJob.printDialog())
5664     {
5665       try
5666       {
5667         printJob.print();
5668       } catch (Exception PrintException)
5669       {
5670         PrintException.printStackTrace();
5671       }
5672     }
5673   }
5674 }