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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Rectangle;
  27 import java.awt.Toolkit;
  28 import java.awt.datatransfer.Clipboard;
  29 import java.awt.datatransfer.DataFlavor;
  30 import java.awt.datatransfer.StringSelection;
  31 import java.awt.datatransfer.Transferable;
  32 import java.awt.dnd.DnDConstants;
  33 import java.awt.dnd.DropTargetDragEvent;
  34 import java.awt.dnd.DropTargetDropEvent;
  35 import java.awt.dnd.DropTargetEvent;
  36 import java.awt.dnd.DropTargetListener;
  37 import java.awt.event.ActionEvent;
  38 import java.awt.event.ActionListener;
  39 import java.awt.event.FocusAdapter;
  40 import java.awt.event.FocusEvent;
  41 import java.awt.event.ItemEvent;
  42 import java.awt.event.ItemListener;
  43 import java.awt.event.KeyAdapter;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.print.PageFormat;
  47 import java.awt.print.PrinterJob;
  48 import java.beans.PropertyChangeEvent;
  49 import java.io.File;
  50 import java.io.FileWriter;
  51 import java.io.PrintWriter;
  52 import java.net.URL;
  53 import java.util.ArrayList;
  54 import java.util.Arrays;
  55 import java.util.Deque;
  56 import java.util.Enumeration;
  57 import java.util.Hashtable;
  58 import java.util.List;
  59 import java.util.Vector;
  60
  61 import javax.swing.ButtonGroup;
  62 import javax.swing.JCheckBoxMenuItem;
  63 import javax.swing.JComponent;
  64 import javax.swing.JEditorPane;
  65 import javax.swing.JInternalFrame;
  66 import javax.swing.JLabel;
  67 import javax.swing.JLayeredPane;
  68 import javax.swing.JMenu;
  69 import javax.swing.JMenuItem;
  70 import javax.swing.JPanel;
  71 import javax.swing.JScrollPane;
  72 import javax.swing.SwingUtilities;
  73
  74 import ext.vamsas.ServiceHandle;
  75 import jalview.analysis.AlignmentSorter;
  76 import jalview.analysis.AlignmentUtils;
  77 import jalview.analysis.CrossRef;
  78 import jalview.analysis.Dna;
  79 import jalview.analysis.GeneticCodeI;
  80 import jalview.analysis.ParseProperties;
  81 import jalview.analysis.SequenceIdMatcher;
  82 import jalview.api.AlignExportSettingsI;
  83 import jalview.api.AlignViewControllerGuiI;
  84 import jalview.api.AlignViewControllerI;
  85 import jalview.api.AlignViewportI;
  86 import jalview.api.AlignmentViewPanel;
  87 import jalview.api.FeatureSettingsControllerI;
  88 import jalview.api.FeatureSettingsModelI;
  89 import jalview.api.SplitContainerI;
  90 import jalview.api.ViewStyleI;
  91 import jalview.api.analysis.SimilarityParamsI;
  92 import jalview.bin.Cache;
  93 import jalview.bin.Jalview;
  94 import jalview.commands.CommandI;
  95 import jalview.commands.EditCommand;
  96 import jalview.commands.EditCommand.Action;
  97 import jalview.commands.OrderCommand;
  98 import jalview.commands.RemoveGapColCommand;
  99 import jalview.commands.RemoveGapsCommand;
 100 import jalview.commands.SlideSequencesCommand;
 101 import jalview.commands.TrimRegionCommand;
 102 import jalview.datamodel.AlignExportSettingsAdapter;
 103 import jalview.datamodel.AlignedCodonFrame;
 104 import jalview.datamodel.Alignment;
 105 import jalview.datamodel.AlignmentAnnotation;
 106 import jalview.datamodel.AlignmentExportData;
 107 import jalview.datamodel.AlignmentI;
 108 import jalview.datamodel.AlignmentOrder;
 109 import jalview.datamodel.AlignmentView;
 110 import jalview.datamodel.ColumnSelection;
 111 import jalview.datamodel.HiddenColumns;
 112 import jalview.datamodel.PDBEntry;
 113 import jalview.datamodel.SeqCigar;
 114 import jalview.datamodel.Sequence;
 115 import jalview.datamodel.SequenceGroup;
 116 import jalview.datamodel.SequenceI;
 117 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 118 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 119 import jalview.io.AlignmentProperties;
 120 import jalview.io.AnnotationFile;
 121 import jalview.io.BackupFiles;
 122 import jalview.io.BioJsHTMLOutput;
 123 import jalview.io.DataSourceType;
 124 import jalview.io.FileFormat;
 125 import jalview.io.FileFormatI;
 126 import jalview.io.FileFormats;
 127 import jalview.io.FileLoader;
 128 import jalview.io.FileParse;
 129 import jalview.io.FormatAdapter;
 130 import jalview.io.HtmlSvgOutput;
 131 import jalview.io.IdentifyFile;
 132 import jalview.io.JPredFile;
 133 import jalview.io.JalviewFileChooser;
 134 import jalview.io.JalviewFileView;
 135 import jalview.io.JnetAnnotationMaker;
 136 import jalview.io.NewickFile;
 137 import jalview.io.ScoreMatrixFile;
 138 import jalview.io.TCoffeeScoreFile;
 139 import jalview.io.vcf.VCFLoader;
 140 import jalview.jbgui.GAlignFrame;
 141 import jalview.project.Jalview2XML;
 142 import jalview.schemes.ColourSchemeI;
 143 import jalview.schemes.ColourSchemes;
 144 import jalview.schemes.ResidueColourScheme;
 145 import jalview.schemes.TCoffeeColourScheme;
 146 import jalview.util.ImageMaker.TYPE;
 147 import jalview.util.MessageManager;
 148 import jalview.util.Platform;
 149 import jalview.viewmodel.AlignmentViewport;
 150 import jalview.viewmodel.ViewportRanges;
 151 import jalview.ws.DBRefFetcher;
 152 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 153 import jalview.ws.jws1.Discoverer;
 154 import jalview.ws.jws2.Jws2Discoverer;
 155 import jalview.ws.jws2.jabaws2.Jws2Instance;
 156 import jalview.ws.seqfetcher.DbSourceProxy;
 157
 158 /**
 159  * DOCUMENT ME!
 160  *
 161  * @author $author$
 162  * @version $Revision$
 163  */
 164 @SuppressWarnings("serial")
 165 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 166         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 167 {
 168
 169   public static final int DEFAULT_WIDTH = 700;
 170
 171   public static final int DEFAULT_HEIGHT = 500;
 172
 173   /*
 174    * The currently displayed panel (selected tabbed view if more than one)
 175    */
 176   public AlignmentPanel alignPanel;
 177
 178   AlignViewport viewport;
 179
 180   public AlignViewControllerI avc;
 181
 182   List<AlignmentPanel> alignPanels = new ArrayList<>();
 183
 184   /**
 185    * Last format used to load or save alignments in this window
 186    */
 187   FileFormatI currentFileFormat = null;
 188
 189   /**
 190    * Current filename for this alignment
 191    */
 192   String fileName = null;
 193
 194   File fileObject;
 195
 196   /**
 197    * Creates a new AlignFrame object with specific width and height.
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    */
 203   public AlignFrame(AlignmentI al, int width, int height)
 204   {
 205     this(al, null, width, height);
 206   }
 207
 208   /**
 209    * Creates a new AlignFrame object with specific width, height and
 210    * sequenceSetId
 211    *
 212    * @param al
 213    * @param width
 214    * @param height
 215    * @param sequenceSetId
 216    */
 217   public AlignFrame(AlignmentI al, int width, int height,
 218           String sequenceSetId)
 219   {
 220     this(al, null, width, height, sequenceSetId);
 221   }
 222
 223   /**
 224    * Creates a new AlignFrame object with specific width, height and
 225    * sequenceSetId
 226    *
 227    * @param al
 228    * @param width
 229    * @param height
 230    * @param sequenceSetId
 231    * @param viewId
 232    */
 233   public AlignFrame(AlignmentI al, int width, int height,
 234           String sequenceSetId, String viewId)
 235   {
 236     this(al, null, width, height, sequenceSetId, viewId);
 237   }
 238
 239   /**
 240    * new alignment window with hidden columns
 241    *
 242    * @param al
 243    *          AlignmentI
 244    * @param hiddenColumns
 245    *          ColumnSelection or null
 246    * @param width
 247    *          Width of alignment frame
 248    * @param height
 249    *          height of frame.
 250    */
 251   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 252           int height)
 253   {
 254     this(al, hiddenColumns, width, height, null);
 255   }
 256
 257   /**
 258    * Create alignment frame for al with hiddenColumns, a specific width and
 259    * height, and specific sequenceId
 260    *
 261    * @param al
 262    * @param hiddenColumns
 263    * @param width
 264    * @param height
 265    * @param sequenceSetId
 266    *          (may be null)
 267    */
 268   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 269           int height, String sequenceSetId)
 270   {
 271     this(al, hiddenColumns, width, height, sequenceSetId, null);
 272   }
 273
 274   /**
 275    * Create alignment frame for al with hiddenColumns, a specific width and
 276    * height, and specific sequenceId
 277    *
 278    * @param al
 279    * @param hiddenColumns
 280    * @param width
 281    * @param height
 282    * @param sequenceSetId
 283    *          (may be null)
 284    * @param viewId
 285    *          (may be null)
 286    */
 287   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 288           int height, String sequenceSetId, String viewId)
 289   {
 290     setSize(width, height);
 291
 292     if (al.getDataset() == null)
 293     {
 294       al.setDataset(null);
 295     }
 296
 297     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 298
 299     alignPanel = new AlignmentPanel(this, viewport);
 300
 301     addAlignmentPanel(alignPanel, true);
 302     init();
 303   }
 304
 305   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 306           HiddenColumns hiddenColumns, int width, int height)
 307   {
 308     setSize(width, height);
 309
 310     if (al.getDataset() == null)
 311     {
 312       al.setDataset(null);
 313     }
 314
 315     viewport = new AlignViewport(al, hiddenColumns);
 316
 317     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 318     {
 319       viewport.hideSequence(hiddenSeqs);
 320     }
 321     alignPanel = new AlignmentPanel(this, viewport);
 322     addAlignmentPanel(alignPanel, true);
 323     init();
 324   }
 325
 326   /**
 327    * Make a new AlignFrame from existing alignmentPanels
 328    *
 329    * @param ap
 330    *          AlignmentPanel
 331    * @param av
 332    *          AlignViewport
 333    */
 334   public AlignFrame(AlignmentPanel ap)
 335   {
 336     viewport = ap.av;
 337     alignPanel = ap;
 338     addAlignmentPanel(ap, false);
 339     init();
 340   }
 341
 342   /**
 343    * initalise the alignframe from the underlying viewport data and the
 344    * configurations
 345    */
 346   void init()
 347   {
 348 //        setBackground(Color.white); // BH 2019
 349
 350     if (!Jalview.isHeadlessMode())
 351     {
 352       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 353     }
 354
 355     avc = new jalview.controller.AlignViewController(this, viewport,
 356             alignPanel);
 357     if (viewport.getAlignmentConservationAnnotation() == null)
 358     {
 359       // BLOSUM62Colour.setEnabled(false);
 360       conservationMenuItem.setEnabled(false);
 361       modifyConservation.setEnabled(false);
 362       // PIDColour.setEnabled(false);
 363       // abovePIDThreshold.setEnabled(false);
 364       // modifyPID.setEnabled(false);
 365     }
 366
 367     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 368             "No sort");
 369
 370     if (sortby.equals("Id"))
 371     {
 372       sortIDMenuItem_actionPerformed(null);
 373     }
 374     else if (sortby.equals("Pairwise Identity"))
 375     {
 376       sortPairwiseMenuItem_actionPerformed(null);
 377     }
 378
 379     this.alignPanel.av
 380             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 381
 382     setMenusFromViewport(viewport);
 383     buildSortByAnnotationScoresMenu();
 384     calculateTree.addActionListener(new ActionListener()
 385     {
 386
 387       @Override
 388       public void actionPerformed(ActionEvent e)
 389       {
 390         openTreePcaDialog();
 391       }
 392     });
 393     buildColourMenu();
 394
 395     if (Desktop.desktop != null)
 396     {
 397       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 398       if (!Platform.isJS())
 399       {
 400         addServiceListeners();
 401       }
 402       setGUINucleotide();
 403     }
 404
 405     if (viewport.getWrapAlignment())
 406     {
 407       wrapMenuItem_actionPerformed(null);
 408     }
 409
 410     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 411     {
 412       this.overviewMenuItem_actionPerformed(null);
 413     }
 414
 415     addKeyListener();
 416
 417     final List<AlignmentPanel> selviews = new ArrayList<>();
 418     final List<AlignmentPanel> origview = new ArrayList<>();
 419     final String menuLabel = MessageManager
 420             .getString("label.copy_format_from");
 421     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 422             new ViewSetProvider()
 423             {
 424
 425               @Override
 426               public AlignmentPanel[] getAllAlignmentPanels()
 427               {
 428                 origview.clear();
 429                 origview.add(alignPanel);
 430                 // make an array of all alignment panels except for this one
 431                 List<AlignmentPanel> aps = new ArrayList<>(
 432                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 433                 aps.remove(AlignFrame.this.alignPanel);
 434                 return aps.toArray(new AlignmentPanel[aps.size()]);
 435               }
 436             }, selviews, new ItemListener()
 437             {
 438
 439               @Override
 440               public void itemStateChanged(ItemEvent e)
 441               {
 442                 if (origview.size() > 0)
 443                 {
 444                   final AlignmentPanel ap = origview.get(0);
 445
 446                   /*
 447                    * Copy the ViewStyle of the selected panel to 'this one'.
 448                    * Don't change value of 'scaleProteinAsCdna' unless copying
 449                    * from a SplitFrame.
 450                    */
 451                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 452                           .getViewStyle();
 453                   boolean fromSplitFrame = selviews.get(0)
 454                           .getAlignViewport().getCodingComplement() != null;
 455                   if (!fromSplitFrame)
 456                   {
 457                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 458                             .getViewStyle().isScaleProteinAsCdna());
 459                   }
 460                   ap.getAlignViewport().setViewStyle(vs);
 461
 462                   /*
 463                    * Also rescale ViewStyle of SplitFrame complement if there is
 464                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 465                    * the whole ViewStyle (allow cDNA protein to have different
 466                    * fonts)
 467                    */
 468                   AlignViewportI complement = ap.getAlignViewport()
 469                           .getCodingComplement();
 470                   if (complement != null && vs.isScaleProteinAsCdna())
 471                   {
 472                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 473                     ((SplitFrame) af.getSplitViewContainer())
 474                             .adjustLayout();
 475                     af.setMenusForViewport();
 476                   }
 477
 478                   ap.updateLayout();
 479                   ap.setSelected(true);
 480                   ap.alignFrame.setMenusForViewport();
 481
 482                 }
 483               }
 484             });
 485     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 486             .indexOf("devel") > -1
 487             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 488                     .indexOf("test") > -1)
 489     {
 490       formatMenu.add(vsel);
 491     }
 492     addFocusListener(new FocusAdapter()
 493     {
 494       @Override
 495       public void focusGained(FocusEvent e)
 496       {
 497         Jalview.setCurrentAlignFrame(AlignFrame.this);
 498       }
 499     });
 500
 501   }
 502
 503   /**
 504    * Change the filename and format for the alignment, and enable the 'reload'
 505    * button functionality.
 506    *
 507    * @param file
 508    *          valid filename
 509    * @param format
 510    *          format of file
 511    */
 512   public void setFileName(String file, FileFormatI format)
 513   {
 514     fileName = file;
 515     setFileFormat(format);
 516     reload.setEnabled(true);
 517   }
 518
 519   /**
 520    * JavaScript will have this, maybe others. More dependable than a file name
 521    * and maintains a reference to the actual bytes loaded.
 522    *
 523    * @param file
 524    */
 525   public void setFileObject(File file)
 526   {
 527     this.fileObject = file;
 528   }
 529
 530   /**
 531    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 532    * events
 533    */
 534   void addKeyListener()
 535   {
 536     addKeyListener(new KeyAdapter()
 537     {
 538       @Override
 539       public void keyPressed(KeyEvent evt)
 540       {
 541         if (viewport.cursorMode
 542                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 543                         && evt.getKeyCode() <= KeyEvent.VK_9)
 544                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 545                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 546                 && Character.isDigit(evt.getKeyChar()))
 547         {
 548           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 549         }
 550
 551         switch (evt.getKeyCode())
 552         {
 553
 554         case 27: // escape key
 555           deselectAllSequenceMenuItem_actionPerformed(null);
 556
 557           break;
 558
 559         case KeyEvent.VK_DOWN:
 560           if (evt.isAltDown() || !viewport.cursorMode)
 561           {
 562             moveSelectedSequences(false);
 563           }
 564           if (viewport.cursorMode)
 565           {
 566             alignPanel.getSeqPanel().moveCursor(0, 1);
 567           }
 568           break;
 569
 570         case KeyEvent.VK_UP:
 571           if (evt.isAltDown() || !viewport.cursorMode)
 572           {
 573             moveSelectedSequences(true);
 574           }
 575           if (viewport.cursorMode)
 576           {
 577             alignPanel.getSeqPanel().moveCursor(0, -1);
 578           }
 579
 580           break;
 581
 582         case KeyEvent.VK_LEFT:
 583           if (evt.isAltDown() || !viewport.cursorMode)
 584           {
 585             slideSequences(false,
 586                     alignPanel.getSeqPanel().getKeyboardNo1());
 587           }
 588           else
 589           {
 590             alignPanel.getSeqPanel().moveCursor(-1, 0);
 591           }
 592
 593           break;
 594
 595         case KeyEvent.VK_RIGHT:
 596           if (evt.isAltDown() || !viewport.cursorMode)
 597           {
 598             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 599           }
 600           else
 601           {
 602             alignPanel.getSeqPanel().moveCursor(1, 0);
 603           }
 604           break;
 605
 606         case KeyEvent.VK_SPACE:
 607           if (viewport.cursorMode)
 608           {
 609             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 610                     || evt.isShiftDown() || evt.isAltDown());
 611           }
 612           break;
 613
 614         // case KeyEvent.VK_A:
 615         // if (viewport.cursorMode)
 616         // {
 617         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 618         // //System.out.println("A");
 619         // }
 620         // break;
 621         /*
 622          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 623          * System.out.println("closing bracket"); } break;
 624          */
 625         case KeyEvent.VK_DELETE:
 626         case KeyEvent.VK_BACK_SPACE:
 627           if (!viewport.cursorMode)
 628           {
 629             cut_actionPerformed();
 630           }
 631           else
 632           {
 633             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 634                     || evt.isShiftDown() || evt.isAltDown());
 635           }
 636
 637           break;
 638
 639         case KeyEvent.VK_S:
 640           if (viewport.cursorMode)
 641           {
 642             alignPanel.getSeqPanel().setCursorRow();
 643           }
 644           break;
 645         case KeyEvent.VK_C:
 646           if (viewport.cursorMode && !evt.isControlDown())
 647           {
 648             alignPanel.getSeqPanel().setCursorColumn();
 649           }
 650           break;
 651         case KeyEvent.VK_P:
 652           if (viewport.cursorMode)
 653           {
 654             alignPanel.getSeqPanel().setCursorPosition();
 655           }
 656           break;
 657
 658         case KeyEvent.VK_ENTER:
 659         case KeyEvent.VK_COMMA:
 660           if (viewport.cursorMode)
 661           {
 662             alignPanel.getSeqPanel().setCursorRowAndColumn();
 663           }
 664           break;
 665
 666         case KeyEvent.VK_Q:
 667           if (viewport.cursorMode)
 668           {
 669             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 670           }
 671           break;
 672         case KeyEvent.VK_M:
 673           if (viewport.cursorMode)
 674           {
 675             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 676           }
 677           break;
 678
 679         case KeyEvent.VK_F2:
 680           viewport.cursorMode = !viewport.cursorMode;
 681           setStatus(MessageManager
 682                   .formatMessage("label.keyboard_editing_mode", new String[]
 683                   { (viewport.cursorMode ? "on" : "off") }));
 684           if (viewport.cursorMode)
 685           {
 686             ViewportRanges ranges = viewport.getRanges();
 687             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 688                     .getStartRes();
 689             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 690                     .getStartSeq();
 691           }
 692           alignPanel.getSeqPanel().seqCanvas.repaint();
 693           break;
 694
 695         case KeyEvent.VK_F1:
 696           try
 697           {
 698             Help.showHelpWindow();
 699           } catch (Exception ex)
 700           {
 701             ex.printStackTrace();
 702           }
 703           break;
 704         case KeyEvent.VK_H:
 705         {
 706           boolean toggleSeqs = !evt.isControlDown();
 707           boolean toggleCols = !evt.isShiftDown();
 708           toggleHiddenRegions(toggleSeqs, toggleCols);
 709           break;
 710         }
 711         case KeyEvent.VK_B:
 712         {
 713           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 714           boolean modifyExisting = true; // always modify, don't clear
 715                                          // evt.isShiftDown();
 716           boolean invertHighlighted = evt.isAltDown();
 717           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 718                   toggleSel);
 719           break;
 720         }
 721         case KeyEvent.VK_PAGE_UP:
 722           viewport.getRanges().pageUp();
 723           break;
 724         case KeyEvent.VK_PAGE_DOWN:
 725           viewport.getRanges().pageDown();
 726           break;
 727         }
 728       }
 729
 730       @Override
 731       public void keyReleased(KeyEvent evt)
 732       {
 733         switch (evt.getKeyCode())
 734         {
 735         case KeyEvent.VK_LEFT:
 736           if (evt.isAltDown() || !viewport.cursorMode)
 737           {
 738             viewport.firePropertyChange("alignment", null,
 739                     viewport.getAlignment().getSequences());
 740           }
 741           break;
 742
 743         case KeyEvent.VK_RIGHT:
 744           if (evt.isAltDown() || !viewport.cursorMode)
 745           {
 746             viewport.firePropertyChange("alignment", null,
 747                     viewport.getAlignment().getSequences());
 748           }
 749           break;
 750         }
 751       }
 752     });
 753   }
 754
 755   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 756   {
 757     ap.alignFrame = this;
 758     avc = new jalview.controller.AlignViewController(this, viewport,
 759             alignPanel);
 760
 761     alignPanels.add(ap);
 762
 763     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 764
 765     int aSize = alignPanels.size();
 766
 767     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 768
 769     if (aSize == 1 && ap.av.getViewName() == null)
 770     {
 771       this.getContentPane().add(ap, BorderLayout.CENTER);
 772     }
 773     else
 774     {
 775       if (aSize == 2)
 776       {
 777         setInitialTabVisible();
 778       }
 779
 780       expandViews.setEnabled(true);
 781       gatherViews.setEnabled(true);
 782       tabbedPane.addTab(ap.av.getViewName(), ap);
 783
 784       ap.setVisible(false);
 785     }
 786
 787     if (newPanel)
 788     {
 789       if (ap.av.isPadGaps())
 790       {
 791         ap.av.getAlignment().padGaps();
 792       }
 793       ap.av.updateConservation(ap);
 794       ap.av.updateConsensus(ap);
 795       ap.av.updateStrucConsensus(ap);
 796     }
 797   }
 798
 799   public void setInitialTabVisible()
 800   {
 801     expandViews.setEnabled(true);
 802     gatherViews.setEnabled(true);
 803     tabbedPane.setVisible(true);
 804     AlignmentPanel first = alignPanels.get(0);
 805     tabbedPane.addTab(first.av.getViewName(), first);
 806     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 807   }
 808
 809   public AlignViewport getViewport()
 810   {
 811     return viewport;
 812   }
 813
 814   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 815   private void addServiceListeners()
 816   {
 817     final java.beans.PropertyChangeListener thisListener;
 818     Desktop.instance.addJalviewPropertyChangeListener("services",
 819             thisListener = new java.beans.PropertyChangeListener()
 820             {
 821               @Override
 822               public void propertyChange(PropertyChangeEvent evt)
 823               {
 824                 // // System.out.println("Discoverer property change.");
 825                 // if (evt.getPropertyName().equals("services"))
 826                 {
 827                   SwingUtilities.invokeLater(new Runnable()
 828                   {
 829
 830                     @Override
 831                     public void run()
 832                     {
 833                       System.err.println(
 834                               "Rebuild WS Menu for service change");
 835                       BuildWebServiceMenu();
 836                     }
 837
 838                   });
 839                 }
 840               }
 841             });
 842     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 843     {
 844       @Override
 845       public void internalFrameClosed(
 846               javax.swing.event.InternalFrameEvent evt)
 847       {
 848         // System.out.println("deregistering discoverer listener");
 849         Desktop.instance.removeJalviewPropertyChangeListener("services",
 850                 thisListener);
 851         closeMenuItem_actionPerformed(true);
 852       }
 853     });
 854     // Finally, build the menu once to get current service state
 855     new Thread(new Runnable()
 856     {
 857       @Override
 858       public void run()
 859       {
 860         BuildWebServiceMenu();
 861       }
 862     }).start();
 863   }
 864
 865   /**
 866    * Configure menu items that vary according to whether the alignment is
 867    * nucleotide or protein
 868    */
 869   public void setGUINucleotide()
 870   {
 871     AlignmentI al = getViewport().getAlignment();
 872     boolean nucleotide = al.isNucleotide();
 873
 874     loadVcf.setVisible(nucleotide);
 875     showTranslation.setVisible(nucleotide);
 876     showReverse.setVisible(nucleotide);
 877     showReverseComplement.setVisible(nucleotide);
 878     conservationMenuItem.setEnabled(!nucleotide);
 879     modifyConservation
 880             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 881     showGroupConservation.setEnabled(!nucleotide);
 882
 883     showComplementMenuItem
 884             .setText(nucleotide ? MessageManager.getString("label.protein")
 885                     : MessageManager.getString("label.nucleotide"));
 886   }
 887
 888   /**
 889    * set up menus for the current viewport. This may be called after any
 890    * operation that affects the data in the current view (selection changed,
 891    * etc) to update the menus to reflect the new state.
 892    */
 893   @Override
 894   public void setMenusForViewport()
 895   {
 896     setMenusFromViewport(viewport);
 897   }
 898
 899   /**
 900    * Need to call this method when tabs are selected for multiple views, or when
 901    * loading from Jalview2XML.java
 902    *
 903    * @param av
 904    *          AlignViewport
 905    */
 906   public void setMenusFromViewport(AlignViewport av)
 907   {
 908     padGapsMenuitem.setSelected(av.isPadGaps());
 909     colourTextMenuItem.setSelected(av.isShowColourText());
 910     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 911     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 912     conservationMenuItem.setSelected(av.getConservationSelected());
 913     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 914     seqLimits.setSelected(av.getShowJVSuffix());
 915     idRightAlign.setSelected(av.isRightAlignIds());
 916     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 917     renderGapsMenuItem.setSelected(av.isRenderGaps());
 918     wrapMenuItem.setSelected(av.getWrapAlignment());
 919     scaleAbove.setVisible(av.getWrapAlignment());
 920     scaleLeft.setVisible(av.getWrapAlignment());
 921     scaleRight.setVisible(av.getWrapAlignment());
 922     annotationPanelMenuItem.setState(av.isShowAnnotation());
 923     /*
 924      * Show/hide annotations only enabled if annotation panel is shown
 925      */
 926     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 927     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 928     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 929     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 930     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 931     viewTextMenuItem.setSelected(av.getShowText());
 932     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 933     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 934     showGroupConservation.setSelected(av.isShowGroupConservation());
 935     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 936     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 937     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 938
 939     ColourMenuHelper.setColourSelected(colourMenu,
 940             av.getGlobalColourScheme());
 941
 942     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 943     hiddenMarkers.setState(av.getShowHiddenMarkers());
 944     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 945     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 946     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 947     autoCalculate.setSelected(av.autoCalculateConsensus);
 948     sortByTree.setSelected(av.sortByTree);
 949     listenToViewSelections.setSelected(av.followSelection);
 950
 951     showProducts.setEnabled(canShowProducts());
 952     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 953
 954     updateEditMenuBar();
 955   }
 956
 957   /**
 958    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 959    *
 960    * @param b
 961    */
 962   public void setGroovyEnabled(boolean b)
 963   {
 964     runGroovy.setEnabled(b);
 965   }
 966
 967   private IProgressIndicator progressBar;
 968
 969   /*
 970    * (non-Javadoc)
 971    *
 972    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 973    */
 974   @Override
 975   public void setProgressBar(String message, long id)
 976   {
 977     progressBar.setProgressBar(message, id);
 978   }
 979
 980   @Override
 981   public void registerHandler(final long id,
 982           final IProgressIndicatorHandler handler)
 983   {
 984     progressBar.registerHandler(id, handler);
 985   }
 986
 987   /**
 988    *
 989    * @return true if any progress bars are still active
 990    */
 991   @Override
 992   public boolean operationInProgress()
 993   {
 994     return progressBar.operationInProgress();
 995   }
 996
 997   /**
 998    * Sets the text of the status bar. Note that setting a null or empty value
 999    * will cause the status bar to be hidden, with possibly undesirable flicker
1000    * of the screen layout.
1001    */
1002   @Override
1003   public void setStatus(String text)
1004   {
1005     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1006   }
1007
1008   /*
1009    * Added so Castor Mapping file can obtain Jalview Version
1010    */
1011   public String getVersion()
1012   {
1013     return jalview.bin.Cache.getProperty("VERSION");
1014   }
1015
1016   public FeatureRenderer getFeatureRenderer()
1017   {
1018     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1019   }
1020
1021   @Override
1022   public void fetchSequence_actionPerformed()
1023   {
1024     new SequenceFetcher(this);
1025   }
1026
1027   @Override
1028   public void addFromFile_actionPerformed(ActionEvent e)
1029   {
1030     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1031   }
1032
1033   @Override
1034   public void reload_actionPerformed(ActionEvent e)
1035   {
1036     if (fileName != null)
1037     {
1038       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1039       // originating file's format
1040       // TODO: work out how to recover feature settings for correct view(s) when
1041       // file is reloaded.
1042       if (FileFormat.Jalview.equals(currentFileFormat))
1043       {
1044         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1045         for (int i = 0; i < frames.length; i++)
1046         {
1047           if (frames[i] instanceof AlignFrame && frames[i] != this
1048                   && ((AlignFrame) frames[i]).fileName != null
1049                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1050           {
1051             try
1052             {
1053               frames[i].setSelected(true);
1054               Desktop.instance.closeAssociatedWindows();
1055             } catch (java.beans.PropertyVetoException ex)
1056             {
1057             }
1058           }
1059
1060         }
1061         Desktop.instance.closeAssociatedWindows();
1062
1063         FileLoader loader = new FileLoader();
1064         DataSourceType protocol = fileName.startsWith("http:")
1065                 ? DataSourceType.URL
1066                 : DataSourceType.FILE;
1067         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1068       }
1069       else
1070       {
1071         Rectangle bounds = this.getBounds();
1072
1073         FileLoader loader = new FileLoader();
1074
1075         AlignFrame newframe = null;
1076
1077         if (fileObject == null)
1078         {
1079
1080           DataSourceType protocol = (fileName.startsWith("http:")
1081                   ? DataSourceType.URL
1082                   : DataSourceType.FILE);
1083           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1084                   currentFileFormat);
1085         }
1086         else
1087         {
1088           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1089                   DataSourceType.FILE, currentFileFormat);
1090         }
1091
1092         newframe.setBounds(bounds);
1093         if (featureSettings != null && featureSettings.isShowing())
1094         {
1095           final Rectangle fspos = featureSettings.frame.getBounds();
1096           // TODO: need a 'show feature settings' function that takes bounds -
1097           // need to refactor Desktop.addFrame
1098           newframe.featureSettings_actionPerformed(null);
1099           final FeatureSettings nfs = newframe.featureSettings;
1100           SwingUtilities.invokeLater(new Runnable()
1101           {
1102             @Override
1103             public void run()
1104             {
1105               nfs.frame.setBounds(fspos);
1106             }
1107           });
1108           this.featureSettings.close();
1109           this.featureSettings = null;
1110         }
1111         this.closeMenuItem_actionPerformed(true);
1112       }
1113     }
1114   }
1115
1116   @Override
1117   public void addFromText_actionPerformed(ActionEvent e)
1118   {
1119     Desktop.instance
1120             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1121   }
1122
1123   @Override
1124   public void addFromURL_actionPerformed(ActionEvent e)
1125   {
1126     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1127   }
1128
1129   @Override
1130   public void save_actionPerformed(ActionEvent e)
1131   {
1132     if (fileName == null || (currentFileFormat == null)
1133             || fileName.startsWith("http"))
1134     {
1135       saveAs_actionPerformed();
1136     }
1137     else
1138     {
1139       saveAlignment(fileName, currentFileFormat);
1140     }
1141   }
1142
1143   /**
1144    * Saves the alignment to a file with a name chosen by the user, if necessary
1145    * warning if a file would be overwritten
1146    */
1147   @Override
1148   public void saveAs_actionPerformed()
1149   {
1150     String format = currentFileFormat == null ? null
1151             : currentFileFormat.getName();
1152     JalviewFileChooser chooser = JalviewFileChooser
1153             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1154
1155     chooser.setFileView(new JalviewFileView());
1156     chooser.setDialogTitle(
1157             MessageManager.getString("label.save_alignment_to_file"));
1158     chooser.setToolTipText(MessageManager.getString("action.save"));
1159
1160     int value = chooser.showSaveDialog(this);
1161
1162     if (value != JalviewFileChooser.APPROVE_OPTION)
1163     {
1164       return;
1165     }
1166     currentFileFormat = chooser.getSelectedFormat();
1167     // todo is this (2005) test now obsolete - value is never null?
1168     while (currentFileFormat == null)
1169     {
1170       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1171               MessageManager
1172                       .getString("label.select_file_format_before_saving"),
1173               MessageManager.getString("label.file_format_not_specified"),
1174               JvOptionPane.WARNING_MESSAGE);
1175       currentFileFormat = chooser.getSelectedFormat();
1176       value = chooser.showSaveDialog(this);
1177       if (value != JalviewFileChooser.APPROVE_OPTION)
1178       {
1179         return;
1180       }
1181     }
1182
1183     fileName = chooser.getSelectedFile().getPath();
1184
1185     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1186     Cache.setProperty("LAST_DIRECTORY", fileName);
1187     saveAlignment(fileName, currentFileFormat);
1188   }
1189
1190   boolean lastSaveSuccessful = false;
1191
1192   FileFormatI lastFormatSaved;
1193
1194   String lastFilenameSaved;
1195
1196   /**
1197    * Raise a dialog or status message for the last call to saveAlignment.
1198    *
1199    * @return true if last call to saveAlignment(file, format) was successful.
1200    */
1201   public boolean isSaveAlignmentSuccessful()
1202   {
1203
1204     if (!lastSaveSuccessful)
1205     {
1206       JvOptionPane.showInternalMessageDialog(this, MessageManager
1207               .formatMessage("label.couldnt_save_file", new Object[]
1208               { lastFilenameSaved }),
1209               MessageManager.getString("label.error_saving_file"),
1210               JvOptionPane.WARNING_MESSAGE);
1211     }
1212     else
1213     {
1214
1215       setStatus(MessageManager.formatMessage(
1216               "label.successfully_saved_to_file_in_format", new Object[]
1217               { lastFilenameSaved, lastFormatSaved }));
1218
1219     }
1220     return lastSaveSuccessful;
1221   }
1222
1223   /**
1224    * Saves the alignment to the specified file path, in the specified format,
1225    * which may be an alignment format, or Jalview project format. If the
1226    * alignment has hidden regions, or the format is one capable of including
1227    * non-sequence data (features, annotations, groups), then the user may be
1228    * prompted to specify what to include in the output.
1229    *
1230    * @param file
1231    * @param format
1232    */
1233   public void saveAlignment(String file, FileFormatI format)
1234   {
1235     lastSaveSuccessful = true;
1236     lastFilenameSaved = file;
1237     lastFormatSaved = format;
1238
1239     if (FileFormat.Jalview.equals(format))
1240     {
1241       String shortName = title;
1242       if (shortName.indexOf(File.separatorChar) > -1)
1243       {
1244         shortName = shortName.substring(
1245                 shortName.lastIndexOf(File.separatorChar) + 1);
1246       }
1247       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
1248
1249       statusBar.setText(MessageManager.formatMessage(
1250               "label.successfully_saved_to_file_in_format", new Object[]
1251               { fileName, format }));
1252
1253       return;
1254     }
1255
1256     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1257     Runnable cancelAction = new Runnable()
1258     {
1259       @Override
1260       public void run()
1261       {
1262         lastSaveSuccessful = false;
1263       }
1264     };
1265     Runnable outputAction = new Runnable()
1266     {
1267       @Override
1268       public void run()
1269       {
1270         // todo defer this to inside formatSequences (or later)
1271         AlignmentExportData exportData = viewport
1272                 .getAlignExportData(options);
1273         String output = new FormatAdapter(alignPanel, options)
1274                 .formatSequences(format, exportData.getAlignment(),
1275                         exportData.getOmitHidden(),
1276                         exportData.getStartEndPostions(),
1277                         viewport.getAlignment().getHiddenColumns());
1278         if (output == null)
1279         {
1280           lastSaveSuccessful = false;
1281         }
1282         else
1283         {
1284           // create backupfiles object and get new temp filename destination
1285           boolean doBackup = BackupFiles.getEnabled();
1286           BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1287           try
1288           {
1289             String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
1290                         PrintWriter out = new PrintWriter(
1291                     new FileWriter(tempFilePath));
1292
1293             out.print(output);
1294             out.close();
1295             AlignFrame.this.setTitle(file);
1296             statusBar.setText(MessageManager.formatMessage(
1297                   "label.successfully_saved_to_file_in_format", new Object[]
1298                   { fileName, format.getName() }));
1299             lastSaveSuccessful = true;
1300           } catch (Exception ex)
1301           {
1302             lastSaveSuccessful = false;
1303             ex.printStackTrace();
1304           }
1305
1306           if (doBackup)
1307           {
1308             backupfiles.setWriteSuccess(lastSaveSuccessful);
1309             // do the backup file roll and rename the temp file to actual file
1310             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1311           }
1312         }
1313       }
1314     };
1315
1316     /*
1317      * show dialog with export options if applicable; else just do it
1318      */
1319     if (AlignExportOptions.isNeeded(viewport, format))
1320     {
1321       AlignExportOptions choices = new AlignExportOptions(
1322               alignPanel.getAlignViewport(), format, options);
1323       choices.setResponseAction(0, outputAction);
1324       choices.setResponseAction(1, cancelAction);
1325       choices.showDialog();
1326     }
1327     else
1328     {
1329       outputAction.run();
1330     }
1331   }
1332
1333   /**
1334    * Outputs the alignment to textbox in the requested format, if necessary
1335    * first prompting the user for whether to include hidden regions or
1336    * non-sequence data
1337    *
1338    * @param fileFormatName
1339    */
1340   @Override
1341   protected void outputText_actionPerformed(String fileFormatName)
1342   {
1343     FileFormatI fileFormat = FileFormats.getInstance()
1344             .forName(fileFormatName);
1345     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1346     Runnable outputAction = new Runnable()
1347     {
1348       @Override
1349       public void run()
1350       {
1351         // todo defer this to inside formatSequences (or later)
1352         AlignmentExportData exportData = viewport
1353                 .getAlignExportData(options);
1354         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1355         cap.setForInput(null);
1356         try
1357         {
1358           FileFormatI format = fileFormat;
1359           cap.setText(new FormatAdapter(alignPanel, options)
1360                   .formatSequences(format, exportData.getAlignment(),
1361                           exportData.getOmitHidden(),
1362                           exportData.getStartEndPostions(),
1363                           viewport.getAlignment().getHiddenColumns()));
1364           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1365                   "label.alignment_output_command", new Object[]
1366                   { fileFormat.getName() }), 600, 500);
1367         } catch (OutOfMemoryError oom)
1368         {
1369           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1370                   oom);
1371           cap.dispose();
1372         }
1373       }
1374     };
1375
1376     /*
1377      * show dialog with export options if applicable; else just do it
1378      */
1379     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1380     {
1381       AlignExportOptions choices = new AlignExportOptions(
1382               alignPanel.getAlignViewport(), fileFormat, options);
1383       choices.setResponseAction(0, outputAction);
1384       choices.showDialog();
1385     }
1386     else
1387     {
1388       outputAction.run();
1389     }
1390   }
1391
1392   /**
1393    * DOCUMENT ME!
1394    *
1395    * @param e
1396    *          DOCUMENT ME!
1397    */
1398   @Override
1399   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1400   {
1401     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1402     htmlSVG.exportHTML(null);
1403   }
1404
1405   @Override
1406   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1407   {
1408     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1409     bjs.exportHTML(null);
1410   }
1411
1412   public void createImageMap(File file, String image)
1413   {
1414     alignPanel.makePNGImageMap(file, image);
1415   }
1416
1417   /**
1418    * Creates a PNG image of the alignment and writes it to the given file. If
1419    * the file is null, the user is prompted to choose a file.
1420    *
1421    * @param f
1422    */
1423   @Override
1424   public void createPNG(File f)
1425   {
1426     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1427   }
1428
1429   /**
1430    * Creates an EPS image of the alignment and writes it to the given file. If
1431    * the file is null, the user is prompted to choose a file.
1432    *
1433    * @param f
1434    */
1435   @Override
1436   public void createEPS(File f)
1437   {
1438     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1439   }
1440
1441   /**
1442    * Creates an SVG image of the alignment and writes it to the given file. If
1443    * the file is null, the user is prompted to choose a file.
1444    *
1445    * @param f
1446    */
1447   @Override
1448   public void createSVG(File f)
1449   {
1450     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1451   }
1452
1453   @Override
1454   public void pageSetup_actionPerformed(ActionEvent e)
1455   {
1456     PrinterJob printJob = PrinterJob.getPrinterJob();
1457     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1458   }
1459
1460   /**
1461    * DOCUMENT ME!
1462    *
1463    * @param e
1464    *          DOCUMENT ME!
1465    */
1466   @Override
1467   public void printMenuItem_actionPerformed(ActionEvent e)
1468   {
1469     // Putting in a thread avoids Swing painting problems
1470     PrintThread thread = new PrintThread(alignPanel);
1471     thread.start();
1472   }
1473
1474   @Override
1475   public void exportFeatures_actionPerformed(ActionEvent e)
1476   {
1477     new AnnotationExporter(alignPanel).exportFeatures();
1478   }
1479
1480   @Override
1481   public void exportAnnotations_actionPerformed(ActionEvent e)
1482   {
1483     new AnnotationExporter(alignPanel).exportAnnotations();
1484   }
1485
1486   @Override
1487   public void associatedData_actionPerformed(ActionEvent e)
1488   {
1489     final JalviewFileChooser chooser = new JalviewFileChooser(
1490             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1491     chooser.setFileView(new JalviewFileView());
1492     String tooltip = MessageManager.getString("label.load_jalview_annotations");
1493     chooser.setDialogTitle(tooltip);
1494     chooser.setToolTipText(tooltip);
1495     chooser.setResponseHandler(0, new Runnable()
1496     {
1497       @Override
1498       public void run()
1499       {
1500         String choice = chooser.getSelectedFile().getPath();
1501         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1502         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1503       }
1504     });
1505
1506     chooser.showOpenDialog(this);
1507   }
1508
1509   /**
1510    * Close the current view or all views in the alignment frame. If the frame
1511    * only contains one view then the alignment will be removed from memory.
1512    *
1513    * @param closeAllTabs
1514    */
1515   @Override
1516   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1517   {
1518     if (alignPanels != null && alignPanels.size() < 2)
1519     {
1520       closeAllTabs = true;
1521     }
1522
1523     try
1524     {
1525       if (alignPanels != null)
1526       {
1527         if (closeAllTabs)
1528         {
1529           if (this.isClosed())
1530           {
1531             // really close all the windows - otherwise wait till
1532             // setClosed(true) is called
1533             for (int i = 0; i < alignPanels.size(); i++)
1534             {
1535               AlignmentPanel ap = alignPanels.get(i);
1536               ap.closePanel();
1537             }
1538           }
1539         }
1540         else
1541         {
1542           closeView(alignPanel);
1543         }
1544       }
1545       if (closeAllTabs)
1546       {
1547         if (featureSettings != null && featureSettings.isOpen())
1548         {
1549           featureSettings.close();
1550           featureSettings = null;
1551         }
1552         /*
1553          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1554          * be called recursively, with the frame now in 'closed' state
1555          */
1556         this.setClosed(true);
1557       }
1558     } catch (Exception ex)
1559     {
1560       ex.printStackTrace();
1561     }
1562   }
1563
1564   /**
1565    * Close the specified panel and close up tabs appropriately.
1566    *
1567    * @param panelToClose
1568    */
1569   public void closeView(AlignmentPanel panelToClose)
1570   {
1571     int index = tabbedPane.getSelectedIndex();
1572     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1573     alignPanels.remove(panelToClose);
1574     panelToClose.closePanel();
1575     panelToClose = null;
1576
1577     tabbedPane.removeTabAt(closedindex);
1578     tabbedPane.validate();
1579
1580     if (index > closedindex || index == tabbedPane.getTabCount())
1581     {
1582       // modify currently selected tab index if necessary.
1583       index--;
1584     }
1585
1586     this.tabSelectionChanged(index);
1587   }
1588
1589   /**
1590    * DOCUMENT ME!
1591    */
1592   void updateEditMenuBar()
1593   {
1594
1595     if (viewport.getHistoryList().size() > 0)
1596     {
1597       undoMenuItem.setEnabled(true);
1598       CommandI command = viewport.getHistoryList().peek();
1599       undoMenuItem.setText(MessageManager
1600               .formatMessage("label.undo_command", new Object[]
1601               { command.getDescription() }));
1602     }
1603     else
1604     {
1605       undoMenuItem.setEnabled(false);
1606       undoMenuItem.setText(MessageManager.getString("action.undo"));
1607     }
1608
1609     if (viewport.getRedoList().size() > 0)
1610     {
1611       redoMenuItem.setEnabled(true);
1612
1613       CommandI command = viewport.getRedoList().peek();
1614       redoMenuItem.setText(MessageManager
1615               .formatMessage("label.redo_command", new Object[]
1616               { command.getDescription() }));
1617     }
1618     else
1619     {
1620       redoMenuItem.setEnabled(false);
1621       redoMenuItem.setText(MessageManager.getString("action.redo"));
1622     }
1623   }
1624
1625   @Override
1626   public void addHistoryItem(CommandI command)
1627   {
1628     if (command.getSize() > 0)
1629     {
1630       viewport.addToHistoryList(command);
1631       viewport.clearRedoList();
1632       updateEditMenuBar();
1633       viewport.updateHiddenColumns();
1634       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1635       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1636       // viewport.getColumnSelection()
1637       // .getHiddenColumns().size() > 0);
1638     }
1639   }
1640
1641   /**
1642    *
1643    * @return alignment objects for all views
1644    */
1645   AlignmentI[] getViewAlignments()
1646   {
1647     if (alignPanels != null)
1648     {
1649       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1650       int i = 0;
1651       for (AlignmentPanel ap : alignPanels)
1652       {
1653         als[i++] = ap.av.getAlignment();
1654       }
1655       return als;
1656     }
1657     if (viewport != null)
1658     {
1659       return new AlignmentI[] { viewport.getAlignment() };
1660     }
1661     return null;
1662   }
1663
1664   /**
1665    * DOCUMENT ME!
1666    *
1667    * @param e
1668    *          DOCUMENT ME!
1669    */
1670   @Override
1671   protected void undoMenuItem_actionPerformed(ActionEvent e)
1672   {
1673     if (viewport.getHistoryList().isEmpty())
1674     {
1675       return;
1676     }
1677     CommandI command = viewport.getHistoryList().pop();
1678     viewport.addToRedoList(command);
1679     command.undoCommand(getViewAlignments());
1680
1681     AlignmentViewport originalSource = getOriginatingSource(command);
1682     updateEditMenuBar();
1683
1684     if (originalSource != null)
1685     {
1686       if (originalSource != viewport)
1687       {
1688         Cache.log.warn(
1689                 "Implementation worry: mismatch of viewport origin for undo");
1690       }
1691       originalSource.updateHiddenColumns();
1692       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1693       // null
1694       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1695       // viewport.getColumnSelection()
1696       // .getHiddenColumns().size() > 0);
1697       originalSource.firePropertyChange("alignment", null,
1698               originalSource.getAlignment().getSequences());
1699     }
1700   }
1701
1702   /**
1703    * DOCUMENT ME!
1704    *
1705    * @param e
1706    *          DOCUMENT ME!
1707    */
1708   @Override
1709   protected void redoMenuItem_actionPerformed(ActionEvent e)
1710   {
1711     if (viewport.getRedoList().size() < 1)
1712     {
1713       return;
1714     }
1715
1716     CommandI command = viewport.getRedoList().pop();
1717     viewport.addToHistoryList(command);
1718     command.doCommand(getViewAlignments());
1719
1720     AlignmentViewport originalSource = getOriginatingSource(command);
1721     updateEditMenuBar();
1722
1723     if (originalSource != null)
1724     {
1725
1726       if (originalSource != viewport)
1727       {
1728         Cache.log.warn(
1729                 "Implementation worry: mismatch of viewport origin for redo");
1730       }
1731       originalSource.updateHiddenColumns();
1732       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1733       // null
1734       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1735       // viewport.getColumnSelection()
1736       // .getHiddenColumns().size() > 0);
1737       originalSource.firePropertyChange("alignment", null,
1738               originalSource.getAlignment().getSequences());
1739     }
1740   }
1741
1742   AlignmentViewport getOriginatingSource(CommandI command)
1743   {
1744     AlignmentViewport originalSource = null;
1745     // For sequence removal and addition, we need to fire
1746     // the property change event FROM the viewport where the
1747     // original alignment was altered
1748     AlignmentI al = null;
1749     if (command instanceof EditCommand)
1750     {
1751       EditCommand editCommand = (EditCommand) command;
1752       al = editCommand.getAlignment();
1753       List<Component> comps = PaintRefresher.components
1754               .get(viewport.getSequenceSetId());
1755
1756       for (Component comp : comps)
1757       {
1758         if (comp instanceof AlignmentPanel)
1759         {
1760           if (al == ((AlignmentPanel) comp).av.getAlignment())
1761           {
1762             originalSource = ((AlignmentPanel) comp).av;
1763             break;
1764           }
1765         }
1766       }
1767     }
1768
1769     if (originalSource == null)
1770     {
1771       // The original view is closed, we must validate
1772       // the current view against the closed view first
1773       if (al != null)
1774       {
1775         PaintRefresher.validateSequences(al, viewport.getAlignment());
1776       }
1777
1778       originalSource = viewport;
1779     }
1780
1781     return originalSource;
1782   }
1783
1784   /**
1785    * DOCUMENT ME!
1786    *
1787    * @param up
1788    *          DOCUMENT ME!
1789    */
1790   public void moveSelectedSequences(boolean up)
1791   {
1792     SequenceGroup sg = viewport.getSelectionGroup();
1793
1794     if (sg == null)
1795     {
1796       return;
1797     }
1798     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1799             viewport.getHiddenRepSequences(), up);
1800     alignPanel.paintAlignment(true, false);
1801   }
1802
1803   synchronized void slideSequences(boolean right, int size)
1804   {
1805     List<SequenceI> sg = new ArrayList<>();
1806     if (viewport.cursorMode)
1807     {
1808       sg.add(viewport.getAlignment()
1809               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1810     }
1811     else if (viewport.getSelectionGroup() != null
1812             && viewport.getSelectionGroup().getSize() != viewport
1813                     .getAlignment().getHeight())
1814     {
1815       sg = viewport.getSelectionGroup()
1816               .getSequences(viewport.getHiddenRepSequences());
1817     }
1818
1819     if (sg.size() < 1)
1820     {
1821       return;
1822     }
1823
1824     List<SequenceI> invertGroup = new ArrayList<>();
1825
1826     for (SequenceI seq : viewport.getAlignment().getSequences())
1827     {
1828       if (!sg.contains(seq))
1829       {
1830         invertGroup.add(seq);
1831       }
1832     }
1833
1834     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1835
1836     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1837     for (int i = 0; i < invertGroup.size(); i++)
1838     {
1839       seqs2[i] = invertGroup.get(i);
1840     }
1841
1842     SlideSequencesCommand ssc;
1843     if (right)
1844     {
1845       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1846               viewport.getGapCharacter());
1847     }
1848     else
1849     {
1850       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1851               viewport.getGapCharacter());
1852     }
1853
1854     int groupAdjustment = 0;
1855     if (ssc.getGapsInsertedBegin() && right)
1856     {
1857       if (viewport.cursorMode)
1858       {
1859         alignPanel.getSeqPanel().moveCursor(size, 0);
1860       }
1861       else
1862       {
1863         groupAdjustment = size;
1864       }
1865     }
1866     else if (!ssc.getGapsInsertedBegin() && !right)
1867     {
1868       if (viewport.cursorMode)
1869       {
1870         alignPanel.getSeqPanel().moveCursor(-size, 0);
1871       }
1872       else
1873       {
1874         groupAdjustment = -size;
1875       }
1876     }
1877
1878     if (groupAdjustment != 0)
1879     {
1880       viewport.getSelectionGroup().setStartRes(
1881               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1882       viewport.getSelectionGroup().setEndRes(
1883               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1884     }
1885
1886     /*
1887      * just extend the last slide command if compatible; but not if in
1888      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1889      */
1890     boolean appendHistoryItem = false;
1891     Deque<CommandI> historyList = viewport.getHistoryList();
1892     boolean inSplitFrame = getSplitViewContainer() != null;
1893     if (!inSplitFrame && historyList != null && historyList.size() > 0
1894             && historyList.peek() instanceof SlideSequencesCommand)
1895     {
1896       appendHistoryItem = ssc.appendSlideCommand(
1897               (SlideSequencesCommand) historyList.peek());
1898     }
1899
1900     if (!appendHistoryItem)
1901     {
1902       addHistoryItem(ssc);
1903     }
1904
1905     repaint();
1906   }
1907
1908   /**
1909    * DOCUMENT ME!
1910    *
1911    * @param e
1912    *          DOCUMENT ME!
1913    */
1914   @Override
1915   protected void copy_actionPerformed()
1916   {
1917     if (viewport.getSelectionGroup() == null)
1918     {
1919       return;
1920     }
1921     // TODO: preserve the ordering of displayed alignment annotation in any
1922     // internal paste (particularly sequence associated annotation)
1923     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1924     String[] omitHidden = null;
1925
1926     if (viewport.hasHiddenColumns())
1927     {
1928       omitHidden = viewport.getViewAsString(true);
1929     }
1930
1931     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1932             seqs, omitHidden, null);
1933
1934     StringSelection ss = new StringSelection(output);
1935
1936     try
1937     {
1938       jalview.gui.Desktop.internalCopy = true;
1939       // Its really worth setting the clipboard contents
1940       // to empty before setting the large StringSelection!!
1941       Toolkit.getDefaultToolkit().getSystemClipboard()
1942               .setContents(new StringSelection(""), null);
1943
1944       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1945               Desktop.instance);
1946     } catch (OutOfMemoryError er)
1947     {
1948       new OOMWarning("copying region", er);
1949       return;
1950     }
1951
1952     HiddenColumns hiddenColumns = null;
1953     if (viewport.hasHiddenColumns())
1954     {
1955       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1956       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1957
1958       // create new HiddenColumns object with copy of hidden regions
1959       // between startRes and endRes, offset by startRes
1960       hiddenColumns = new HiddenColumns(
1961               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1962               hiddenCutoff, hiddenOffset);
1963     }
1964
1965     Desktop.jalviewClipboard = new Object[] { seqs,
1966         viewport.getAlignment().getDataset(), hiddenColumns };
1967     setStatus(MessageManager.formatMessage(
1968             "label.copied_sequences_to_clipboard", new Object[]
1969             { Integer.valueOf(seqs.length).toString() }));
1970   }
1971
1972   /**
1973    * DOCUMENT ME!
1974    *
1975    * @param e
1976    *          DOCUMENT ME!
1977    */
1978   @Override
1979   protected void pasteNew_actionPerformed(ActionEvent e)
1980   {
1981     paste(true);
1982   }
1983
1984   /**
1985    * DOCUMENT ME!
1986    *
1987    * @param e
1988    *          DOCUMENT ME!
1989    */
1990   @Override
1991   protected void pasteThis_actionPerformed(ActionEvent e)
1992   {
1993     paste(false);
1994   }
1995
1996   /**
1997    * Paste contents of Jalview clipboard
1998    *
1999    * @param newAlignment
2000    *          true to paste to a new alignment, otherwise add to this.
2001    */
2002   void paste(boolean newAlignment)
2003   {
2004     boolean externalPaste = true;
2005     try
2006     {
2007       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2008       Transferable contents = c.getContents(this);
2009
2010       if (contents == null)
2011       {
2012         return;
2013       }
2014
2015       String str;
2016       FileFormatI format;
2017       try
2018       {
2019         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2020         if (str.length() < 1)
2021         {
2022           return;
2023         }
2024
2025         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2026
2027       } catch (OutOfMemoryError er)
2028       {
2029         new OOMWarning("Out of memory pasting sequences!!", er);
2030         return;
2031       }
2032
2033       SequenceI[] sequences;
2034       boolean annotationAdded = false;
2035       AlignmentI alignment = null;
2036
2037       if (Desktop.jalviewClipboard != null)
2038       {
2039         // The clipboard was filled from within Jalview, we must use the
2040         // sequences
2041         // And dataset from the copied alignment
2042         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2043         // be doubly sure that we create *new* sequence objects.
2044         sequences = new SequenceI[newseq.length];
2045         for (int i = 0; i < newseq.length; i++)
2046         {
2047           sequences[i] = new Sequence(newseq[i]);
2048         }
2049         alignment = new Alignment(sequences);
2050         externalPaste = false;
2051       }
2052       else
2053       {
2054         // parse the clipboard as an alignment.
2055         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2056                 format);
2057         sequences = alignment.getSequencesArray();
2058       }
2059
2060       int alwidth = 0;
2061       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2062       int fgroup = -1;
2063
2064       if (newAlignment)
2065       {
2066
2067         if (Desktop.jalviewClipboard != null)
2068         {
2069           // dataset is inherited
2070           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2071         }
2072         else
2073         {
2074           // new dataset is constructed
2075           alignment.setDataset(null);
2076         }
2077         alwidth = alignment.getWidth() + 1;
2078       }
2079       else
2080       {
2081         AlignmentI pastedal = alignment; // preserve pasted alignment object
2082         // Add pasted sequences and dataset into existing alignment.
2083         alignment = viewport.getAlignment();
2084         alwidth = alignment.getWidth() + 1;
2085         // decide if we need to import sequences from an existing dataset
2086         boolean importDs = Desktop.jalviewClipboard != null
2087                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2088         // importDs==true instructs us to copy over new dataset sequences from
2089         // an existing alignment
2090         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2091                                                                       // create
2092         // minimum dataset set
2093
2094         for (int i = 0; i < sequences.length; i++)
2095         {
2096           if (importDs)
2097           {
2098             newDs.addElement(null);
2099           }
2100           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2101           // paste
2102           if (importDs && ds != null)
2103           {
2104             if (!newDs.contains(ds))
2105             {
2106               newDs.setElementAt(ds, i);
2107               ds = new Sequence(ds);
2108               // update with new dataset sequence
2109               sequences[i].setDatasetSequence(ds);
2110             }
2111             else
2112             {
2113               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2114             }
2115           }
2116           else
2117           {
2118             // copy and derive new dataset sequence
2119             sequences[i] = sequences[i].deriveSequence();
2120             alignment.getDataset()
2121                     .addSequence(sequences[i].getDatasetSequence());
2122             // TODO: avoid creation of duplicate dataset sequences with a
2123             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2124           }
2125           alignment.addSequence(sequences[i]); // merges dataset
2126         }
2127         if (newDs != null)
2128         {
2129           newDs.clear(); // tidy up
2130         }
2131         if (alignment.getAlignmentAnnotation() != null)
2132         {
2133           for (AlignmentAnnotation alan : alignment
2134                   .getAlignmentAnnotation())
2135           {
2136             if (alan.graphGroup > fgroup)
2137             {
2138               fgroup = alan.graphGroup;
2139             }
2140           }
2141         }
2142         if (pastedal.getAlignmentAnnotation() != null)
2143         {
2144           // Add any annotation attached to alignment.
2145           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2146           for (int i = 0; i < alann.length; i++)
2147           {
2148             annotationAdded = true;
2149             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2150             {
2151               AlignmentAnnotation newann = new AlignmentAnnotation(
2152                       alann[i]);
2153               if (newann.graphGroup > -1)
2154               {
2155                 if (newGraphGroups.size() <= newann.graphGroup
2156                         || newGraphGroups.get(newann.graphGroup) == null)
2157                 {
2158                   for (int q = newGraphGroups
2159                           .size(); q <= newann.graphGroup; q++)
2160                   {
2161                     newGraphGroups.add(q, null);
2162                   }
2163                   newGraphGroups.set(newann.graphGroup,
2164                           Integer.valueOf(++fgroup));
2165                 }
2166                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2167                         .intValue();
2168               }
2169
2170               newann.padAnnotation(alwidth);
2171               alignment.addAnnotation(newann);
2172             }
2173           }
2174         }
2175       }
2176       if (!newAlignment)
2177       {
2178         // /////
2179         // ADD HISTORY ITEM
2180         //
2181         addHistoryItem(new EditCommand(
2182                 MessageManager.getString("label.add_sequences"),
2183                 Action.PASTE, sequences, 0, alignment.getWidth(),
2184                 alignment));
2185       }
2186       // Add any annotations attached to sequences
2187       for (int i = 0; i < sequences.length; i++)
2188       {
2189         if (sequences[i].getAnnotation() != null)
2190         {
2191           AlignmentAnnotation newann;
2192           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2193           {
2194             annotationAdded = true;
2195             newann = sequences[i].getAnnotation()[a];
2196             newann.adjustForAlignment();
2197             newann.padAnnotation(alwidth);
2198             if (newann.graphGroup > -1)
2199             {
2200               if (newann.graphGroup > -1)
2201               {
2202                 if (newGraphGroups.size() <= newann.graphGroup
2203                         || newGraphGroups.get(newann.graphGroup) == null)
2204                 {
2205                   for (int q = newGraphGroups
2206                           .size(); q <= newann.graphGroup; q++)
2207                   {
2208                     newGraphGroups.add(q, null);
2209                   }
2210                   newGraphGroups.set(newann.graphGroup,
2211                           Integer.valueOf(++fgroup));
2212                 }
2213                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2214                         .intValue();
2215               }
2216             }
2217             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2218             // was
2219             // duplicated
2220             // earlier
2221             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2222                     a);
2223           }
2224         }
2225       }
2226       if (!newAlignment)
2227       {
2228
2229         // propagate alignment changed.
2230         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2231         if (annotationAdded)
2232         {
2233           // Duplicate sequence annotation in all views.
2234           AlignmentI[] alview = this.getViewAlignments();
2235           for (int i = 0; i < sequences.length; i++)
2236           {
2237             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2238             if (sann == null)
2239             {
2240               continue;
2241             }
2242             for (int avnum = 0; avnum < alview.length; avnum++)
2243             {
2244               if (alview[avnum] != alignment)
2245               {
2246                 // duplicate in a view other than the one with input focus
2247                 int avwidth = alview[avnum].getWidth() + 1;
2248                 // this relies on sann being preserved after we
2249                 // modify the sequence's annotation array for each duplication
2250                 for (int a = 0; a < sann.length; a++)
2251                 {
2252                   AlignmentAnnotation newann = new AlignmentAnnotation(
2253                           sann[a]);
2254                   sequences[i].addAlignmentAnnotation(newann);
2255                   newann.padAnnotation(avwidth);
2256                   alview[avnum].addAnnotation(newann); // annotation was
2257                   // duplicated earlier
2258                   // TODO JAL-1145 graphGroups are not updated for sequence
2259                   // annotation added to several views. This may cause
2260                   // strangeness
2261                   alview[avnum].setAnnotationIndex(newann, a);
2262                 }
2263               }
2264             }
2265           }
2266           buildSortByAnnotationScoresMenu();
2267         }
2268         viewport.firePropertyChange("alignment", null,
2269                 alignment.getSequences());
2270         if (alignPanels != null)
2271         {
2272           for (AlignmentPanel ap : alignPanels)
2273           {
2274             ap.validateAnnotationDimensions(false);
2275           }
2276         }
2277         else
2278         {
2279           alignPanel.validateAnnotationDimensions(false);
2280         }
2281
2282       }
2283       else
2284       {
2285         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2286                 DEFAULT_HEIGHT);
2287         String newtitle = new String("Copied sequences");
2288
2289         if (Desktop.jalviewClipboard != null
2290                 && Desktop.jalviewClipboard[2] != null)
2291         {
2292           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2293           af.viewport.setHiddenColumns(hc);
2294         }
2295
2296         // >>>This is a fix for the moment, until a better solution is
2297         // found!!<<<
2298         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2299                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2300                         .getFeatureRenderer());
2301
2302         // TODO: maintain provenance of an alignment, rather than just make the
2303         // title a concatenation of operations.
2304         if (!externalPaste)
2305         {
2306           if (title.startsWith("Copied sequences"))
2307           {
2308             newtitle = title;
2309           }
2310           else
2311           {
2312             newtitle = newtitle.concat("- from " + title);
2313           }
2314         }
2315         else
2316         {
2317           newtitle = new String("Pasted sequences");
2318         }
2319
2320         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2321                 DEFAULT_HEIGHT);
2322
2323       }
2324
2325     } catch (Exception ex)
2326     {
2327       ex.printStackTrace();
2328       System.out.println("Exception whilst pasting: " + ex);
2329       // could be anything being pasted in here
2330     }
2331
2332   }
2333
2334   @Override
2335   protected void expand_newalign(ActionEvent e)
2336   {
2337     try
2338     {
2339       AlignmentI alignment = AlignmentUtils
2340               .expandContext(getViewport().getAlignment(), -1);
2341       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2342               DEFAULT_HEIGHT);
2343       String newtitle = new String("Flanking alignment");
2344
2345       if (Desktop.jalviewClipboard != null
2346               && Desktop.jalviewClipboard[2] != null)
2347       {
2348         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2349         af.viewport.setHiddenColumns(hc);
2350       }
2351
2352       // >>>This is a fix for the moment, until a better solution is
2353       // found!!<<<
2354       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2355               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2356                       .getFeatureRenderer());
2357
2358       // TODO: maintain provenance of an alignment, rather than just make the
2359       // title a concatenation of operations.
2360       {
2361         if (title.startsWith("Copied sequences"))
2362         {
2363           newtitle = title;
2364         }
2365         else
2366         {
2367           newtitle = newtitle.concat("- from " + title);
2368         }
2369       }
2370
2371       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2372
2373     } catch (Exception ex)
2374     {
2375       ex.printStackTrace();
2376       System.out.println("Exception whilst pasting: " + ex);
2377       // could be anything being pasted in here
2378     } catch (OutOfMemoryError oom)
2379     {
2380       new OOMWarning("Viewing flanking region of alignment", oom);
2381     }
2382   }
2383
2384   /**
2385    * Action Cut (delete and copy) the selected region
2386    */
2387   @Override
2388   protected void cut_actionPerformed()
2389   {
2390     copy_actionPerformed();
2391     delete_actionPerformed();
2392   }
2393
2394   /**
2395    * Performs menu option to Delete the currently selected region
2396    */
2397   @Override
2398   protected void delete_actionPerformed()
2399   {
2400
2401     SequenceGroup sg = viewport.getSelectionGroup();
2402     if (sg == null)
2403     {
2404       return;
2405     }
2406
2407     Runnable okAction = new Runnable()
2408     {
2409                 @Override
2410                 public void run()
2411                 {
2412                     SequenceI[] cut = sg.getSequences()
2413                             .toArray(new SequenceI[sg.getSize()]);
2414
2415                     addHistoryItem(new EditCommand(
2416                             MessageManager.getString("label.cut_sequences"), Action.CUT,
2417                             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2418                             viewport.getAlignment()));
2419
2420                     viewport.setSelectionGroup(null);
2421                     viewport.sendSelection();
2422                     viewport.getAlignment().deleteGroup(sg);
2423
2424                     viewport.firePropertyChange("alignment", null,
2425                             viewport.getAlignment().getSequences());
2426                     if (viewport.getAlignment().getHeight() < 1)
2427                     {
2428                       try
2429                       {
2430                         AlignFrame.this.setClosed(true);
2431                       } catch (Exception ex)
2432                       {
2433                       }
2434                     }
2435                 }};
2436
2437     /*
2438      * If the cut affects all sequences, prompt for confirmation
2439      */
2440     boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2441     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2442             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2443         if (wholeHeight && wholeWidth)
2444         {
2445             JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2446                 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2447             Object[] options = new Object[] { MessageManager.getString("action.ok"),
2448                     MessageManager.getString("action.cancel") };
2449                 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2450                     MessageManager.getString("label.delete_all"),
2451                     JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2452                     options, options[0]);
2453         } else
2454         {
2455                 okAction.run();
2456         }
2457   }
2458
2459   /**
2460    * DOCUMENT ME!
2461    *
2462    * @param e
2463    *          DOCUMENT ME!
2464    */
2465   @Override
2466   protected void deleteGroups_actionPerformed(ActionEvent e)
2467   {
2468     if (avc.deleteGroups())
2469     {
2470       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2471       alignPanel.updateAnnotation();
2472       alignPanel.paintAlignment(true, true);
2473     }
2474   }
2475
2476   /**
2477    * DOCUMENT ME!
2478    *
2479    * @param e
2480    *          DOCUMENT ME!
2481    */
2482   @Override
2483   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2484   {
2485     SequenceGroup sg = new SequenceGroup(
2486             viewport.getAlignment().getSequences());
2487
2488     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2489     viewport.setSelectionGroup(sg);
2490     viewport.isSelectionGroupChanged(true);
2491     viewport.sendSelection();
2492     // JAL-2034 - should delegate to
2493     // alignPanel to decide if overview needs
2494     // updating.
2495     alignPanel.paintAlignment(false, false);
2496     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2497   }
2498
2499   /**
2500    * DOCUMENT ME!
2501    *
2502    * @param e
2503    *          DOCUMENT ME!
2504    */
2505   @Override
2506   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2507   {
2508     if (viewport.cursorMode)
2509     {
2510       alignPanel.getSeqPanel().keyboardNo1 = null;
2511       alignPanel.getSeqPanel().keyboardNo2 = null;
2512     }
2513     viewport.setSelectionGroup(null);
2514     viewport.getColumnSelection().clear();
2515     viewport.setSelectionGroup(null);
2516     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2517     // JAL-2034 - should delegate to
2518     // alignPanel to decide if overview needs
2519     // updating.
2520     alignPanel.paintAlignment(false, false);
2521     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2522     viewport.sendSelection();
2523   }
2524
2525   /**
2526    * DOCUMENT ME!
2527    *
2528    * @param e
2529    *          DOCUMENT ME!
2530    */
2531   @Override
2532   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2533   {
2534     SequenceGroup sg = viewport.getSelectionGroup();
2535
2536     if (sg == null)
2537     {
2538       selectAllSequenceMenuItem_actionPerformed(null);
2539
2540       return;
2541     }
2542
2543     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2544     {
2545       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2546     }
2547     // JAL-2034 - should delegate to
2548     // alignPanel to decide if overview needs
2549     // updating.
2550
2551     alignPanel.paintAlignment(true, false);
2552     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2553     viewport.sendSelection();
2554   }
2555
2556   @Override
2557   public void invertColSel_actionPerformed(ActionEvent e)
2558   {
2559     viewport.invertColumnSelection();
2560     alignPanel.paintAlignment(true, false);
2561     viewport.sendSelection();
2562   }
2563
2564   /**
2565    * DOCUMENT ME!
2566    *
2567    * @param e
2568    *          DOCUMENT ME!
2569    */
2570   @Override
2571   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2572   {
2573     trimAlignment(true);
2574   }
2575
2576   /**
2577    * DOCUMENT ME!
2578    *
2579    * @param e
2580    *          DOCUMENT ME!
2581    */
2582   @Override
2583   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2584   {
2585     trimAlignment(false);
2586   }
2587
2588   void trimAlignment(boolean trimLeft)
2589   {
2590     ColumnSelection colSel = viewport.getColumnSelection();
2591     int column;
2592
2593     if (!colSel.isEmpty())
2594     {
2595       if (trimLeft)
2596       {
2597         column = colSel.getMin();
2598       }
2599       else
2600       {
2601         column = colSel.getMax();
2602       }
2603
2604       SequenceI[] seqs;
2605       if (viewport.getSelectionGroup() != null)
2606       {
2607         seqs = viewport.getSelectionGroup()
2608                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2609       }
2610       else
2611       {
2612         seqs = viewport.getAlignment().getSequencesArray();
2613       }
2614
2615       TrimRegionCommand trimRegion;
2616       if (trimLeft)
2617       {
2618         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2619                 column, viewport.getAlignment());
2620         viewport.getRanges().setStartRes(0);
2621       }
2622       else
2623       {
2624         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2625                 column, viewport.getAlignment());
2626       }
2627
2628       setStatus(MessageManager
2629               .formatMessage("label.removed_columns", new String[]
2630               { Integer.valueOf(trimRegion.getSize()).toString() }));
2631
2632       addHistoryItem(trimRegion);
2633
2634       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2635       {
2636         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2637                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2638         {
2639           viewport.getAlignment().deleteGroup(sg);
2640         }
2641       }
2642
2643       viewport.firePropertyChange("alignment", null,
2644               viewport.getAlignment().getSequences());
2645     }
2646   }
2647
2648   /**
2649    * DOCUMENT ME!
2650    *
2651    * @param e
2652    *          DOCUMENT ME!
2653    */
2654   @Override
2655   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2656   {
2657     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2658
2659     SequenceI[] seqs;
2660     if (viewport.getSelectionGroup() != null)
2661     {
2662       seqs = viewport.getSelectionGroup()
2663               .getSequencesAsArray(viewport.getHiddenRepSequences());
2664       start = viewport.getSelectionGroup().getStartRes();
2665       end = viewport.getSelectionGroup().getEndRes();
2666     }
2667     else
2668     {
2669       seqs = viewport.getAlignment().getSequencesArray();
2670     }
2671
2672     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2673             "Remove Gapped Columns", seqs, start, end,
2674             viewport.getAlignment());
2675
2676     addHistoryItem(removeGapCols);
2677
2678     setStatus(MessageManager
2679             .formatMessage("label.removed_empty_columns", new Object[]
2680             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2681
2682     // This is to maintain viewport position on first residue
2683     // of first sequence
2684     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2685     ViewportRanges ranges = viewport.getRanges();
2686     int startRes = seq.findPosition(ranges.getStartRes());
2687     // ShiftList shifts;
2688     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2689     // edit.alColumnChanges=shifts.getInverse();
2690     // if (viewport.hasHiddenColumns)
2691     // viewport.getColumnSelection().compensateForEdits(shifts);
2692     ranges.setStartRes(seq.findIndex(startRes) - 1);
2693     viewport.firePropertyChange("alignment", null,
2694             viewport.getAlignment().getSequences());
2695
2696   }
2697
2698   /**
2699    * DOCUMENT ME!
2700    *
2701    * @param e
2702    *          DOCUMENT ME!
2703    */
2704   @Override
2705   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2706   {
2707     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2708
2709     SequenceI[] seqs;
2710     if (viewport.getSelectionGroup() != null)
2711     {
2712       seqs = viewport.getSelectionGroup()
2713               .getSequencesAsArray(viewport.getHiddenRepSequences());
2714       start = viewport.getSelectionGroup().getStartRes();
2715       end = viewport.getSelectionGroup().getEndRes();
2716     }
2717     else
2718     {
2719       seqs = viewport.getAlignment().getSequencesArray();
2720     }
2721
2722     // This is to maintain viewport position on first residue
2723     // of first sequence
2724     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2725     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2726
2727     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2728             viewport.getAlignment()));
2729
2730     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2731
2732     viewport.firePropertyChange("alignment", null,
2733             viewport.getAlignment().getSequences());
2734
2735   }
2736
2737   /**
2738    * DOCUMENT ME!
2739    *
2740    * @param e
2741    *          DOCUMENT ME!
2742    */
2743   @Override
2744   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2745   {
2746     viewport.setPadGaps(padGapsMenuitem.isSelected());
2747     viewport.firePropertyChange("alignment", null,
2748             viewport.getAlignment().getSequences());
2749   }
2750
2751   /**
2752    * DOCUMENT ME!
2753    *
2754    * @param e
2755    *          DOCUMENT ME!
2756    */
2757   @Override
2758   public void findMenuItem_actionPerformed(ActionEvent e)
2759   {
2760     new Finder();
2761   }
2762
2763   /**
2764    * Create a new view of the current alignment.
2765    */
2766   @Override
2767   public void newView_actionPerformed(ActionEvent e)
2768   {
2769     newView(null, true);
2770   }
2771
2772   /**
2773    * Creates and shows a new view of the current alignment.
2774    *
2775    * @param viewTitle
2776    *          title of newly created view; if null, one will be generated
2777    * @param copyAnnotation
2778    *          if true then duplicate all annnotation, groups and settings
2779    * @return new alignment panel, already displayed.
2780    */
2781   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2782   {
2783     /*
2784      * Create a new AlignmentPanel (with its own, new Viewport)
2785      */
2786     AlignmentPanel newap = new jalview.project.Jalview2XML()
2787             .copyAlignPanel(alignPanel);
2788     if (!copyAnnotation)
2789     {
2790       /*
2791        * remove all groups and annotation except for the automatic stuff
2792        */
2793       newap.av.getAlignment().deleteAllGroups();
2794       newap.av.getAlignment().deleteAllAnnotations(false);
2795     }
2796
2797     newap.av.setGatherViewsHere(false);
2798
2799     if (viewport.getViewName() == null)
2800     {
2801       viewport.setViewName(MessageManager
2802               .getString("label.view_name_original"));
2803     }
2804
2805     /*
2806      * Views share the same edits undo and redo stacks
2807      */
2808     newap.av.setHistoryList(viewport.getHistoryList());
2809     newap.av.setRedoList(viewport.getRedoList());
2810
2811     /*
2812      * copy any visualisation settings that are not saved in the project
2813      */
2814     newap.av.setColourAppliesToAllGroups(
2815             viewport.getColourAppliesToAllGroups());
2816
2817     /*
2818      * Views share the same mappings; need to deregister any new mappings
2819      * created by copyAlignPanel, and register the new reference to the shared
2820      * mappings
2821      */
2822     newap.av.replaceMappings(viewport.getAlignment());
2823
2824     /*
2825      * start up cDNA consensus (if applicable) now mappings are in place
2826      */
2827     if (newap.av.initComplementConsensus())
2828     {
2829       newap.refresh(true); // adjust layout of annotations
2830     }
2831
2832     newap.av.setViewName(getNewViewName(viewTitle));
2833
2834     addAlignmentPanel(newap, true);
2835     newap.alignmentChanged();
2836
2837     if (alignPanels.size() == 2)
2838     {
2839       viewport.setGatherViewsHere(true);
2840     }
2841     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2842     return newap;
2843   }
2844
2845   /**
2846    * Make a new name for the view, ensuring it is unique within the current
2847    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2848    * these now use viewId. Unique view names are still desirable for usability.)
2849    *
2850    * @param viewTitle
2851    * @return
2852    */
2853   protected String getNewViewName(String viewTitle)
2854   {
2855     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2856     boolean addFirstIndex = false;
2857     if (viewTitle == null || viewTitle.trim().length() == 0)
2858     {
2859       viewTitle = MessageManager.getString("action.view");
2860       addFirstIndex = true;
2861     }
2862     else
2863     {
2864       index = 1;// we count from 1 if given a specific name
2865     }
2866     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2867
2868     List<Component> comps = PaintRefresher.components
2869             .get(viewport.getSequenceSetId());
2870
2871     List<String> existingNames = getExistingViewNames(comps);
2872
2873     while (existingNames.contains(newViewName))
2874     {
2875       newViewName = viewTitle + " " + (++index);
2876     }
2877     return newViewName;
2878   }
2879
2880   /**
2881    * Returns a list of distinct view names found in the given list of
2882    * components. View names are held on the viewport of an AlignmentPanel.
2883    *
2884    * @param comps
2885    * @return
2886    */
2887   protected List<String> getExistingViewNames(List<Component> comps)
2888   {
2889     List<String> existingNames = new ArrayList<>();
2890     for (Component comp : comps)
2891     {
2892       if (comp instanceof AlignmentPanel)
2893       {
2894         AlignmentPanel ap = (AlignmentPanel) comp;
2895         if (!existingNames.contains(ap.av.getViewName()))
2896         {
2897           existingNames.add(ap.av.getViewName());
2898         }
2899       }
2900     }
2901     return existingNames;
2902   }
2903
2904   /**
2905    * Explode tabbed views into separate windows.
2906    */
2907   @Override
2908   public void expandViews_actionPerformed(ActionEvent e)
2909   {
2910     Desktop.explodeViews(this);
2911   }
2912
2913   /**
2914    * Gather views in separate windows back into a tabbed presentation.
2915    */
2916   @Override
2917   public void gatherViews_actionPerformed(ActionEvent e)
2918   {
2919     Desktop.instance.gatherViews(this);
2920   }
2921
2922   /**
2923    * DOCUMENT ME!
2924    *
2925    * @param e
2926    *          DOCUMENT ME!
2927    */
2928   @Override
2929   public void font_actionPerformed(ActionEvent e)
2930   {
2931     new FontChooser(alignPanel);
2932   }
2933
2934   /**
2935    * DOCUMENT ME!
2936    *
2937    * @param e
2938    *          DOCUMENT ME!
2939    */
2940   @Override
2941   protected void seqLimit_actionPerformed(ActionEvent e)
2942   {
2943     viewport.setShowJVSuffix(seqLimits.isSelected());
2944
2945     alignPanel.getIdPanel().getIdCanvas()
2946             .setPreferredSize(alignPanel.calculateIdWidth());
2947     alignPanel.paintAlignment(true, false);
2948   }
2949
2950   @Override
2951   public void idRightAlign_actionPerformed(ActionEvent e)
2952   {
2953     viewport.setRightAlignIds(idRightAlign.isSelected());
2954     alignPanel.paintAlignment(false, false);
2955   }
2956
2957   @Override
2958   public void centreColumnLabels_actionPerformed(ActionEvent e)
2959   {
2960     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2961     alignPanel.paintAlignment(false, false);
2962   }
2963
2964   /*
2965    * (non-Javadoc)
2966    *
2967    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2968    */
2969   @Override
2970   protected void followHighlight_actionPerformed()
2971   {
2972     /*
2973      * Set the 'follow' flag on the Viewport (and scroll to position if now
2974      * true).
2975      */
2976     final boolean state = this.followHighlightMenuItem.getState();
2977     viewport.setFollowHighlight(state);
2978     if (state)
2979     {
2980       alignPanel.scrollToPosition(viewport.getSearchResults());
2981     }
2982   }
2983
2984   /**
2985    * DOCUMENT ME!
2986    *
2987    * @param e
2988    *          DOCUMENT ME!
2989    */
2990   @Override
2991   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2992   {
2993     viewport.setColourText(colourTextMenuItem.isSelected());
2994     alignPanel.paintAlignment(false, false);
2995   }
2996
2997   /**
2998    * DOCUMENT ME!
2999    *
3000    * @param e
3001    *          DOCUMENT ME!
3002    */
3003   @Override
3004   public void wrapMenuItem_actionPerformed(ActionEvent e)
3005   {
3006     scaleAbove.setVisible(wrapMenuItem.isSelected());
3007     scaleLeft.setVisible(wrapMenuItem.isSelected());
3008     scaleRight.setVisible(wrapMenuItem.isSelected());
3009     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3010     alignPanel.updateLayout();
3011   }
3012
3013   @Override
3014   public void showAllSeqs_actionPerformed(ActionEvent e)
3015   {
3016     viewport.showAllHiddenSeqs();
3017   }
3018
3019   @Override
3020   public void showAllColumns_actionPerformed(ActionEvent e)
3021   {
3022     viewport.showAllHiddenColumns();
3023     alignPanel.paintAlignment(true, true);
3024     viewport.sendSelection();
3025   }
3026
3027   @Override
3028   public void hideSelSequences_actionPerformed(ActionEvent e)
3029   {
3030     viewport.hideAllSelectedSeqs();
3031   }
3032
3033   /**
3034    * called by key handler and the hide all/show all menu items
3035    *
3036    * @param toggleSeqs
3037    * @param toggleCols
3038    */
3039   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3040   {
3041
3042     boolean hide = false;
3043     SequenceGroup sg = viewport.getSelectionGroup();
3044     if (!toggleSeqs && !toggleCols)
3045     {
3046       // Hide everything by the current selection - this is a hack - we do the
3047       // invert and then hide
3048       // first check that there will be visible columns after the invert.
3049       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3050               && sg.getStartRes() <= sg.getEndRes()))
3051       {
3052         // now invert the sequence set, if required - empty selection implies
3053         // that no hiding is required.
3054         if (sg != null)
3055         {
3056           invertSequenceMenuItem_actionPerformed(null);
3057           sg = viewport.getSelectionGroup();
3058           toggleSeqs = true;
3059
3060         }
3061         viewport.expandColSelection(sg, true);
3062         // finally invert the column selection and get the new sequence
3063         // selection.
3064         invertColSel_actionPerformed(null);
3065         toggleCols = true;
3066       }
3067     }
3068
3069     if (toggleSeqs)
3070     {
3071       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3072       {
3073         hideSelSequences_actionPerformed(null);
3074         hide = true;
3075       }
3076       else if (!(toggleCols && viewport.hasSelectedColumns()))
3077       {
3078         showAllSeqs_actionPerformed(null);
3079       }
3080     }
3081
3082     if (toggleCols)
3083     {
3084       if (viewport.hasSelectedColumns())
3085       {
3086         hideSelColumns_actionPerformed(null);
3087         if (!toggleSeqs)
3088         {
3089           viewport.setSelectionGroup(sg);
3090         }
3091       }
3092       else if (!hide)
3093       {
3094         showAllColumns_actionPerformed(null);
3095       }
3096     }
3097   }
3098
3099   /*
3100    * (non-Javadoc)
3101    *
3102    * @see
3103    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3104    * event.ActionEvent)
3105    */
3106   @Override
3107   public void hideAllButSelection_actionPerformed(ActionEvent e)
3108   {
3109     toggleHiddenRegions(false, false);
3110     viewport.sendSelection();
3111   }
3112
3113   /*
3114    * (non-Javadoc)
3115    *
3116    * @see
3117    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3118    * .ActionEvent)
3119    */
3120   @Override
3121   public void hideAllSelection_actionPerformed(ActionEvent e)
3122   {
3123     SequenceGroup sg = viewport.getSelectionGroup();
3124     viewport.expandColSelection(sg, false);
3125     viewport.hideAllSelectedSeqs();
3126     viewport.hideSelectedColumns();
3127     alignPanel.updateLayout();
3128     alignPanel.paintAlignment(true, true);
3129     viewport.sendSelection();
3130   }
3131
3132   /*
3133    * (non-Javadoc)
3134    *
3135    * @see
3136    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3137    * ActionEvent)
3138    */
3139   @Override
3140   public void showAllhidden_actionPerformed(ActionEvent e)
3141   {
3142     viewport.showAllHiddenColumns();
3143     viewport.showAllHiddenSeqs();
3144     alignPanel.paintAlignment(true, true);
3145     viewport.sendSelection();
3146   }
3147
3148   @Override
3149   public void hideSelColumns_actionPerformed(ActionEvent e)
3150   {
3151     viewport.hideSelectedColumns();
3152     alignPanel.updateLayout();
3153     alignPanel.paintAlignment(true, true);
3154     viewport.sendSelection();
3155   }
3156
3157   @Override
3158   public void hiddenMarkers_actionPerformed(ActionEvent e)
3159   {
3160     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3161     repaint();
3162   }
3163
3164   /**
3165    * DOCUMENT ME!
3166    *
3167    * @param e
3168    *          DOCUMENT ME!
3169    */
3170   @Override
3171   protected void scaleAbove_actionPerformed(ActionEvent e)
3172   {
3173     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3174     alignPanel.updateLayout();
3175     alignPanel.paintAlignment(true, false);
3176   }
3177
3178   /**
3179    * DOCUMENT ME!
3180    *
3181    * @param e
3182    *          DOCUMENT ME!
3183    */
3184   @Override
3185   protected void scaleLeft_actionPerformed(ActionEvent e)
3186   {
3187     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3188     alignPanel.updateLayout();
3189     alignPanel.paintAlignment(true, false);
3190   }
3191
3192   /**
3193    * DOCUMENT ME!
3194    *
3195    * @param e
3196    *          DOCUMENT ME!
3197    */
3198   @Override
3199   protected void scaleRight_actionPerformed(ActionEvent e)
3200   {
3201     viewport.setScaleRightWrapped(scaleRight.isSelected());
3202     alignPanel.updateLayout();
3203     alignPanel.paintAlignment(true, false);
3204   }
3205
3206   /**
3207    * DOCUMENT ME!
3208    *
3209    * @param e
3210    *          DOCUMENT ME!
3211    */
3212   @Override
3213   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3214   {
3215     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3216     alignPanel.paintAlignment(false, false);
3217   }
3218
3219   /**
3220    * DOCUMENT ME!
3221    *
3222    * @param e
3223    *          DOCUMENT ME!
3224    */
3225   @Override
3226   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3227   {
3228     viewport.setShowText(viewTextMenuItem.isSelected());
3229     alignPanel.paintAlignment(false, false);
3230   }
3231
3232   /**
3233    * DOCUMENT ME!
3234    *
3235    * @param e
3236    *          DOCUMENT ME!
3237    */
3238   @Override
3239   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3240   {
3241     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3242     alignPanel.paintAlignment(false, false);
3243   }
3244
3245   public FeatureSettings featureSettings;
3246
3247   @Override
3248   public FeatureSettingsControllerI getFeatureSettingsUI()
3249   {
3250     return featureSettings;
3251   }
3252
3253   @Override
3254   public void featureSettings_actionPerformed(ActionEvent e)
3255   {
3256     showFeatureSettingsUI();
3257   }
3258
3259   @Override
3260   public FeatureSettingsControllerI showFeatureSettingsUI()
3261   {
3262     if (featureSettings != null)
3263     {
3264       featureSettings.closeOldSettings();
3265       featureSettings = null;
3266     }
3267     if (!showSeqFeatures.isSelected())
3268     {
3269       // make sure features are actually displayed
3270       showSeqFeatures.setSelected(true);
3271       showSeqFeatures_actionPerformed(null);
3272     }
3273     featureSettings = new FeatureSettings(this);
3274     return featureSettings;
3275   }
3276
3277   /**
3278    * Set or clear 'Show Sequence Features'
3279    *
3280    * @param evt
3281    *          DOCUMENT ME!
3282    */
3283   @Override
3284   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3285   {
3286     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3287     alignPanel.paintAlignment(true, true);
3288   }
3289
3290   /**
3291    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3292    * the annotations panel as a whole.
3293    *
3294    * The options to show/hide all annotations should be enabled when the panel
3295    * is shown, and disabled when the panel is hidden.
3296    *
3297    * @param e
3298    */
3299   @Override
3300   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3301   {
3302     final boolean setVisible = annotationPanelMenuItem.isSelected();
3303     viewport.setShowAnnotation(setVisible);
3304     this.showAllSeqAnnotations.setEnabled(setVisible);
3305     this.hideAllSeqAnnotations.setEnabled(setVisible);
3306     this.showAllAlAnnotations.setEnabled(setVisible);
3307     this.hideAllAlAnnotations.setEnabled(setVisible);
3308     alignPanel.updateLayout();
3309   }
3310
3311   @Override
3312   public void alignmentProperties()
3313   {
3314     JComponent pane;
3315     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3316
3317             .formatAsHtml();
3318     String content = MessageManager.formatMessage("label.html_content",
3319             new Object[]
3320             { contents.toString() });
3321     contents = null;
3322
3323     if (Platform.isJS())
3324     {
3325       JLabel textLabel = new JLabel();
3326       textLabel.setText(content);
3327       textLabel.setBackground(Color.WHITE);
3328
3329       pane = new JPanel(new BorderLayout());
3330       ((JPanel) pane).setOpaque(true);
3331       pane.setBackground(Color.WHITE);
3332       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3333     }
3334     else
3335     /**
3336      * Java only
3337      *
3338      * @j2sIgnore
3339      */
3340     {
3341       JEditorPane editPane = new JEditorPane("text/html", "");
3342       editPane.setEditable(false);
3343       editPane.setText(content);
3344       pane = editPane;
3345     }
3346
3347     JInternalFrame frame = new JInternalFrame();
3348
3349     frame.getContentPane().add(new JScrollPane(pane));
3350
3351     Desktop.addInternalFrame(frame, MessageManager
3352             .formatMessage("label.alignment_properties", new Object[]
3353             { getTitle() }), 500, 400);
3354   }
3355
3356   /**
3357    * DOCUMENT ME!
3358    *
3359    * @param e
3360    *          DOCUMENT ME!
3361    */
3362   @Override
3363   public void overviewMenuItem_actionPerformed(ActionEvent e)
3364   {
3365     if (alignPanel.overviewPanel != null)
3366     {
3367       return;
3368     }
3369
3370     JInternalFrame frame = new JInternalFrame();
3371     final OverviewPanel overview = new OverviewPanel(alignPanel);
3372     frame.setContentPane(overview);
3373     Desktop.addInternalFrame(frame, MessageManager
3374             .formatMessage("label.overview_params", new Object[]
3375             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3376             true, true);
3377     frame.pack();
3378     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3379     frame.addInternalFrameListener(
3380             new javax.swing.event.InternalFrameAdapter()
3381             {
3382               @Override
3383               public void internalFrameClosed(
3384                       javax.swing.event.InternalFrameEvent evt)
3385               {
3386                 overview.dispose();
3387                 alignPanel.setOverviewPanel(null);
3388               }
3389             });
3390     if (getKeyListeners().length > 0)
3391     {
3392       frame.addKeyListener(getKeyListeners()[0]);
3393     }
3394
3395     alignPanel.setOverviewPanel(overview);
3396   }
3397
3398   @Override
3399   public void textColour_actionPerformed()
3400   {
3401     new TextColourChooser().chooseColour(alignPanel, null);
3402   }
3403
3404   /*
3405    * public void covariationColour_actionPerformed() {
3406    * changeColour(new
3407    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3408    * ()[0])); }
3409    */
3410   @Override
3411   public void annotationColour_actionPerformed()
3412   {
3413     new AnnotationColourChooser(viewport, alignPanel);
3414   }
3415
3416   @Override
3417   public void annotationColumn_actionPerformed(ActionEvent e)
3418   {
3419     new AnnotationColumnChooser(viewport, alignPanel);
3420   }
3421
3422   /**
3423    * Action on the user checking or unchecking the option to apply the selected
3424    * colour scheme to all groups. If unchecked, groups may have their own
3425    * independent colour schemes.
3426    *
3427    * @param selected
3428    */
3429   @Override
3430   public void applyToAllGroups_actionPerformed(boolean selected)
3431   {
3432     viewport.setColourAppliesToAllGroups(selected);
3433   }
3434
3435   /**
3436    * Action on user selecting a colour from the colour menu
3437    *
3438    * @param name
3439    *          the name (not the menu item label!) of the colour scheme
3440    */
3441   @Override
3442   public void changeColour_actionPerformed(String name)
3443   {
3444     /*
3445      * 'User Defined' opens a panel to configure or load a
3446      * user-defined colour scheme
3447      */
3448     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3449     {
3450       new UserDefinedColours(alignPanel);
3451       return;
3452     }
3453
3454     /*
3455      * otherwise set the chosen colour scheme (or null for 'None')
3456      */
3457     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3458             viewport,
3459             viewport.getAlignment(), viewport.getHiddenRepSequences());
3460     changeColour(cs);
3461   }
3462
3463   /**
3464    * Actions on setting or changing the alignment colour scheme
3465    *
3466    * @param cs
3467    */
3468   @Override
3469   public void changeColour(ColourSchemeI cs)
3470   {
3471     // TODO: pull up to controller method
3472     ColourMenuHelper.setColourSelected(colourMenu, cs);
3473
3474     viewport.setGlobalColourScheme(cs);
3475
3476     alignPanel.paintAlignment(true, true);
3477   }
3478
3479   /**
3480    * Show the PID threshold slider panel
3481    */
3482   @Override
3483   protected void modifyPID_actionPerformed()
3484   {
3485     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3486             alignPanel.getViewName());
3487     SliderPanel.showPIDSlider();
3488   }
3489
3490   /**
3491    * Show the Conservation slider panel
3492    */
3493   @Override
3494   protected void modifyConservation_actionPerformed()
3495   {
3496     SliderPanel.setConservationSlider(alignPanel,
3497             viewport.getResidueShading(), alignPanel.getViewName());
3498     SliderPanel.showConservationSlider();
3499   }
3500
3501   /**
3502    * Action on selecting or deselecting (Colour) By Conservation
3503    */
3504   @Override
3505   public void conservationMenuItem_actionPerformed(boolean selected)
3506   {
3507     modifyConservation.setEnabled(selected);
3508     viewport.setConservationSelected(selected);
3509     viewport.getResidueShading().setConservationApplied(selected);
3510
3511     changeColour(viewport.getGlobalColourScheme());
3512     if (selected)
3513     {
3514       modifyConservation_actionPerformed();
3515     }
3516     else
3517     {
3518       SliderPanel.hideConservationSlider();
3519     }
3520   }
3521
3522   /**
3523    * Action on selecting or deselecting (Colour) Above PID Threshold
3524    */
3525   @Override
3526   public void abovePIDThreshold_actionPerformed(boolean selected)
3527   {
3528     modifyPID.setEnabled(selected);
3529     viewport.setAbovePIDThreshold(selected);
3530     if (!selected)
3531     {
3532       viewport.getResidueShading().setThreshold(0,
3533               viewport.isIgnoreGapsConsensus());
3534     }
3535
3536     changeColour(viewport.getGlobalColourScheme());
3537     if (selected)
3538     {
3539       modifyPID_actionPerformed();
3540     }
3541     else
3542     {
3543       SliderPanel.hidePIDSlider();
3544     }
3545   }
3546
3547   /**
3548    * DOCUMENT ME!
3549    *
3550    * @param e
3551    *          DOCUMENT ME!
3552    */
3553   @Override
3554   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3555   {
3556     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3557     AlignmentSorter.sortByPID(viewport.getAlignment(),
3558             viewport.getAlignment().getSequenceAt(0));
3559     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3560             viewport.getAlignment()));
3561     alignPanel.paintAlignment(true, false);
3562   }
3563
3564   /**
3565    * DOCUMENT ME!
3566    *
3567    * @param e
3568    *          DOCUMENT ME!
3569    */
3570   @Override
3571   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3572   {
3573     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3574     AlignmentSorter.sortByID(viewport.getAlignment());
3575     addHistoryItem(
3576             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3577     alignPanel.paintAlignment(true, false);
3578   }
3579
3580   /**
3581    * DOCUMENT ME!
3582    *
3583    * @param e
3584    *          DOCUMENT ME!
3585    */
3586   @Override
3587   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3588   {
3589     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3590     AlignmentSorter.sortByLength(viewport.getAlignment());
3591     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3592             viewport.getAlignment()));
3593     alignPanel.paintAlignment(true, false);
3594   }
3595
3596   /**
3597    * DOCUMENT ME!
3598    *
3599    * @param e
3600    *          DOCUMENT ME!
3601    */
3602   @Override
3603   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3604   {
3605     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3606     AlignmentSorter.sortByGroup(viewport.getAlignment());
3607     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3608             viewport.getAlignment()));
3609
3610     alignPanel.paintAlignment(true, false);
3611   }
3612
3613   /**
3614    * DOCUMENT ME!
3615    *
3616    * @param e
3617    *          DOCUMENT ME!
3618    */
3619   @Override
3620   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3621   {
3622     new RedundancyPanel(alignPanel, this);
3623   }
3624
3625   /**
3626    * DOCUMENT ME!
3627    *
3628    * @param e
3629    *          DOCUMENT ME!
3630    */
3631   @Override
3632   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3633   {
3634     if ((viewport.getSelectionGroup() == null)
3635             || (viewport.getSelectionGroup().getSize() < 2))
3636     {
3637       JvOptionPane.showInternalMessageDialog(this,
3638               MessageManager.getString(
3639                       "label.you_must_select_least_two_sequences"),
3640               MessageManager.getString("label.invalid_selection"),
3641               JvOptionPane.WARNING_MESSAGE);
3642     }
3643     else
3644     {
3645       JInternalFrame frame = new JInternalFrame();
3646       frame.setContentPane(new PairwiseAlignPanel(viewport));
3647       Desktop.addInternalFrame(frame,
3648               MessageManager.getString("action.pairwise_alignment"), 600,
3649               500);
3650     }
3651   }
3652
3653   @Override
3654   public void autoCalculate_actionPerformed(ActionEvent e)
3655   {
3656     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3657     if (viewport.autoCalculateConsensus)
3658     {
3659       viewport.firePropertyChange("alignment", null,
3660               viewport.getAlignment().getSequences());
3661     }
3662   }
3663
3664   @Override
3665   public void sortByTreeOption_actionPerformed(ActionEvent e)
3666   {
3667     viewport.sortByTree = sortByTree.isSelected();
3668   }
3669
3670   @Override
3671   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3672   {
3673     viewport.followSelection = listenToViewSelections.isSelected();
3674   }
3675
3676   /**
3677    * Constructs a tree panel and adds it to the desktop
3678    *
3679    * @param type
3680    *          tree type (NJ or AV)
3681    * @param modelName
3682    *          name of score model used to compute the tree
3683    * @param options
3684    *          parameters for the distance or similarity calculation
3685    */
3686   void newTreePanel(String type, String modelName,
3687           SimilarityParamsI options)
3688   {
3689     String frameTitle = "";
3690     TreePanel tp;
3691
3692     boolean onSelection = false;
3693     if (viewport.getSelectionGroup() != null
3694             && viewport.getSelectionGroup().getSize() > 0)
3695     {
3696       SequenceGroup sg = viewport.getSelectionGroup();
3697
3698       /* Decide if the selection is a column region */
3699       for (SequenceI _s : sg.getSequences())
3700       {
3701         if (_s.getLength() < sg.getEndRes())
3702         {
3703           JvOptionPane.showMessageDialog(Desktop.desktop,
3704                   MessageManager.getString(
3705                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3706                   MessageManager.getString(
3707                           "label.sequences_selection_not_aligned"),
3708                   JvOptionPane.WARNING_MESSAGE);
3709
3710           return;
3711         }
3712       }
3713       onSelection = true;
3714     }
3715     else
3716     {
3717       if (viewport.getAlignment().getHeight() < 2)
3718       {
3719         return;
3720       }
3721     }
3722
3723     tp = new TreePanel(alignPanel, type, modelName, options);
3724     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3725
3726     frameTitle += " from ";
3727
3728     if (viewport.getViewName() != null)
3729     {
3730       frameTitle += viewport.getViewName() + " of ";
3731     }
3732
3733     frameTitle += this.title;
3734
3735     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3736   }
3737
3738   /**
3739    * DOCUMENT ME!
3740    *
3741    * @param title
3742    *          DOCUMENT ME!
3743    * @param order
3744    *          DOCUMENT ME!
3745    */
3746   public void addSortByOrderMenuItem(String title,
3747           final AlignmentOrder order)
3748   {
3749     final JMenuItem item = new JMenuItem(MessageManager
3750             .formatMessage("action.by_title_param", new Object[]
3751             { title }));
3752     sort.add(item);
3753     item.addActionListener(new java.awt.event.ActionListener()
3754     {
3755       @Override
3756       public void actionPerformed(ActionEvent e)
3757       {
3758         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3759
3760         // TODO: JBPNote - have to map order entries to curent SequenceI
3761         // pointers
3762         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3763
3764         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3765                 viewport.getAlignment()));
3766
3767         alignPanel.paintAlignment(true, false);
3768       }
3769     });
3770   }
3771
3772   /**
3773    * Add a new sort by annotation score menu item
3774    *
3775    * @param sort
3776    *          the menu to add the option to
3777    * @param scoreLabel
3778    *          the label used to retrieve scores for each sequence on the
3779    *          alignment
3780    */
3781   public void addSortByAnnotScoreMenuItem(JMenu sort,
3782           final String scoreLabel)
3783   {
3784     final JMenuItem item = new JMenuItem(scoreLabel);
3785     sort.add(item);
3786     item.addActionListener(new java.awt.event.ActionListener()
3787     {
3788       @Override
3789       public void actionPerformed(ActionEvent e)
3790       {
3791         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3792         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3793                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3794         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3795                 viewport.getAlignment()));
3796         alignPanel.paintAlignment(true, false);
3797       }
3798     });
3799   }
3800
3801   /**
3802    * last hash for alignment's annotation array - used to minimise cost of
3803    * rebuild.
3804    */
3805   protected int _annotationScoreVectorHash;
3806
3807   /**
3808    * search the alignment and rebuild the sort by annotation score submenu the
3809    * last alignment annotation vector hash is stored to minimize cost of
3810    * rebuilding in subsequence calls.
3811    *
3812    */
3813   @Override
3814   public void buildSortByAnnotationScoresMenu()
3815   {
3816     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3817     {
3818       return;
3819     }
3820
3821     if (viewport.getAlignment().getAlignmentAnnotation()
3822             .hashCode() != _annotationScoreVectorHash)
3823     {
3824       sortByAnnotScore.removeAll();
3825       // almost certainly a quicker way to do this - but we keep it simple
3826       Hashtable<String, String> scoreSorts = new Hashtable<>();
3827       AlignmentAnnotation aann[];
3828       for (SequenceI sqa : viewport.getAlignment().getSequences())
3829       {
3830         aann = sqa.getAnnotation();
3831         for (int i = 0; aann != null && i < aann.length; i++)
3832         {
3833           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3834           {
3835             scoreSorts.put(aann[i].label, aann[i].label);
3836           }
3837         }
3838       }
3839       Enumeration<String> labels = scoreSorts.keys();
3840       while (labels.hasMoreElements())
3841       {
3842         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3843                 labels.nextElement());
3844       }
3845       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3846       scoreSorts.clear();
3847
3848       _annotationScoreVectorHash = viewport.getAlignment()
3849               .getAlignmentAnnotation().hashCode();
3850     }
3851   }
3852
3853   /**
3854    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3855    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3856    * call. Listeners are added to remove the menu item when the treePanel is
3857    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3858    * modified.
3859    */
3860   @Override
3861   public void buildTreeSortMenu()
3862   {
3863     sortByTreeMenu.removeAll();
3864
3865     List<Component> comps = PaintRefresher.components
3866             .get(viewport.getSequenceSetId());
3867     List<TreePanel> treePanels = new ArrayList<>();
3868     for (Component comp : comps)
3869     {
3870       if (comp instanceof TreePanel)
3871       {
3872         treePanels.add((TreePanel) comp);
3873       }
3874     }
3875
3876     if (treePanels.size() < 1)
3877     {
3878       sortByTreeMenu.setVisible(false);
3879       return;
3880     }
3881
3882     sortByTreeMenu.setVisible(true);
3883
3884     for (final TreePanel tp : treePanels)
3885     {
3886       final JMenuItem item = new JMenuItem(tp.getTitle());
3887       item.addActionListener(new java.awt.event.ActionListener()
3888       {
3889         @Override
3890         public void actionPerformed(ActionEvent e)
3891         {
3892           tp.sortByTree_actionPerformed();
3893           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3894
3895         }
3896       });
3897
3898       sortByTreeMenu.add(item);
3899     }
3900   }
3901
3902   public boolean sortBy(AlignmentOrder alorder, String undoname)
3903   {
3904     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3905     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3906     if (undoname != null)
3907     {
3908       addHistoryItem(new OrderCommand(undoname, oldOrder,
3909               viewport.getAlignment()));
3910     }
3911     alignPanel.paintAlignment(true, false);
3912     return true;
3913   }
3914
3915   /**
3916    * Work out whether the whole set of sequences or just the selected set will
3917    * be submitted for multiple alignment.
3918    *
3919    */
3920   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3921   {
3922     // Now, check we have enough sequences
3923     AlignmentView msa = null;
3924
3925     if ((viewport.getSelectionGroup() != null)
3926             && (viewport.getSelectionGroup().getSize() > 1))
3927     {
3928       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3929       // some common interface!
3930       /*
3931        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3932        * SequenceI[sz = seqs.getSize(false)];
3933        *
3934        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3935        * seqs.getSequenceAt(i); }
3936        */
3937       msa = viewport.getAlignmentView(true);
3938     }
3939     else if (viewport.getSelectionGroup() != null
3940             && viewport.getSelectionGroup().getSize() == 1)
3941     {
3942       int option = JvOptionPane.showConfirmDialog(this,
3943               MessageManager.getString("warn.oneseq_msainput_selection"),
3944               MessageManager.getString("label.invalid_selection"),
3945               JvOptionPane.OK_CANCEL_OPTION);
3946       if (option == JvOptionPane.OK_OPTION)
3947       {
3948         msa = viewport.getAlignmentView(false);
3949       }
3950     }
3951     else
3952     {
3953       msa = viewport.getAlignmentView(false);
3954     }
3955     return msa;
3956   }
3957
3958   /**
3959    * Decides what is submitted to a secondary structure prediction service: the
3960    * first sequence in the alignment, or in the current selection, or, if the
3961    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3962    * region or the whole alignment. (where the first sequence in the set is the
3963    * one that the prediction will be for).
3964    */
3965   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3966   {
3967     AlignmentView seqs = null;
3968
3969     if ((viewport.getSelectionGroup() != null)
3970             && (viewport.getSelectionGroup().getSize() > 0))
3971     {
3972       seqs = viewport.getAlignmentView(true);
3973     }
3974     else
3975     {
3976       seqs = viewport.getAlignmentView(false);
3977     }
3978     // limit sequences - JBPNote in future - could spawn multiple prediction
3979     // jobs
3980     // TODO: viewport.getAlignment().isAligned is a global state - the local
3981     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3982     if (!viewport.getAlignment().isAligned(false))
3983     {
3984       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3985       // TODO: if seqs.getSequences().length>1 then should really have warned
3986       // user!
3987
3988     }
3989     return seqs;
3990   }
3991
3992   /**
3993    * DOCUMENT ME!
3994    *
3995    * @param e
3996    *          DOCUMENT ME!
3997    */
3998   @Override
3999   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4000   {
4001     // Pick the tree file
4002     JalviewFileChooser chooser = new JalviewFileChooser(
4003             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4004     chooser.setFileView(new JalviewFileView());
4005     chooser.setDialogTitle(
4006             MessageManager.getString("label.select_newick_like_tree_file"));
4007     chooser.setToolTipText(
4008             MessageManager.getString("label.load_tree_file"));
4009
4010     chooser.setResponseHandler(0,new Runnable()
4011     {
4012       @Override
4013       public void run()
4014       {
4015         String filePath = chooser.getSelectedFile().getPath();
4016         Cache.setProperty("LAST_DIRECTORY", filePath);
4017         NewickFile fin = null;
4018         try
4019         {
4020           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4021                   DataSourceType.FILE));
4022           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4023         } catch (Exception ex)
4024         {
4025           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4026                   MessageManager
4027                           .getString("label.problem_reading_tree_file"),
4028                   JvOptionPane.WARNING_MESSAGE);
4029           ex.printStackTrace();
4030         }
4031         if (fin != null && fin.hasWarningMessage())
4032         {
4033           JvOptionPane.showMessageDialog(Desktop.desktop,
4034                   fin.getWarningMessage(),
4035                   MessageManager.getString(
4036                           "label.possible_problem_with_tree_file"),
4037                   JvOptionPane.WARNING_MESSAGE);
4038         }
4039       }
4040     });
4041     chooser.showOpenDialog(this);
4042   }
4043
4044   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4045   {
4046     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4047   }
4048
4049   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4050           int h, int x, int y)
4051   {
4052     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4053   }
4054
4055   /**
4056    * Add a treeviewer for the tree extracted from a Newick file object to the
4057    * current alignment view
4058    *
4059    * @param nf
4060    *          the tree
4061    * @param title
4062    *          tree viewer title
4063    * @param input
4064    *          Associated alignment input data (or null)
4065    * @param w
4066    *          width
4067    * @param h
4068    *          height
4069    * @param x
4070    *          position
4071    * @param y
4072    *          position
4073    * @return TreePanel handle
4074    */
4075   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4076           AlignmentView input, int w, int h, int x, int y)
4077   {
4078     TreePanel tp = null;
4079
4080     try
4081     {
4082       nf.parse();
4083
4084       if (nf.getTree() != null)
4085       {
4086         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4087
4088         tp.setSize(w, h);
4089
4090         if (x > 0 && y > 0)
4091         {
4092           tp.setLocation(x, y);
4093         }
4094
4095         Desktop.addInternalFrame(tp, treeTitle, w, h);
4096       }
4097     } catch (Exception ex)
4098     {
4099       ex.printStackTrace();
4100     }
4101
4102     return tp;
4103   }
4104
4105   private boolean buildingMenu = false;
4106
4107   /**
4108    * Generates menu items and listener event actions for web service clients
4109    *
4110    */
4111   public void BuildWebServiceMenu()
4112   {
4113     while (buildingMenu)
4114     {
4115       try
4116       {
4117         System.err.println("Waiting for building menu to finish.");
4118         Thread.sleep(10);
4119       } catch (Exception e)
4120       {
4121       }
4122     }
4123     final AlignFrame me = this;
4124     buildingMenu = true;
4125     new Thread(new Runnable()
4126     {
4127       @Override
4128       public void run()
4129       {
4130         final List<JMenuItem> legacyItems = new ArrayList<>();
4131         try
4132         {
4133           // System.err.println("Building ws menu again "
4134           // + Thread.currentThread());
4135           // TODO: add support for context dependent disabling of services based
4136           // on
4137           // alignment and current selection
4138           // TODO: add additional serviceHandle parameter to specify abstract
4139           // handler
4140           // class independently of AbstractName
4141           // TODO: add in rediscovery GUI function to restart discoverer
4142           // TODO: group services by location as well as function and/or
4143           // introduce
4144           // object broker mechanism.
4145           final Vector<JMenu> wsmenu = new Vector<>();
4146           final IProgressIndicator af = me;
4147
4148           /*
4149            * do not i18n these strings - they are hard-coded in class
4150            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4151            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4152            */
4153           final JMenu msawsmenu = new JMenu("Alignment");
4154           final JMenu secstrmenu = new JMenu(
4155                   "Secondary Structure Prediction");
4156           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4157           final JMenu analymenu = new JMenu("Analysis");
4158           final JMenu dismenu = new JMenu("Protein Disorder");
4159           // JAL-940 - only show secondary structure prediction services from
4160           // the legacy server
4161           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4162               // &&
4163           Discoverer.services != null && (Discoverer.services.size() > 0))
4164           {
4165             // TODO: refactor to allow list of AbstractName/Handler bindings to
4166             // be
4167             // stored or retrieved from elsewhere
4168             // No MSAWS used any more:
4169             // Vector msaws = null; // (Vector)
4170             // Discoverer.services.get("MsaWS");
4171             Vector<ServiceHandle> secstrpr = Discoverer.services
4172                     .get("SecStrPred");
4173             if (secstrpr != null)
4174             {
4175               // Add any secondary structure prediction services
4176               for (int i = 0, j = secstrpr.size(); i < j; i++)
4177               {
4178                 final ext.vamsas.ServiceHandle sh = secstrpr
4179                         .get(i);
4180                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4181                         .getServiceClient(sh);
4182                 int p = secstrmenu.getItemCount();
4183                 impl.attachWSMenuEntry(secstrmenu, me);
4184                 int q = secstrmenu.getItemCount();
4185                 for (int litm = p; litm < q; litm++)
4186                 {
4187                   legacyItems.add(secstrmenu.getItem(litm));
4188                 }
4189               }
4190             }
4191           }
4192
4193           // Add all submenus in the order they should appear on the web
4194           // services menu
4195           wsmenu.add(msawsmenu);
4196           wsmenu.add(secstrmenu);
4197           wsmenu.add(dismenu);
4198           wsmenu.add(analymenu);
4199           // No search services yet
4200           // wsmenu.add(seqsrchmenu);
4201
4202           javax.swing.SwingUtilities.invokeLater(new Runnable()
4203           {
4204             @Override
4205             public void run()
4206             {
4207               try
4208               {
4209                 webService.removeAll();
4210                 // first, add discovered services onto the webservices menu
4211                 if (wsmenu.size() > 0)
4212                 {
4213                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4214                   {
4215                     webService.add(wsmenu.get(i));
4216                   }
4217                 }
4218                 else
4219                 {
4220                   webService.add(me.webServiceNoServices);
4221                 }
4222                 // TODO: move into separate menu builder class.
4223                 boolean new_sspred = false;
4224                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4225                 {
4226                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4227                   if (jws2servs != null)
4228                   {
4229                     if (jws2servs.hasServices())
4230                     {
4231                       jws2servs.attachWSMenuEntry(webService, me);
4232                       for (Jws2Instance sv : jws2servs.getServices())
4233                       {
4234                         if (sv.description.toLowerCase().contains("jpred"))
4235                         {
4236                           for (JMenuItem jmi : legacyItems)
4237                           {
4238                             jmi.setVisible(false);
4239                           }
4240                         }
4241                       }
4242
4243                     }
4244                     if (jws2servs.isRunning())
4245                     {
4246                       JMenuItem tm = new JMenuItem(
4247                               "Still discovering JABA Services");
4248                       tm.setEnabled(false);
4249                       webService.add(tm);
4250                     }
4251                   }
4252                 }
4253                 build_urlServiceMenu(me.webService);
4254                 build_fetchdbmenu(webService);
4255                 for (JMenu item : wsmenu)
4256                 {
4257                   if (item.getItemCount() == 0)
4258                   {
4259                     item.setEnabled(false);
4260                   }
4261                   else
4262                   {
4263                     item.setEnabled(true);
4264                   }
4265                 }
4266               } catch (Exception e)
4267               {
4268                 Cache.log.debug(
4269                         "Exception during web service menu building process.",
4270                         e);
4271               }
4272             }
4273           });
4274         } catch (Exception e)
4275         {
4276         }
4277         buildingMenu = false;
4278       }
4279     }).start();
4280
4281   }
4282
4283   /**
4284    * construct any groupURL type service menu entries.
4285    *
4286    * @param webService
4287    */
4288   protected void build_urlServiceMenu(JMenu webService)
4289   {
4290     // TODO: remove this code when 2.7 is released
4291     // DEBUG - alignmentView
4292     /*
4293      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4294      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4295      *
4296      * @Override public void actionPerformed(ActionEvent e) {
4297      * jalview.datamodel.AlignmentView
4298      * .testSelectionViews(af.viewport.getAlignment(),
4299      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4300      *
4301      * }); webService.add(testAlView);
4302      */
4303     // TODO: refactor to RestClient discoverer and merge menu entries for
4304     // rest-style services with other types of analysis/calculation service
4305     // SHmmr test client - still being implemented.
4306     // DEBUG - alignmentView
4307
4308     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4309             .getRestClients())
4310     {
4311       client.attachWSMenuEntry(
4312               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4313               this);
4314     }
4315   }
4316
4317   /**
4318    * Searches the alignment sequences for xRefs and builds the Show
4319    * Cross-References menu (formerly called Show Products), with database
4320    * sources for which cross-references are found (protein sources for a
4321    * nucleotide alignment and vice versa)
4322    *
4323    * @return true if Show Cross-references menu should be enabled
4324    */
4325   public boolean canShowProducts()
4326   {
4327     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4328     AlignmentI dataset = viewport.getAlignment().getDataset();
4329
4330     showProducts.removeAll();
4331     final boolean dna = viewport.getAlignment().isNucleotide();
4332
4333     if (seqs == null || seqs.length == 0)
4334     {
4335       // nothing to see here.
4336       return false;
4337     }
4338
4339     boolean showp = false;
4340     try
4341     {
4342       List<String> ptypes = new CrossRef(seqs, dataset)
4343               .findXrefSourcesForSequences(dna);
4344
4345       for (final String source : ptypes)
4346       {
4347         showp = true;
4348         final AlignFrame af = this;
4349         JMenuItem xtype = new JMenuItem(source);
4350         xtype.addActionListener(new ActionListener()
4351         {
4352           @Override
4353           public void actionPerformed(ActionEvent e)
4354           {
4355             showProductsFor(af.viewport.getSequenceSelection(), dna,
4356                     source);
4357           }
4358         });
4359         showProducts.add(xtype);
4360       }
4361       showProducts.setVisible(showp);
4362       showProducts.setEnabled(showp);
4363     } catch (Exception e)
4364     {
4365       Cache.log.warn(
4366               "canShowProducts threw an exception - please report to help@jalview.org",
4367               e);
4368       return false;
4369     }
4370     return showp;
4371   }
4372
4373   /**
4374    * Finds and displays cross-references for the selected sequences (protein
4375    * products for nucleotide sequences, dna coding sequences for peptides).
4376    *
4377    * @param sel
4378    *          the sequences to show cross-references for
4379    * @param dna
4380    *          true if from a nucleotide alignment (so showing proteins)
4381    * @param source
4382    *          the database to show cross-references for
4383    */
4384   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4385           final String source)
4386   {
4387     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4388             .start();
4389   }
4390
4391   /**
4392    * Construct and display a new frame containing the translation of this
4393    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4394    */
4395   @Override
4396   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4397   {
4398     AlignmentI al = null;
4399     try
4400     {
4401       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4402
4403       al = dna.translateCdna(codeTable);
4404     } catch (Exception ex)
4405     {
4406       jalview.bin.Cache.log.error(
4407               "Exception during translation. Please report this !", ex);
4408       final String msg = MessageManager.getString(
4409               "label.error_when_translating_sequences_submit_bug_report");
4410       final String errorTitle = MessageManager
4411               .getString("label.implementation_error")
4412               + MessageManager.getString("label.translation_failed");
4413       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4414               JvOptionPane.ERROR_MESSAGE);
4415       return;
4416     }
4417     if (al == null || al.getHeight() == 0)
4418     {
4419       final String msg = MessageManager.getString(
4420               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4421       final String errorTitle = MessageManager
4422               .getString("label.translation_failed");
4423       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4424               JvOptionPane.WARNING_MESSAGE);
4425     }
4426     else
4427     {
4428       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4429       af.setFileFormat(this.currentFileFormat);
4430       final String newTitle = MessageManager
4431               .formatMessage("label.translation_of_params", new Object[]
4432               { this.getTitle(), codeTable.getId() });
4433       af.setTitle(newTitle);
4434       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4435       {
4436         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4437         viewport.openSplitFrame(af, new Alignment(seqs));
4438       }
4439       else
4440       {
4441         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4442                 DEFAULT_HEIGHT);
4443       }
4444     }
4445   }
4446
4447   /**
4448    * Set the file format
4449    *
4450    * @param format
4451    */
4452   public void setFileFormat(FileFormatI format)
4453   {
4454     this.currentFileFormat = format;
4455   }
4456
4457   /**
4458    * Try to load a features file onto the alignment.
4459    *
4460    * @param file
4461    *          contents or path to retrieve file or a File object
4462    * @param sourceType
4463    *          access mode of file (see jalview.io.AlignFile)
4464    * @return true if features file was parsed correctly.
4465    */
4466   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4467   {
4468     // BH 2018
4469     return avc.parseFeaturesFile(file, sourceType,
4470             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4471
4472   }
4473
4474   @Override
4475   public void refreshFeatureUI(boolean enableIfNecessary)
4476   {
4477     // note - currently this is only still here rather than in the controller
4478     // because of the featureSettings hard reference that is yet to be
4479     // abstracted
4480     if (enableIfNecessary)
4481     {
4482       viewport.setShowSequenceFeatures(true);
4483       showSeqFeatures.setSelected(true);
4484     }
4485
4486   }
4487
4488   @Override
4489   public void dragEnter(DropTargetDragEvent evt)
4490   {
4491   }
4492
4493   @Override
4494   public void dragExit(DropTargetEvent evt)
4495   {
4496   }
4497
4498   @Override
4499   public void dragOver(DropTargetDragEvent evt)
4500   {
4501   }
4502
4503   @Override
4504   public void dropActionChanged(DropTargetDragEvent evt)
4505   {
4506   }
4507
4508   @Override
4509   public void drop(DropTargetDropEvent evt)
4510   {
4511     // JAL-1552 - acceptDrop required before getTransferable call for
4512     // Java's Transferable for native dnd
4513     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4514     Transferable t = evt.getTransferable();
4515
4516     final AlignFrame thisaf = this;
4517     final List<Object> files = new ArrayList<>();
4518     List<DataSourceType> protocols = new ArrayList<>();
4519
4520     try
4521     {
4522       Desktop.transferFromDropTarget(files, protocols, evt, t);
4523     } catch (Exception e)
4524     {
4525       e.printStackTrace();
4526     }
4527     if (files != null)
4528     {
4529       new Thread(new Runnable()
4530       {
4531         @Override
4532         public void run()
4533         {
4534           try
4535           {
4536             // check to see if any of these files have names matching sequences
4537             // in
4538             // the alignment
4539             SequenceIdMatcher idm = new SequenceIdMatcher(
4540                     viewport.getAlignment().getSequencesArray());
4541             /**
4542              * Object[] { String,SequenceI}
4543              */
4544             ArrayList<Object[]> filesmatched = new ArrayList<>();
4545             ArrayList<Object> filesnotmatched = new ArrayList<>();
4546             for (int i = 0; i < files.size(); i++)
4547             {
4548               // BH 2018
4549               Object file = files.get(i);
4550               String fileName = file.toString();
4551               String pdbfn = "";
4552               DataSourceType protocol = (file instanceof File
4553                       ? DataSourceType.FILE
4554                       : FormatAdapter.checkProtocol(fileName));
4555               if (protocol == DataSourceType.FILE)
4556               {
4557                 File fl;
4558                 if (file instanceof File) {
4559                   fl = (File) file;
4560                   Platform.cacheFileData(fl);
4561                 } else {
4562                   fl = new File(fileName);
4563                 }
4564                 pdbfn = fl.getName();
4565               }
4566               else if (protocol == DataSourceType.URL)
4567               {
4568                 URL url = new URL(fileName);
4569                 pdbfn = url.getFile();
4570               }
4571               if (pdbfn.length() > 0)
4572               {
4573                 // attempt to find a match in the alignment
4574                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4575                 int l = 0, c = pdbfn.indexOf(".");
4576                 while (mtch == null && c != -1)
4577                 {
4578                   do
4579                   {
4580                     l = c;
4581                   } while ((c = pdbfn.indexOf(".", l)) > l);
4582                   if (l > -1)
4583                   {
4584                     pdbfn = pdbfn.substring(0, l);
4585                   }
4586                   mtch = idm.findAllIdMatches(pdbfn);
4587                 }
4588                 if (mtch != null)
4589                 {
4590                   FileFormatI type;
4591                   try
4592                   {
4593                     type = new IdentifyFile().identify(file, protocol);
4594                   } catch (Exception ex)
4595                   {
4596                     type = null;
4597                   }
4598                   if (type != null && type.isStructureFile())
4599                   {
4600                     filesmatched.add(new Object[] { file, protocol, mtch });
4601                     continue;
4602                   }
4603                 }
4604                 // File wasn't named like one of the sequences or wasn't a PDB
4605                 // file.
4606                 filesnotmatched.add(file);
4607               }
4608             }
4609             int assocfiles = 0;
4610             if (filesmatched.size() > 0)
4611             {
4612               boolean autoAssociate = Cache
4613                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4614               if (!autoAssociate)
4615               {
4616                 String msg = MessageManager.formatMessage(
4617                         "label.automatically_associate_structure_files_with_sequences_same_name",
4618                         new Object[]
4619                         { Integer.valueOf(filesmatched.size())
4620                                 .toString() });
4621                 String ttl = MessageManager.getString(
4622                         "label.automatically_associate_structure_files_by_name");
4623                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4624                         ttl, JvOptionPane.YES_NO_OPTION);
4625                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4626               }
4627               if (autoAssociate)
4628               {
4629                 for (Object[] fm : filesmatched)
4630                 {
4631                   // try and associate
4632                   // TODO: may want to set a standard ID naming formalism for
4633                   // associating PDB files which have no IDs.
4634                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4635                   {
4636                     PDBEntry pe = new AssociatePdbFileWithSeq()
4637                             .associatePdbWithSeq(fm[0].toString(),
4638                                     (DataSourceType) fm[1], toassoc, false,
4639                                     Desktop.instance);
4640                     if (pe != null)
4641                     {
4642                       System.err.println("Associated file : "
4643                               + (fm[0].toString()) + " with "
4644                               + toassoc.getDisplayId(true));
4645                       assocfiles++;
4646                     }
4647                   }
4648                   // TODO: do we need to update overview ? only if features are
4649                   // shown I guess
4650                   alignPanel.paintAlignment(true, false);
4651                 }
4652               }
4653               else
4654               {
4655                 /*
4656                  * add declined structures as sequences
4657                  */
4658                 for (Object[] o : filesmatched)
4659                 {
4660                   filesnotmatched.add(o[0]);
4661                 }
4662               }
4663             }
4664             if (filesnotmatched.size() > 0)
4665             {
4666               if (assocfiles > 0 && (Cache.getDefault(
4667                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4668                       || JvOptionPane.showConfirmDialog(thisaf,
4669                               "<html>" + MessageManager.formatMessage(
4670                                       "label.ignore_unmatched_dropped_files_info",
4671                                       new Object[]
4672                                       { Integer.valueOf(
4673                                               filesnotmatched.size())
4674                                               .toString() })
4675                                       + "</html>",
4676                               MessageManager.getString(
4677                                       "label.ignore_unmatched_dropped_files"),
4678                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4679               {
4680                 return;
4681               }
4682               for (Object fn : filesnotmatched)
4683               {
4684                 loadJalviewDataFile(fn, null, null, null);
4685               }
4686
4687             }
4688           } catch (Exception ex)
4689           {
4690             ex.printStackTrace();
4691           }
4692         }
4693       }).start();
4694     }
4695   }
4696
4697   /**
4698    * Attempt to load a "dropped" file or URL string, by testing in turn for
4699    * <ul>
4700    * <li>an Annotation file</li>
4701    * <li>a JNet file</li>
4702    * <li>a features file</li>
4703    * <li>else try to interpret as an alignment file</li>
4704    * </ul>
4705    *
4706    * @param file
4707    *          either a filename or a URL string.
4708    */
4709   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4710           FileFormatI format, SequenceI assocSeq)
4711   {
4712     // BH 2018 was String file
4713     try
4714     {
4715       if (sourceType == null)
4716       {
4717         sourceType = FormatAdapter.checkProtocol(file);
4718       }
4719       // if the file isn't identified, or not positively identified as some
4720       // other filetype (PFAM is default unidentified alignment file type) then
4721       // try to parse as annotation.
4722       boolean isAnnotation = (format == null
4723               || FileFormat.Pfam.equals(format))
4724                       ? new AnnotationFile().annotateAlignmentView(viewport,
4725                               file, sourceType)
4726                       : false;
4727
4728       if (!isAnnotation)
4729       {
4730         // first see if its a T-COFFEE score file
4731         TCoffeeScoreFile tcf = null;
4732         try
4733         {
4734           tcf = new TCoffeeScoreFile(file, sourceType);
4735           if (tcf.isValid())
4736           {
4737             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4738             {
4739               buildColourMenu();
4740               changeColour(
4741                       new TCoffeeColourScheme(viewport.getAlignment()));
4742               isAnnotation = true;
4743               setStatus(MessageManager.getString(
4744                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4745             }
4746             else
4747             {
4748               // some problem - if no warning its probable that the ID matching
4749               // process didn't work
4750               JvOptionPane.showMessageDialog(Desktop.desktop,
4751                       tcf.getWarningMessage() == null
4752                               ? MessageManager.getString(
4753                                       "label.check_file_matches_sequence_ids_alignment")
4754                               : tcf.getWarningMessage(),
4755                       MessageManager.getString(
4756                               "label.problem_reading_tcoffee_score_file"),
4757                       JvOptionPane.WARNING_MESSAGE);
4758             }
4759           }
4760           else
4761           {
4762             tcf = null;
4763           }
4764         } catch (Exception x)
4765         {
4766           Cache.log.debug(
4767                   "Exception when processing data source as T-COFFEE score file",
4768                   x);
4769           tcf = null;
4770         }
4771         if (tcf == null)
4772         {
4773           // try to see if its a JNet 'concise' style annotation file *before*
4774           // we
4775           // try to parse it as a features file
4776           if (format == null)
4777           {
4778             format = new IdentifyFile().identify(file, sourceType);
4779           }
4780           if (FileFormat.ScoreMatrix == format)
4781           {
4782             ScoreMatrixFile sm = new ScoreMatrixFile(
4783                     new FileParse(file, sourceType));
4784             sm.parse();
4785             // todo: i18n this message
4786             setStatus(MessageManager.formatMessage(
4787                     "label.successfully_loaded_matrix",
4788                     sm.getMatrixName()));
4789           }
4790           else if (FileFormat.Jnet.equals(format))
4791           {
4792             JPredFile predictions = new JPredFile(file, sourceType);
4793             new JnetAnnotationMaker();
4794             JnetAnnotationMaker.add_annotation(predictions,
4795                     viewport.getAlignment(), 0, false);
4796             viewport.getAlignment().setupJPredAlignment();
4797             isAnnotation = true;
4798           }
4799           // else if (IdentifyFile.FeaturesFile.equals(format))
4800           else if (FileFormat.Features.equals(format))
4801           {
4802             if (parseFeaturesFile(file, sourceType))
4803             {
4804               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4805               if (splitFrame != null)
4806               {
4807                 splitFrame.repaint();
4808               }
4809               else
4810               {
4811                 alignPanel.paintAlignment(true, true);
4812               }
4813             }
4814           }
4815           else
4816           {
4817             new FileLoader().LoadFile(viewport, file, sourceType, format);
4818           }
4819         }
4820       }
4821       if (isAnnotation)
4822       {
4823         updateForAnnotations();
4824       }
4825     } catch (Exception ex)
4826     {
4827       ex.printStackTrace();
4828     } catch (OutOfMemoryError oom)
4829     {
4830       try
4831       {
4832         System.gc();
4833       } catch (Exception x)
4834       {
4835       }
4836       new OOMWarning(
4837               "loading data "
4838                       + (sourceType != null
4839                               ? (sourceType == DataSourceType.PASTE
4840                                       ? "from clipboard."
4841                                       : "using " + sourceType + " from "
4842                                               + file)
4843                               : ".")
4844                       + (format != null
4845                               ? "(parsing as '" + format + "' file)"
4846                               : ""),
4847               oom, Desktop.desktop);
4848     }
4849   }
4850
4851   /**
4852    * Do all updates necessary after an annotation file such as jnet. Also called
4853    * from Jalview.loadAppletParams for "annotations", "jnetFile"
4854    */
4855
4856   public void updateForAnnotations()
4857   {
4858     alignPanel.adjustAnnotationHeight();
4859     viewport.updateSequenceIdColours();
4860     buildSortByAnnotationScoresMenu();
4861     alignPanel.paintAlignment(true, true);
4862   }
4863
4864   /**
4865    * Change the display state for the given feature groups -- Added by BH from
4866    * JalviewLite
4867    *
4868    * @param groups
4869    *          list of group strings
4870    * @param state
4871    *          visible or invisible
4872    */
4873   public void setFeatureGroupState(String[] groups, boolean state)
4874   {
4875     jalview.api.FeatureRenderer fr = null;
4876     viewport.setShowSequenceFeatures(true);
4877     if (alignPanel != null
4878             && (fr = alignPanel.getFeatureRenderer()) != null)
4879     {
4880
4881       fr.setGroupVisibility(Arrays.asList(groups), state);
4882       alignPanel.getSeqPanel().seqCanvas.repaint();
4883       if (alignPanel.overviewPanel != null)
4884       {
4885         alignPanel.overviewPanel.updateOverviewImage();
4886       }
4887     }
4888   }
4889
4890
4891   /**
4892    * Method invoked by the ChangeListener on the tabbed pane, in other words
4893    * when a different tabbed pane is selected by the user or programmatically.
4894    */
4895   @Override
4896   public void tabSelectionChanged(int index)
4897   {
4898     if (index > -1)
4899     {
4900       alignPanel = alignPanels.get(index);
4901       viewport = alignPanel.av;
4902       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4903       setMenusFromViewport(viewport);
4904       if (featureSettings != null && featureSettings.isOpen()
4905               && featureSettings.fr.getViewport() != viewport)
4906       {
4907         if (viewport.isShowSequenceFeatures())
4908         {
4909           // refresh the featureSettings to reflect UI change
4910           showFeatureSettingsUI();
4911         }
4912         else
4913         {
4914           // close feature settings for this view.
4915           featureSettings.close();
4916         }
4917       }
4918
4919     }
4920
4921     /*
4922      * 'focus' any colour slider that is open to the selected viewport
4923      */
4924     if (viewport.getConservationSelected())
4925     {
4926       SliderPanel.setConservationSlider(alignPanel,
4927               viewport.getResidueShading(), alignPanel.getViewName());
4928     }
4929     else
4930     {
4931       SliderPanel.hideConservationSlider();
4932     }
4933     if (viewport.getAbovePIDThreshold())
4934     {
4935       SliderPanel.setPIDSliderSource(alignPanel,
4936               viewport.getResidueShading(), alignPanel.getViewName());
4937     }
4938     else
4939     {
4940       SliderPanel.hidePIDSlider();
4941     }
4942
4943     /*
4944      * If there is a frame linked to this one in a SplitPane, switch it to the
4945      * same view tab index. No infinite recursion of calls should happen, since
4946      * tabSelectionChanged() should not get invoked on setting the selected
4947      * index to an unchanged value. Guard against setting an invalid index
4948      * before the new view peer tab has been created.
4949      */
4950     final AlignViewportI peer = viewport.getCodingComplement();
4951     if (peer != null)
4952     {
4953       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4954               .getAlignPanel().alignFrame;
4955       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4956       {
4957         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4958       }
4959     }
4960   }
4961
4962   /**
4963    * On right mouse click on view tab, prompt for and set new view name.
4964    */
4965   @Override
4966   public void tabbedPane_mousePressed(MouseEvent e)
4967   {
4968     if (e.isPopupTrigger())
4969     {
4970       String msg = MessageManager.getString("label.enter_view_name");
4971       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4972       String reply = JvOptionPane.showInputDialog(msg, ttl);
4973
4974       if (reply != null)
4975       {
4976         viewport.setViewName(reply);
4977         // TODO warn if reply is in getExistingViewNames()?
4978         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4979       }
4980     }
4981   }
4982
4983   public AlignViewport getCurrentView()
4984   {
4985     return viewport;
4986   }
4987
4988   /**
4989    * Open the dialog for regex description parsing.
4990    */
4991   @Override
4992   protected void extractScores_actionPerformed(ActionEvent e)
4993   {
4994     ParseProperties pp = new jalview.analysis.ParseProperties(
4995             viewport.getAlignment());
4996     // TODO: verify regex and introduce GUI dialog for version 2.5
4997     // if (pp.getScoresFromDescription("col", "score column ",
4998     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4999     // true)>0)
5000     if (pp.getScoresFromDescription("description column",
5001             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5002     {
5003       buildSortByAnnotationScoresMenu();
5004     }
5005   }
5006
5007   /*
5008    * (non-Javadoc)
5009    *
5010    * @see
5011    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5012    * )
5013    */
5014   @Override
5015   protected void showDbRefs_actionPerformed(ActionEvent e)
5016   {
5017     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5018   }
5019
5020   /*
5021    * (non-Javadoc)
5022    *
5023    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5024    * ActionEvent)
5025    */
5026   @Override
5027   protected void showNpFeats_actionPerformed(ActionEvent e)
5028   {
5029     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5030   }
5031
5032   /**
5033    * find the viewport amongst the tabs in this alignment frame and close that
5034    * tab
5035    *
5036    * @param av
5037    */
5038   public boolean closeView(AlignViewportI av)
5039   {
5040     if (viewport == av)
5041     {
5042       this.closeMenuItem_actionPerformed(false);
5043       return true;
5044     }
5045     Component[] comp = tabbedPane.getComponents();
5046     for (int i = 0; comp != null && i < comp.length; i++)
5047     {
5048       if (comp[i] instanceof AlignmentPanel)
5049       {
5050         if (((AlignmentPanel) comp[i]).av == av)
5051         {
5052           // close the view.
5053           closeView((AlignmentPanel) comp[i]);
5054           return true;
5055         }
5056       }
5057     }
5058     return false;
5059   }
5060
5061   protected void build_fetchdbmenu(JMenu webService)
5062   {
5063     // Temporary hack - DBRef Fetcher always top level ws entry.
5064     // TODO We probably want to store a sequence database checklist in
5065     // preferences and have checkboxes.. rather than individual sources selected
5066     // here
5067     final JMenu rfetch = new JMenu(
5068             MessageManager.getString("action.fetch_db_references"));
5069     rfetch.setToolTipText(MessageManager.getString(
5070             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5071     webService.add(rfetch);
5072
5073     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5074             MessageManager.getString("option.trim_retrieved_seqs"));
5075     trimrs.setToolTipText(
5076             MessageManager.getString("label.trim_retrieved_sequences"));
5077     trimrs.setSelected(
5078             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5079     trimrs.addActionListener(new ActionListener()
5080     {
5081       @Override
5082       public void actionPerformed(ActionEvent e)
5083       {
5084         trimrs.setSelected(trimrs.isSelected());
5085         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5086                 Boolean.valueOf(trimrs.isSelected()).toString());
5087       }
5088     });
5089     rfetch.add(trimrs);
5090     JMenuItem fetchr = new JMenuItem(
5091             MessageManager.getString("label.standard_databases"));
5092     fetchr.setToolTipText(
5093             MessageManager.getString("label.fetch_embl_uniprot"));
5094     fetchr.addActionListener(new ActionListener()
5095     {
5096
5097       @Override
5098       public void actionPerformed(ActionEvent e)
5099       {
5100         new Thread(new Runnable()
5101         {
5102           @Override
5103           public void run()
5104           {
5105             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5106                     .getAlignment().isNucleotide();
5107             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5108                     alignPanel.av.getSequenceSelection(),
5109                     alignPanel.alignFrame, null,
5110                     alignPanel.alignFrame.featureSettings, isNucleotide);
5111             dbRefFetcher.addListener(new FetchFinishedListenerI()
5112             {
5113               @Override
5114               public void finished()
5115               {
5116
5117                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5118                         .getFeatureSettingsModels())
5119                 {
5120
5121                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5122                 }
5123                 AlignFrame.this.setMenusForViewport();
5124               }
5125             });
5126             dbRefFetcher.fetchDBRefs(false);
5127           }
5128         }).start();
5129
5130       }
5131
5132     });
5133     rfetch.add(fetchr);
5134     new Thread(new Runnable()
5135     {
5136       @Override
5137       public void run()
5138       {
5139         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5140                 .getSequenceFetcherSingleton();
5141         javax.swing.SwingUtilities.invokeLater(new Runnable()
5142         {
5143           @Override
5144           public void run()
5145           {
5146             String[] dbclasses = sf.getNonAlignmentSources();
5147             List<DbSourceProxy> otherdb;
5148             JMenu dfetch = new JMenu();
5149             JMenu ifetch = new JMenu();
5150             JMenuItem fetchr = null;
5151             int comp = 0, icomp = 0, mcomp = 15;
5152             String mname = null;
5153             int dbi = 0;
5154             for (String dbclass : dbclasses)
5155             {
5156               otherdb = sf.getSourceProxy(dbclass);
5157               // add a single entry for this class, or submenu allowing 'fetch
5158               // all' or pick one
5159               if (otherdb == null || otherdb.size() < 1)
5160               {
5161                 continue;
5162               }
5163               if (mname == null)
5164               {
5165                 mname = "From " + dbclass;
5166               }
5167               if (otherdb.size() == 1)
5168               {
5169                 final DbSourceProxy[] dassource = otherdb
5170                         .toArray(new DbSourceProxy[0]);
5171                 DbSourceProxy src = otherdb.get(0);
5172                 fetchr = new JMenuItem(src.getDbSource());
5173                 fetchr.addActionListener(new ActionListener()
5174                 {
5175
5176                   @Override
5177                   public void actionPerformed(ActionEvent e)
5178                   {
5179                     new Thread(new Runnable()
5180                     {
5181
5182                       @Override
5183                       public void run()
5184                       {
5185                         boolean isNucleotide = alignPanel.alignFrame
5186                                 .getViewport().getAlignment()
5187                                 .isNucleotide();
5188                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5189                                 alignPanel.av.getSequenceSelection(),
5190                                 alignPanel.alignFrame, dassource,
5191                                 alignPanel.alignFrame.featureSettings,
5192                                 isNucleotide);
5193                         dbRefFetcher
5194                                 .addListener(new FetchFinishedListenerI()
5195                                 {
5196                                   @Override
5197                                   public void finished()
5198                                   {
5199                                     FeatureSettingsModelI srcSettings = dassource[0]
5200                                             .getFeatureColourScheme();
5201                                     alignPanel.av.mergeFeaturesStyle(
5202                                             srcSettings);
5203                                     AlignFrame.this.setMenusForViewport();
5204                                   }
5205                                 });
5206                         dbRefFetcher.fetchDBRefs(false);
5207                       }
5208                     }).start();
5209                   }
5210
5211                 });
5212                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5213                         MessageManager.formatMessage(
5214                                 "label.fetch_retrieve_from", new Object[]
5215                                 { src.getDbName() })));
5216                 dfetch.add(fetchr);
5217                 comp++;
5218               }
5219               else
5220               {
5221                 final DbSourceProxy[] dassource = otherdb
5222                         .toArray(new DbSourceProxy[0]);
5223                 // fetch all entry
5224                 DbSourceProxy src = otherdb.get(0);
5225                 fetchr = new JMenuItem(MessageManager
5226                         .formatMessage("label.fetch_all_param", new Object[]
5227                         { src.getDbSource() }));
5228                 fetchr.addActionListener(new ActionListener()
5229                 {
5230                   @Override
5231                   public void actionPerformed(ActionEvent e)
5232                   {
5233                     new Thread(new Runnable()
5234                     {
5235
5236                       @Override
5237                       public void run()
5238                       {
5239                         boolean isNucleotide = alignPanel.alignFrame
5240                                 .getViewport().getAlignment()
5241                                 .isNucleotide();
5242                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5243                                 alignPanel.av.getSequenceSelection(),
5244                                 alignPanel.alignFrame, dassource,
5245                                 alignPanel.alignFrame.featureSettings,
5246                                 isNucleotide);
5247                         dbRefFetcher
5248                                 .addListener(new FetchFinishedListenerI()
5249                                 {
5250                                   @Override
5251                                   public void finished()
5252                                   {
5253                                     AlignFrame.this.setMenusForViewport();
5254                                   }
5255                                 });
5256                         dbRefFetcher.fetchDBRefs(false);
5257                       }
5258                     }).start();
5259                   }
5260                 });
5261
5262                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5263                         MessageManager.formatMessage(
5264                                 "label.fetch_retrieve_from_all_sources",
5265                                 new Object[]
5266                                 { Integer.valueOf(otherdb.size())
5267                                         .toString(),
5268                                     src.getDbSource(), src.getDbName() })));
5269                 dfetch.add(fetchr);
5270                 comp++;
5271                 // and then build the rest of the individual menus
5272                 ifetch = new JMenu(MessageManager.formatMessage(
5273                         "label.source_from_db_source", new Object[]
5274                         { src.getDbSource() }));
5275                 icomp = 0;
5276                 String imname = null;
5277                 int i = 0;
5278                 for (DbSourceProxy sproxy : otherdb)
5279                 {
5280                   String dbname = sproxy.getDbName();
5281                   String sname = dbname.length() > 5
5282                           ? dbname.substring(0, 5) + "..."
5283                           : dbname;
5284                   String msname = dbname.length() > 10
5285                           ? dbname.substring(0, 10) + "..."
5286                           : dbname;
5287                   if (imname == null)
5288                   {
5289                     imname = MessageManager
5290                             .formatMessage("label.from_msname", new Object[]
5291                             { sname });
5292                   }
5293                   fetchr = new JMenuItem(msname);
5294                   final DbSourceProxy[] dassrc = { sproxy };
5295                   fetchr.addActionListener(new ActionListener()
5296                   {
5297
5298                     @Override
5299                     public void actionPerformed(ActionEvent e)
5300                     {
5301                       new Thread(new Runnable()
5302                       {
5303
5304                         @Override
5305                         public void run()
5306                         {
5307                           boolean isNucleotide = alignPanel.alignFrame
5308                                   .getViewport().getAlignment()
5309                                   .isNucleotide();
5310                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5311                                   alignPanel.av.getSequenceSelection(),
5312                                   alignPanel.alignFrame, dassrc,
5313                                   alignPanel.alignFrame.featureSettings,
5314                                   isNucleotide);
5315                           dbRefFetcher
5316                                   .addListener(new FetchFinishedListenerI()
5317                                   {
5318                                     @Override
5319                                     public void finished()
5320                                     {
5321                                       AlignFrame.this.setMenusForViewport();
5322                                     }
5323                                   });
5324                           dbRefFetcher.fetchDBRefs(false);
5325                         }
5326                       }).start();
5327                     }
5328
5329                   });
5330                   fetchr.setToolTipText(
5331                           "<html>" + MessageManager.formatMessage(
5332                                   "label.fetch_retrieve_from", new Object[]
5333                                   { dbname }));
5334                   ifetch.add(fetchr);
5335                   ++i;
5336                   if (++icomp >= mcomp || i == (otherdb.size()))
5337                   {
5338                     ifetch.setText(MessageManager.formatMessage(
5339                             "label.source_to_target", imname, sname));
5340                     dfetch.add(ifetch);
5341                     ifetch = new JMenu();
5342                     imname = null;
5343                     icomp = 0;
5344                     comp++;
5345                   }
5346                 }
5347               }
5348               ++dbi;
5349               if (comp >= mcomp || dbi >= (dbclasses.length))
5350               {
5351                 dfetch.setText(MessageManager.formatMessage(
5352                         "label.source_to_target", mname, dbclass));
5353                 rfetch.add(dfetch);
5354                 dfetch = new JMenu();
5355                 mname = null;
5356                 comp = 0;
5357               }
5358             }
5359           }
5360         });
5361       }
5362     }).start();
5363
5364   }
5365
5366   /**
5367    * Left justify the whole alignment.
5368    */
5369   @Override
5370   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5371   {
5372     AlignmentI al = viewport.getAlignment();
5373     al.justify(false);
5374     viewport.firePropertyChange("alignment", null, al);
5375   }
5376
5377   /**
5378    * Right justify the whole alignment.
5379    */
5380   @Override
5381   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5382   {
5383     AlignmentI al = viewport.getAlignment();
5384     al.justify(true);
5385     viewport.firePropertyChange("alignment", null, al);
5386   }
5387
5388   @Override
5389   public void setShowSeqFeatures(boolean b)
5390   {
5391     showSeqFeatures.setSelected(b);
5392     viewport.setShowSequenceFeatures(b);
5393   }
5394
5395   /*
5396    * (non-Javadoc)
5397    *
5398    * @see
5399    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5400    * awt.event.ActionEvent)
5401    */
5402   @Override
5403   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5404   {
5405     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5406     alignPanel.paintAlignment(false, false);
5407   }
5408
5409   /*
5410    * (non-Javadoc)
5411    *
5412    * @see
5413    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5414    * .ActionEvent)
5415    */
5416   @Override
5417   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5418   {
5419     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5420     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5421
5422   }
5423
5424   /*
5425    * (non-Javadoc)
5426    *
5427    * @see
5428    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5429    * .event.ActionEvent)
5430    */
5431   @Override
5432   protected void showGroupConservation_actionPerformed(ActionEvent e)
5433   {
5434     viewport.setShowGroupConservation(showGroupConservation.getState());
5435     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5436   }
5437
5438   /*
5439    * (non-Javadoc)
5440    *
5441    * @see
5442    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5443    * .event.ActionEvent)
5444    */
5445   @Override
5446   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5447   {
5448     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5449     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5450   }
5451
5452   /*
5453    * (non-Javadoc)
5454    *
5455    * @see
5456    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5457    * .event.ActionEvent)
5458    */
5459   @Override
5460   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5461   {
5462     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5463     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5464   }
5465
5466   @Override
5467   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5468   {
5469     showSequenceLogo.setState(true);
5470     viewport.setShowSequenceLogo(true);
5471     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5472     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5473   }
5474
5475   @Override
5476   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5477   {
5478     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5479   }
5480
5481   /*
5482    * (non-Javadoc)
5483    *
5484    * @see
5485    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5486    * .event.ActionEvent)
5487    */
5488   @Override
5489   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5490   {
5491     if (avc.makeGroupsFromSelection())
5492     {
5493       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5494       alignPanel.updateAnnotation();
5495       alignPanel.paintAlignment(true,
5496               viewport.needToUpdateStructureViews());
5497     }
5498   }
5499
5500   public void clearAlignmentSeqRep()
5501   {
5502     // TODO refactor alignmentseqrep to controller
5503     if (viewport.getAlignment().hasSeqrep())
5504     {
5505       viewport.getAlignment().setSeqrep(null);
5506       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5507       alignPanel.updateAnnotation();
5508       alignPanel.paintAlignment(true, true);
5509     }
5510   }
5511
5512   @Override
5513   protected void createGroup_actionPerformed(ActionEvent e)
5514   {
5515     if (avc.createGroup())
5516     {
5517       if (applyAutoAnnotationSettings.isSelected())
5518       {
5519         alignPanel.updateAnnotation(true, false);
5520       }
5521       alignPanel.alignmentChanged();
5522     }
5523   }
5524
5525   @Override
5526   protected void unGroup_actionPerformed(ActionEvent e)
5527   {
5528     if (avc.unGroup())
5529     {
5530       alignPanel.alignmentChanged();
5531     }
5532   }
5533
5534   /**
5535    * make the given alignmentPanel the currently selected tab
5536    *
5537    * @param alignmentPanel
5538    */
5539   public void setDisplayedView(AlignmentPanel alignmentPanel)
5540   {
5541     if (!viewport.getSequenceSetId()
5542             .equals(alignmentPanel.av.getSequenceSetId()))
5543     {
5544       throw new Error(MessageManager.getString(
5545               "error.implementation_error_cannot_show_view_alignment_frame"));
5546     }
5547     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5548             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5549     {
5550       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5551     }
5552   }
5553
5554   /**
5555    * Action on selection of menu options to Show or Hide annotations.
5556    *
5557    * @param visible
5558    * @param forSequences
5559    *          update sequence-related annotations
5560    * @param forAlignment
5561    *          update non-sequence-related annotations
5562    */
5563   @Override
5564   protected void setAnnotationsVisibility(boolean visible,
5565           boolean forSequences, boolean forAlignment)
5566   {
5567     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5568             .getAlignmentAnnotation();
5569     if (anns == null)
5570     {
5571       return;
5572     }
5573     for (AlignmentAnnotation aa : anns)
5574     {
5575       /*
5576        * don't display non-positional annotations on an alignment
5577        */
5578       if (aa.annotations == null)
5579       {
5580         continue;
5581       }
5582       boolean apply = (aa.sequenceRef == null && forAlignment)
5583               || (aa.sequenceRef != null && forSequences);
5584       if (apply)
5585       {
5586         aa.visible = visible;
5587       }
5588     }
5589     alignPanel.validateAnnotationDimensions(true);
5590     alignPanel.alignmentChanged();
5591   }
5592
5593   /**
5594    * Store selected annotation sort order for the view and repaint.
5595    */
5596   @Override
5597   protected void sortAnnotations_actionPerformed()
5598   {
5599     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5600     this.alignPanel.av
5601             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5602     alignPanel.paintAlignment(false, false);
5603   }
5604
5605   /**
5606    *
5607    * @return alignment panels in this alignment frame
5608    */
5609   public List<? extends AlignmentViewPanel> getAlignPanels()
5610   {
5611     // alignPanels is never null
5612     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5613     return alignPanels;
5614   }
5615
5616   /**
5617    * Open a new alignment window, with the cDNA associated with this (protein)
5618    * alignment, aligned as is the protein.
5619    */
5620   protected void viewAsCdna_actionPerformed()
5621   {
5622     // TODO no longer a menu action - refactor as required
5623     final AlignmentI alignment = getViewport().getAlignment();
5624     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5625     if (mappings == null)
5626     {
5627       return;
5628     }
5629     List<SequenceI> cdnaSeqs = new ArrayList<>();
5630     for (SequenceI aaSeq : alignment.getSequences())
5631     {
5632       for (AlignedCodonFrame acf : mappings)
5633       {
5634         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5635         if (dnaSeq != null)
5636         {
5637           /*
5638            * There is a cDNA mapping for this protein sequence - add to new
5639            * alignment. It will share the same dataset sequence as other mapped
5640            * cDNA (no new mappings need to be created).
5641            */
5642           final Sequence newSeq = new Sequence(dnaSeq);
5643           newSeq.setDatasetSequence(dnaSeq);
5644           cdnaSeqs.add(newSeq);
5645         }
5646       }
5647     }
5648     if (cdnaSeqs.size() == 0)
5649     {
5650       // show a warning dialog no mapped cDNA
5651       return;
5652     }
5653     AlignmentI cdna = new Alignment(
5654             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5655     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5656             AlignFrame.DEFAULT_HEIGHT);
5657     cdna.alignAs(alignment);
5658     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5659             + this.title;
5660     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5661             AlignFrame.DEFAULT_HEIGHT);
5662   }
5663
5664   /**
5665    * Set visibility of dna/protein complement view (available when shown in a
5666    * split frame).
5667    *
5668    * @param show
5669    */
5670   @Override
5671   protected void showComplement_actionPerformed(boolean show)
5672   {
5673     SplitContainerI sf = getSplitViewContainer();
5674     if (sf != null)
5675     {
5676       sf.setComplementVisible(this, show);
5677     }
5678   }
5679
5680   /**
5681    * Generate the reverse (optionally complemented) of the selected sequences,
5682    * and add them to the alignment
5683    */
5684   @Override
5685   protected void showReverse_actionPerformed(boolean complement)
5686   {
5687     AlignmentI al = null;
5688     try
5689     {
5690       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5691       al = dna.reverseCdna(complement);
5692       viewport.addAlignment(al, "");
5693       addHistoryItem(new EditCommand(
5694               MessageManager.getString("label.add_sequences"), Action.PASTE,
5695               al.getSequencesArray(), 0, al.getWidth(),
5696               viewport.getAlignment()));
5697     } catch (Exception ex)
5698     {
5699       System.err.println(ex.getMessage());
5700       return;
5701     }
5702   }
5703
5704   /**
5705    * Try to run a script in the Groovy console, having first ensured that this
5706    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5707    * be targeted at this alignment.
5708    */
5709   @Override
5710   protected void runGroovy_actionPerformed()
5711   {
5712     Jalview.setCurrentAlignFrame(this);
5713     groovy.ui.Console console = Desktop.getGroovyConsole();
5714     if (console != null)
5715     {
5716       try
5717       {
5718         console.runScript();
5719       } catch (Exception ex)
5720       {
5721         System.err.println((ex.toString()));
5722         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5723                 MessageManager.getString("label.couldnt_run_groovy_script"),
5724                 MessageManager.getString("label.groovy_support_failed"),
5725                 JvOptionPane.ERROR_MESSAGE);
5726       }
5727     }
5728     else
5729     {
5730       System.err.println("Can't run Groovy script as console not found");
5731     }
5732   }
5733
5734   /**
5735    * Hides columns containing (or not containing) a specified feature, provided
5736    * that would not leave all columns hidden
5737    *
5738    * @param featureType
5739    * @param columnsContaining
5740    * @return
5741    */
5742   public boolean hideFeatureColumns(String featureType,
5743           boolean columnsContaining)
5744   {
5745     boolean notForHiding = avc.markColumnsContainingFeatures(
5746             columnsContaining, false, false, featureType);
5747     if (notForHiding)
5748     {
5749       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5750               false, featureType))
5751       {
5752         getViewport().hideSelectedColumns();
5753         return true;
5754       }
5755     }
5756     return false;
5757   }
5758
5759   @Override
5760   protected void selectHighlightedColumns_actionPerformed(
5761           ActionEvent actionEvent)
5762   {
5763     // include key modifier check in case user selects from menu
5764     avc.markHighlightedColumns(
5765             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5766             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5767                     | ActionEvent.CTRL_MASK)) != 0);
5768   }
5769
5770   /**
5771    * Rebuilds the Colour menu, including any user-defined colours which have
5772    * been loaded either on startup or during the session
5773    */
5774   public void buildColourMenu()
5775   {
5776     colourMenu.removeAll();
5777
5778     colourMenu.add(applyToAllGroups);
5779     colourMenu.add(textColour);
5780     colourMenu.addSeparator();
5781
5782     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5783             viewport.getAlignment(), false);
5784
5785     colourMenu.add(annotationColour);
5786     bg.add(annotationColour);
5787     colourMenu.addSeparator();
5788     colourMenu.add(conservationMenuItem);
5789     colourMenu.add(modifyConservation);
5790     colourMenu.add(abovePIDThreshold);
5791     colourMenu.add(modifyPID);
5792
5793     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5794     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5795   }
5796
5797   /**
5798    * Open a dialog (if not already open) that allows the user to select and
5799    * calculate PCA or Tree analysis
5800    */
5801   protected void openTreePcaDialog()
5802   {
5803     if (alignPanel.getCalculationDialog() == null)
5804     {
5805       new CalculationChooser(AlignFrame.this);
5806     }
5807   }
5808
5809   @Override
5810   protected void loadVcf_actionPerformed()
5811   {
5812     JalviewFileChooser chooser = new JalviewFileChooser(
5813             Cache.getProperty("LAST_DIRECTORY"));
5814     chooser.setFileView(new JalviewFileView());
5815     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5816     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5817     final AlignFrame us = this;
5818     chooser.setResponseHandler(0, new Runnable()
5819     {
5820       @Override
5821       public void run()
5822       {
5823         String choice = chooser.getSelectedFile().getPath();
5824         Cache.setProperty("LAST_DIRECTORY", choice);
5825         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5826         new VCFLoader(choice).loadVCF(seqs, us);
5827       }
5828     });
5829     chooser.showOpenDialog(null);
5830
5831   }
5832
5833   private Rectangle lastFeatureSettingsBounds = null;
5834   @Override
5835   public void setFeatureSettingsGeometry(Rectangle bounds)
5836   {
5837     lastFeatureSettingsBounds = bounds;
5838   }
5839
5840   @Override
5841   public Rectangle getFeatureSettingsGeometry()
5842   {
5843     return lastFeatureSettingsBounds;
5844   }
5845 }
5846
5847 class PrintThread extends Thread
5848 {
5849   AlignmentPanel ap;
5850
5851   public PrintThread(AlignmentPanel ap)
5852   {
5853     this.ap = ap;
5854   }
5855
5856   static PageFormat pf;
5857
5858   @Override
5859   public void run()
5860   {
5861     PrinterJob printJob = PrinterJob.getPrinterJob();
5862
5863     if (pf != null)
5864     {
5865       printJob.setPrintable(ap, pf);
5866     }
5867     else
5868     {
5869       printJob.setPrintable(ap);
5870     }
5871
5872     if (printJob.printDialog())
5873     {
5874       try
5875       {
5876         printJob.print();
5877       } catch (Exception PrintException)
5878       {
5879         PrintException.printStackTrace();
5880       }
5881     }
5882   }
5883 }