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.util.Locale;
  24
  25 import java.awt.BorderLayout;
  26 import java.awt.Color;
  27 import java.awt.Component;
  28 import java.awt.Rectangle;
  29 import java.awt.Toolkit;
  30 import java.awt.datatransfer.Clipboard;
  31 import java.awt.datatransfer.DataFlavor;
  32 import java.awt.datatransfer.StringSelection;
  33 import java.awt.datatransfer.Transferable;
  34 import java.awt.dnd.DnDConstants;
  35 import java.awt.dnd.DropTargetDragEvent;
  36 import java.awt.dnd.DropTargetDropEvent;
  37 import java.awt.dnd.DropTargetEvent;
  38 import java.awt.dnd.DropTargetListener;
  39 import java.awt.event.ActionEvent;
  40 import java.awt.event.ActionListener;
  41 import java.awt.event.FocusAdapter;
  42 import java.awt.event.FocusEvent;
  43 import java.awt.event.ItemEvent;
  44 import java.awt.event.ItemListener;
  45 import java.awt.event.KeyAdapter;
  46 import java.awt.event.KeyEvent;
  47 import java.awt.event.MouseEvent;
  48 import java.awt.print.PageFormat;
  49 import java.awt.print.PrinterJob;
  50 import java.beans.PropertyChangeEvent;
  51 import java.io.File;
  52 import java.io.FileWriter;
  53 import java.io.IOException;
  54 import java.io.PrintWriter;
  55 import java.net.URL;
  56 import java.util.ArrayList;
  57 import java.util.Arrays;
  58 import java.util.Deque;
  59 import java.util.Enumeration;
  60 import java.util.Hashtable;
  61 import java.util.List;
  62 import java.util.Vector;
  63
  64 import javax.swing.ButtonGroup;
  65 import javax.swing.JCheckBoxMenuItem;
  66 import javax.swing.JComponent;
  67 import javax.swing.JEditorPane;
  68 import javax.swing.JInternalFrame;
  69 import javax.swing.JLabel;
  70 import javax.swing.JLayeredPane;
  71 import javax.swing.JMenu;
  72 import javax.swing.JMenuItem;
  73 import javax.swing.JPanel;
  74 import javax.swing.JScrollPane;
  75 import javax.swing.SwingUtilities;
  76
  77 import ext.vamsas.ServiceHandle;
  78 import jalview.analysis.AlignmentSorter;
  79 import jalview.analysis.AlignmentUtils;
  80 import jalview.analysis.CrossRef;
  81 import jalview.analysis.Dna;
  82 import jalview.analysis.GeneticCodeI;
  83 import jalview.analysis.ParseProperties;
  84 import jalview.analysis.SequenceIdMatcher;
  85 import jalview.api.AlignExportSettingsI;
  86 import jalview.api.AlignViewControllerGuiI;
  87 import jalview.api.AlignViewControllerI;
  88 import jalview.api.AlignViewportI;
  89 import jalview.api.AlignmentViewPanel;
  90 import jalview.api.FeatureSettingsControllerI;
  91 import jalview.api.FeatureSettingsModelI;
  92 import jalview.api.SplitContainerI;
  93 import jalview.api.ViewStyleI;
  94 import jalview.api.analysis.SimilarityParamsI;
  95 import jalview.bin.Cache;
  96 import jalview.bin.Console;
  97 import jalview.bin.Jalview;
  98 import jalview.commands.CommandI;
  99 import jalview.commands.EditCommand;
 100 import jalview.commands.EditCommand.Action;
 101 import jalview.commands.OrderCommand;
 102 import jalview.commands.RemoveGapColCommand;
 103 import jalview.commands.RemoveGapsCommand;
 104 import jalview.commands.SlideSequencesCommand;
 105 import jalview.commands.TrimRegionCommand;
 106 import jalview.datamodel.AlignExportSettingsAdapter;
 107 import jalview.datamodel.AlignedCodonFrame;
 108 import jalview.datamodel.Alignment;
 109 import jalview.datamodel.AlignmentAnnotation;
 110 import jalview.datamodel.AlignmentExportData;
 111 import jalview.datamodel.AlignmentI;
 112 import jalview.datamodel.AlignmentOrder;
 113 import jalview.datamodel.AlignmentView;
 114 import jalview.datamodel.ColumnSelection;
 115 import jalview.datamodel.HiddenColumns;
 116 import jalview.datamodel.PDBEntry;
 117 import jalview.datamodel.SeqCigar;
 118 import jalview.datamodel.Sequence;
 119 import jalview.datamodel.SequenceGroup;
 120 import jalview.datamodel.SequenceI;
 121 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 122 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 123 import jalview.io.AlignmentProperties;
 124 import jalview.io.AnnotationFile;
 125 import jalview.io.BackupFiles;
 126 import jalview.io.BioJsHTMLOutput;
 127 import jalview.io.DataSourceType;
 128 import jalview.io.FileFormat;
 129 import jalview.io.FileFormatI;
 130 import jalview.io.FileFormats;
 131 import jalview.io.FileLoader;
 132 import jalview.io.FileParse;
 133 import jalview.io.FormatAdapter;
 134 import jalview.io.HtmlSvgOutput;
 135 import jalview.io.IdentifyFile;
 136 import jalview.io.JPredFile;
 137 import jalview.io.JalviewFileChooser;
 138 import jalview.io.JalviewFileView;
 139 import jalview.io.JnetAnnotationMaker;
 140 import jalview.io.NewickFile;
 141 import jalview.io.ScoreMatrixFile;
 142 import jalview.io.TCoffeeScoreFile;
 143 import jalview.io.vcf.VCFLoader;
 144 import jalview.jbgui.GAlignFrame;
 145 import jalview.project.Jalview2XML;
 146 import jalview.schemes.ColourSchemeI;
 147 import jalview.schemes.ColourSchemes;
 148 import jalview.schemes.ResidueColourScheme;
 149 import jalview.schemes.TCoffeeColourScheme;
 150 import jalview.util.HttpUtils;
 151 import jalview.util.ImageMaker.TYPE;
 152 import jalview.util.MessageManager;
 153 import jalview.util.Platform;
 154 import jalview.viewmodel.AlignmentViewport;
 155 import jalview.viewmodel.ViewportRanges;
 156 import jalview.ws.DBRefFetcher;
 157 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 158 import jalview.ws.jws1.Discoverer;
 159 import jalview.ws.jws2.Jws2Discoverer;
 160 import jalview.ws.jws2.jabaws2.Jws2Instance;
 161 import jalview.ws.seqfetcher.DbSourceProxy;
 162
 163 /**
 164  * DOCUMENT ME!
 165  *
 166  * @author $author$
 167  * @version $Revision$
 168  */
 169 @SuppressWarnings("serial")
 170 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 171         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 172 {
 173
 174   public static final int DEFAULT_WIDTH = 700;
 175
 176   public static final int DEFAULT_HEIGHT = 500;
 177
 178   /*
 179    * The currently displayed panel (selected tabbed view if more than one)
 180    */
 181   public AlignmentPanel alignPanel;
 182
 183   AlignViewport viewport;
 184
 185   public AlignViewControllerI avc;
 186
 187   List<AlignmentPanel> alignPanels = new ArrayList<>();
 188
 189   /**
 190    * Last format used to load or save alignments in this window
 191    */
 192   FileFormatI currentFileFormat = null;
 193
 194   /**
 195    * Current filename for this alignment
 196    */
 197   String fileName = null;
 198
 199   File fileObject;
 200
 201   /**
 202    * Creates a new AlignFrame object with specific width and height.
 203    *
 204    * @param al
 205    * @param width
 206    * @param height
 207    */
 208   public AlignFrame(AlignmentI al, int width, int height)
 209   {
 210     this(al, null, width, height);
 211   }
 212
 213   /**
 214    * Creates a new AlignFrame object with specific width, height and
 215    * sequenceSetId
 216    *
 217    * @param al
 218    * @param width
 219    * @param height
 220    * @param sequenceSetId
 221    */
 222   public AlignFrame(AlignmentI al, int width, int height,
 223           String sequenceSetId)
 224   {
 225     this(al, null, width, height, sequenceSetId);
 226   }
 227
 228   /**
 229    * Creates a new AlignFrame object with specific width, height and
 230    * sequenceSetId
 231    *
 232    * @param al
 233    * @param width
 234    * @param height
 235    * @param sequenceSetId
 236    * @param viewId
 237    */
 238   public AlignFrame(AlignmentI al, int width, int height,
 239           String sequenceSetId, String viewId)
 240   {
 241     this(al, null, width, height, sequenceSetId, viewId);
 242   }
 243
 244   /**
 245    * new alignment window with hidden columns
 246    *
 247    * @param al
 248    *          AlignmentI
 249    * @param hiddenColumns
 250    *          ColumnSelection or null
 251    * @param width
 252    *          Width of alignment frame
 253    * @param height
 254    *          height of frame.
 255    */
 256   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 257           int height)
 258   {
 259     this(al, hiddenColumns, width, height, null);
 260   }
 261
 262   /**
 263    * Create alignment frame for al with hiddenColumns, a specific width and
 264    * height, and specific sequenceId
 265    *
 266    * @param al
 267    * @param hiddenColumns
 268    * @param width
 269    * @param height
 270    * @param sequenceSetId
 271    *          (may be null)
 272    */
 273   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 274           int height, String sequenceSetId)
 275   {
 276     this(al, hiddenColumns, width, height, sequenceSetId, null);
 277   }
 278
 279   /**
 280    * Create alignment frame for al with hiddenColumns, a specific width and
 281    * height, and specific sequenceId
 282    *
 283    * @param al
 284    * @param hiddenColumns
 285    * @param width
 286    * @param height
 287    * @param sequenceSetId
 288    *          (may be null)
 289    * @param viewId
 290    *          (may be null)
 291    */
 292   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 293           int height, String sequenceSetId, String viewId)
 294   {
 295     setSize(width, height);
 296
 297     if (al.getDataset() == null)
 298     {
 299       al.setDataset(null);
 300     }
 301
 302     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 303
 304     alignPanel = new AlignmentPanel(this, viewport);
 305
 306     addAlignmentPanel(alignPanel, true);
 307     init();
 308   }
 309
 310   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 311           HiddenColumns hiddenColumns, int width, int height)
 312   {
 313     setSize(width, height);
 314
 315     if (al.getDataset() == null)
 316     {
 317       al.setDataset(null);
 318     }
 319
 320     viewport = new AlignViewport(al, hiddenColumns);
 321
 322     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 323     {
 324       viewport.hideSequence(hiddenSeqs);
 325     }
 326     alignPanel = new AlignmentPanel(this, viewport);
 327     addAlignmentPanel(alignPanel, true);
 328     init();
 329   }
 330
 331   /**
 332    * Make a new AlignFrame from existing alignmentPanels
 333    *
 334    * @param ap
 335    *          AlignmentPanel
 336    * @param av
 337    *          AlignViewport
 338    */
 339   public AlignFrame(AlignmentPanel ap)
 340   {
 341     viewport = ap.av;
 342     alignPanel = ap;
 343     addAlignmentPanel(ap, false);
 344     init();
 345   }
 346
 347   /**
 348    * initalise the alignframe from the underlying viewport data and the
 349    * configurations
 350    */
 351   void init()
 352   {
 353     // setBackground(Color.white); // BH 2019
 354
 355     if (!Jalview.isHeadlessMode())
 356     {
 357       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 358     }
 359
 360     avc = new jalview.controller.AlignViewController(this, viewport,
 361             alignPanel);
 362     if (viewport.getAlignmentConservationAnnotation() == null)
 363     {
 364       // BLOSUM62Colour.setEnabled(false);
 365       conservationMenuItem.setEnabled(false);
 366       modifyConservation.setEnabled(false);
 367       // PIDColour.setEnabled(false);
 368       // abovePIDThreshold.setEnabled(false);
 369       // modifyPID.setEnabled(false);
 370     }
 371
 372     String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 373
 374     if (sortby.equals("Id"))
 375     {
 376       sortIDMenuItem_actionPerformed(null);
 377     }
 378     else if (sortby.equals("Pairwise Identity"))
 379     {
 380       sortPairwiseMenuItem_actionPerformed(null);
 381     }
 382
 383     this.alignPanel.av
 384             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 385
 386     setMenusFromViewport(viewport);
 387     buildSortByAnnotationScoresMenu();
 388     calculateTree.addActionListener(new ActionListener()
 389     {
 390
 391       @Override
 392       public void actionPerformed(ActionEvent e)
 393       {
 394         openTreePcaDialog();
 395       }
 396     });
 397     buildColourMenu();
 398
 399     if (Desktop.desktop != null)
 400     {
 401       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 402       if (!Platform.isJS())
 403       {
 404         addServiceListeners();
 405       }
 406       setGUINucleotide();
 407     }
 408
 409     if (viewport.getWrapAlignment())
 410     {
 411       wrapMenuItem_actionPerformed(null);
 412     }
 413
 414     if (Cache.getDefault("SHOW_OVERVIEW", false))
 415     {
 416       this.overviewMenuItem_actionPerformed(null);
 417     }
 418
 419     addKeyListener();
 420
 421     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 422     final List<AlignmentPanel> origview = new ArrayList<>();
 423     final String menuLabel = MessageManager
 424             .getString("label.copy_format_from");
 425     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 426             new ViewSetProvider()
 427             {
 428
 429               @Override
 430               public AlignmentPanel[] getAllAlignmentPanels()
 431               {
 432                 origview.clear();
 433                 origview.add(alignPanel);
 434                 // make an array of all alignment panels except for this one
 435                 List<AlignmentPanel> aps = new ArrayList<>(
 436                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 437                 aps.remove(AlignFrame.this.alignPanel);
 438                 return aps.toArray(new AlignmentPanel[aps.size()]);
 439               }
 440             }, selviews, new ItemListener()
 441             {
 442
 443               @Override
 444               public void itemStateChanged(ItemEvent e)
 445               {
 446                 if (origview.size() > 0)
 447                 {
 448                   final AlignmentPanel ap = origview.get(0);
 449
 450                   /*
 451                    * Copy the ViewStyle of the selected panel to 'this one'.
 452                    * Don't change value of 'scaleProteinAsCdna' unless copying
 453                    * from a SplitFrame.
 454                    */
 455                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 456                           .getViewStyle();
 457                   boolean fromSplitFrame = selviews.get(0)
 458                           .getAlignViewport().getCodingComplement() != null;
 459                   if (!fromSplitFrame)
 460                   {
 461                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 462                             .getViewStyle().isScaleProteinAsCdna());
 463                   }
 464                   ap.getAlignViewport().setViewStyle(vs);
 465
 466                   /*
 467                    * Also rescale ViewStyle of SplitFrame complement if there is
 468                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 469                    * the whole ViewStyle (allow cDNA protein to have different
 470                    * fonts)
 471                    */
 472                   AlignViewportI complement = ap.getAlignViewport()
 473                           .getCodingComplement();
 474                   if (complement != null && vs.isScaleProteinAsCdna())
 475                   {
 476                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 477                     ((SplitFrame) af.getSplitViewContainer())
 478                             .adjustLayout();
 479                     af.setMenusForViewport();
 480                   }
 481
 482                   ap.updateLayout();
 483                   ap.setSelected(true);
 484                   ap.alignFrame.setMenusForViewport();
 485
 486                 }
 487               }
 488             });
 489     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
 490             .indexOf("devel") > -1
 491             || Cache.getDefault("VERSION", "DEVELOPMENT")
 492                     .toLowerCase(Locale.ROOT).indexOf("test") > -1)
 493     {
 494       formatMenu.add(vsel);
 495     }
 496     addFocusListener(new FocusAdapter()
 497     {
 498       @Override
 499       public void focusGained(FocusEvent e)
 500       {
 501         Jalview.setCurrentAlignFrame(AlignFrame.this);
 502       }
 503     });
 504
 505   }
 506
 507   /**
 508    * Change the filename and format for the alignment, and enable the 'reload'
 509    * button functionality.
 510    *
 511    * @param file
 512    *          valid filename
 513    * @param format
 514    *          format of file
 515    */
 516   public void setFileName(String file, FileFormatI format)
 517   {
 518     fileName = file;
 519     setFileFormat(format);
 520     reload.setEnabled(true);
 521   }
 522
 523   /**
 524    * JavaScript will have this, maybe others. More dependable than a file name
 525    * and maintains a reference to the actual bytes loaded.
 526    *
 527    * @param file
 528    */
 529   public void setFileObject(File file)
 530   {
 531     this.fileObject = file;
 532   }
 533
 534   /**
 535    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 536    * events
 537    */
 538   void addKeyListener()
 539   {
 540     addKeyListener(new KeyAdapter()
 541     {
 542       @Override
 543       public void keyPressed(KeyEvent evt)
 544       {
 545         if (viewport.cursorMode
 546                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 547                         && evt.getKeyCode() <= KeyEvent.VK_9)
 548                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 549                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 550                 && Character.isDigit(evt.getKeyChar()))
 551         {
 552           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 553         }
 554
 555         switch (evt.getKeyCode())
 556         {
 557
 558         case 27: // escape key
 559           deselectAllSequenceMenuItem_actionPerformed(null);
 560
 561           break;
 562
 563         case KeyEvent.VK_DOWN:
 564           if (evt.isAltDown() || !viewport.cursorMode)
 565           {
 566             moveSelectedSequences(false);
 567           }
 568           if (viewport.cursorMode)
 569           {
 570             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 571           }
 572           break;
 573
 574         case KeyEvent.VK_UP:
 575           if (evt.isAltDown() || !viewport.cursorMode)
 576           {
 577             moveSelectedSequences(true);
 578           }
 579           if (viewport.cursorMode)
 580           {
 581             alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
 582           }
 583
 584           break;
 585
 586         case KeyEvent.VK_LEFT:
 587           if (evt.isAltDown() || !viewport.cursorMode)
 588           {
 589             slideSequences(false,
 590                     alignPanel.getSeqPanel().getKeyboardNo1());
 591           }
 592           else
 593           {
 594             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 595           }
 596
 597           break;
 598
 599         case KeyEvent.VK_RIGHT:
 600           if (evt.isAltDown() || !viewport.cursorMode)
 601           {
 602             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 603           }
 604           else
 605           {
 606             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 607           }
 608           break;
 609
 610         case KeyEvent.VK_SPACE:
 611           if (viewport.cursorMode)
 612           {
 613             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 614                     || evt.isShiftDown() || evt.isAltDown());
 615           }
 616           break;
 617
 618         // case KeyEvent.VK_A:
 619         // if (viewport.cursorMode)
 620         // {
 621         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 622         // //System.out.println("A");
 623         // }
 624         // break;
 625         /*
 626          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 627          * System.out.println("closing bracket"); } break;
 628          */
 629         case KeyEvent.VK_DELETE:
 630         case KeyEvent.VK_BACK_SPACE:
 631           if (!viewport.cursorMode)
 632           {
 633             cut_actionPerformed();
 634           }
 635           else
 636           {
 637             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 638                     || evt.isShiftDown() || evt.isAltDown());
 639           }
 640
 641           break;
 642
 643         case KeyEvent.VK_S:
 644           if (viewport.cursorMode)
 645           {
 646             alignPanel.getSeqPanel().setCursorRow();
 647           }
 648           break;
 649         case KeyEvent.VK_C:
 650           if (viewport.cursorMode && !evt.isControlDown())
 651           {
 652             alignPanel.getSeqPanel().setCursorColumn();
 653           }
 654           break;
 655         case KeyEvent.VK_P:
 656           if (viewport.cursorMode)
 657           {
 658             alignPanel.getSeqPanel().setCursorPosition();
 659           }
 660           break;
 661
 662         case KeyEvent.VK_ENTER:
 663         case KeyEvent.VK_COMMA:
 664           if (viewport.cursorMode)
 665           {
 666             alignPanel.getSeqPanel().setCursorRowAndColumn();
 667           }
 668           break;
 669
 670         case KeyEvent.VK_Q:
 671           if (viewport.cursorMode)
 672           {
 673             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 674           }
 675           break;
 676         case KeyEvent.VK_M:
 677           if (viewport.cursorMode)
 678           {
 679             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 680           }
 681           break;
 682
 683         case KeyEvent.VK_F2:
 684           viewport.cursorMode = !viewport.cursorMode;
 685           setStatus(MessageManager
 686                   .formatMessage("label.keyboard_editing_mode", new String[]
 687                   { (viewport.cursorMode ? "on" : "off") }));
 688           if (viewport.cursorMode)
 689           {
 690             ViewportRanges ranges = viewport.getRanges();
 691             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 692                     .getStartRes();
 693             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 694                     .getStartSeq();
 695           }
 696           alignPanel.getSeqPanel().seqCanvas.repaint();
 697           break;
 698
 699         case KeyEvent.VK_F1:
 700           try
 701           {
 702             Help.showHelpWindow();
 703           } catch (Exception ex)
 704           {
 705             ex.printStackTrace();
 706           }
 707           break;
 708         case KeyEvent.VK_H:
 709         {
 710           boolean toggleSeqs = !evt.isControlDown();
 711           boolean toggleCols = !evt.isShiftDown();
 712           toggleHiddenRegions(toggleSeqs, toggleCols);
 713           break;
 714         }
 715         case KeyEvent.VK_B:
 716         {
 717           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 718           boolean modifyExisting = true; // always modify, don't clear
 719                                          // evt.isShiftDown();
 720           boolean invertHighlighted = evt.isAltDown();
 721           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 722                   toggleSel);
 723           break;
 724         }
 725         case KeyEvent.VK_PAGE_UP:
 726           viewport.getRanges().pageUp();
 727           break;
 728         case KeyEvent.VK_PAGE_DOWN:
 729           viewport.getRanges().pageDown();
 730           break;
 731         }
 732       }
 733
 734       @Override
 735       public void keyReleased(KeyEvent evt)
 736       {
 737         switch (evt.getKeyCode())
 738         {
 739         case KeyEvent.VK_LEFT:
 740           if (evt.isAltDown() || !viewport.cursorMode)
 741           {
 742             viewport.firePropertyChange("alignment", null,
 743                     viewport.getAlignment().getSequences());
 744           }
 745           break;
 746
 747         case KeyEvent.VK_RIGHT:
 748           if (evt.isAltDown() || !viewport.cursorMode)
 749           {
 750             viewport.firePropertyChange("alignment", null,
 751                     viewport.getAlignment().getSequences());
 752           }
 753           break;
 754         }
 755       }
 756     });
 757   }
 758
 759   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 760   {
 761     ap.alignFrame = this;
 762     avc = new jalview.controller.AlignViewController(this, viewport,
 763             alignPanel);
 764
 765     alignPanels.add(ap);
 766
 767     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 768
 769     int aSize = alignPanels.size();
 770
 771     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 772
 773     if (aSize == 1 && ap.av.getViewName() == null)
 774     {
 775       this.getContentPane().add(ap, BorderLayout.CENTER);
 776     }
 777     else
 778     {
 779       if (aSize == 2)
 780       {
 781         setInitialTabVisible();
 782       }
 783
 784       expandViews.setEnabled(true);
 785       gatherViews.setEnabled(true);
 786       tabbedPane.addTab(ap.av.getViewName(), ap);
 787
 788       ap.setVisible(false);
 789     }
 790
 791     if (newPanel)
 792     {
 793       if (ap.av.isPadGaps())
 794       {
 795         ap.av.getAlignment().padGaps();
 796       }
 797       ap.av.updateConservation(ap);
 798       ap.av.updateConsensus(ap);
 799       ap.av.updateStrucConsensus(ap);
 800     }
 801   }
 802
 803   public void setInitialTabVisible()
 804   {
 805     expandViews.setEnabled(true);
 806     gatherViews.setEnabled(true);
 807     tabbedPane.setVisible(true);
 808     AlignmentPanel first = alignPanels.get(0);
 809     tabbedPane.addTab(first.av.getViewName(), first);
 810     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 811   }
 812
 813   public AlignViewport getViewport()
 814   {
 815     return viewport;
 816   }
 817
 818   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 819   private void addServiceListeners()
 820   {
 821     final java.beans.PropertyChangeListener thisListener;
 822     Desktop.instance.addJalviewPropertyChangeListener("services",
 823             thisListener = new java.beans.PropertyChangeListener()
 824             {
 825               @Override
 826               public void propertyChange(PropertyChangeEvent evt)
 827               {
 828                 // // System.out.println("Discoverer property change.");
 829                 // if (evt.getPropertyName().equals("services"))
 830                 {
 831                   SwingUtilities.invokeLater(new Runnable()
 832                   {
 833
 834                     @Override
 835                     public void run()
 836                     {
 837                       System.err.println(
 838                               "Rebuild WS Menu for service change");
 839                       BuildWebServiceMenu();
 840                     }
 841
 842                   });
 843                 }
 844               }
 845             });
 846     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 847     {
 848       @Override
 849       public void internalFrameClosed(
 850               javax.swing.event.InternalFrameEvent evt)
 851       {
 852         // System.out.println("deregistering discoverer listener");
 853         Desktop.instance.removeJalviewPropertyChangeListener("services",
 854                 thisListener);
 855         closeMenuItem_actionPerformed(true);
 856       }
 857     });
 858     // Finally, build the menu once to get current service state
 859     new Thread(new Runnable()
 860     {
 861       @Override
 862       public void run()
 863       {
 864         BuildWebServiceMenu();
 865       }
 866     }).start();
 867   }
 868
 869   /**
 870    * Configure menu items that vary according to whether the alignment is
 871    * nucleotide or protein
 872    */
 873   public void setGUINucleotide()
 874   {
 875     AlignmentI al = getViewport().getAlignment();
 876     boolean nucleotide = al.isNucleotide();
 877
 878     loadVcf.setVisible(nucleotide);
 879     showTranslation.setVisible(nucleotide);
 880     showReverse.setVisible(nucleotide);
 881     showReverseComplement.setVisible(nucleotide);
 882     conservationMenuItem.setEnabled(!nucleotide);
 883     modifyConservation
 884             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 885     showGroupConservation.setEnabled(!nucleotide);
 886
 887     showComplementMenuItem
 888             .setText(nucleotide ? MessageManager.getString("label.protein")
 889                     : MessageManager.getString("label.nucleotide"));
 890   }
 891
 892   /**
 893    * set up menus for the current viewport. This may be called after any
 894    * operation that affects the data in the current view (selection changed,
 895    * etc) to update the menus to reflect the new state.
 896    */
 897   @Override
 898   public void setMenusForViewport()
 899   {
 900     setMenusFromViewport(viewport);
 901   }
 902
 903   /**
 904    * Need to call this method when tabs are selected for multiple views, or when
 905    * loading from Jalview2XML.java
 906    *
 907    * @param av
 908    *          AlignViewport
 909    */
 910   public void setMenusFromViewport(AlignViewport av)
 911   {
 912     padGapsMenuitem.setSelected(av.isPadGaps());
 913     colourTextMenuItem.setSelected(av.isShowColourText());
 914     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 915     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 916     conservationMenuItem.setSelected(av.getConservationSelected());
 917     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 918     seqLimits.setSelected(av.getShowJVSuffix());
 919     idRightAlign.setSelected(av.isRightAlignIds());
 920     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 921     renderGapsMenuItem.setSelected(av.isRenderGaps());
 922     wrapMenuItem.setSelected(av.getWrapAlignment());
 923     scaleAbove.setVisible(av.getWrapAlignment());
 924     scaleLeft.setVisible(av.getWrapAlignment());
 925     scaleRight.setVisible(av.getWrapAlignment());
 926     annotationPanelMenuItem.setState(av.isShowAnnotation());
 927     /*
 928      * Show/hide annotations only enabled if annotation panel is shown
 929      */
 930     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 931     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 932     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 933     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 934     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 935     viewTextMenuItem.setSelected(av.getShowText());
 936     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 937     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 938     showGroupConservation.setSelected(av.isShowGroupConservation());
 939     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 940     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 941     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 942
 943     ColourMenuHelper.setColourSelected(colourMenu,
 944             av.getGlobalColourScheme());
 945
 946     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 947     hiddenMarkers.setState(av.getShowHiddenMarkers());
 948     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 949     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 950     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 951     autoCalculate.setSelected(av.autoCalculateConsensus);
 952     sortByTree.setSelected(av.sortByTree);
 953     listenToViewSelections.setSelected(av.followSelection);
 954
 955     showProducts.setEnabled(canShowProducts());
 956     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 957
 958     updateEditMenuBar();
 959   }
 960
 961   /**
 962    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 963    *
 964    * @param b
 965    */
 966   public void setGroovyEnabled(boolean b)
 967   {
 968     runGroovy.setEnabled(b);
 969   }
 970
 971   private IProgressIndicator progressBar;
 972
 973   /*
 974    * (non-Javadoc)
 975    *
 976    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 977    */
 978   @Override
 979   public void setProgressBar(String message, long id)
 980   {
 981     progressBar.setProgressBar(message, id);
 982   }
 983
 984   @Override
 985   public void registerHandler(final long id,
 986           final IProgressIndicatorHandler handler)
 987   {
 988     progressBar.registerHandler(id, handler);
 989   }
 990
 991   /**
 992    *
 993    * @return true if any progress bars are still active
 994    */
 995   @Override
 996   public boolean operationInProgress()
 997   {
 998     return progressBar.operationInProgress();
 999   }
1000
1001   /**
1002    * Sets the text of the status bar. Note that setting a null or empty value
1003    * will cause the status bar to be hidden, with possibly undesirable flicker
1004    * of the screen layout.
1005    */
1006   @Override
1007   public void setStatus(String text)
1008   {
1009     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1010   }
1011
1012   /*
1013    * Added so Castor Mapping file can obtain Jalview Version
1014    */
1015   public String getVersion()
1016   {
1017     return Cache.getProperty("VERSION");
1018   }
1019
1020   public FeatureRenderer getFeatureRenderer()
1021   {
1022     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1023   }
1024
1025   @Override
1026   public void fetchSequence_actionPerformed()
1027   {
1028     new SequenceFetcher(this);
1029   }
1030
1031   @Override
1032   public void addFromFile_actionPerformed(ActionEvent e)
1033   {
1034     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1035   }
1036
1037   @Override
1038   public void reload_actionPerformed(ActionEvent e)
1039   {
1040     if (fileName != null)
1041     {
1042       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1043       // originating file's format
1044       // TODO: work out how to recover feature settings for correct view(s) when
1045       // file is reloaded.
1046       if (FileFormat.Jalview.equals(currentFileFormat))
1047       {
1048         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1049         for (int i = 0; i < frames.length; i++)
1050         {
1051           if (frames[i] instanceof AlignFrame && frames[i] != this
1052                   && ((AlignFrame) frames[i]).fileName != null
1053                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1054           {
1055             try
1056             {
1057               frames[i].setSelected(true);
1058               Desktop.instance.closeAssociatedWindows();
1059             } catch (java.beans.PropertyVetoException ex)
1060             {
1061             }
1062           }
1063
1064         }
1065         Desktop.instance.closeAssociatedWindows();
1066
1067         FileLoader loader = new FileLoader();
1068         DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1069                 ? DataSourceType.URL
1070                 : DataSourceType.FILE;
1071         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1072       }
1073       else
1074       {
1075         Rectangle bounds = this.getBounds();
1076
1077         FileLoader loader = new FileLoader();
1078
1079         AlignFrame newframe = null;
1080
1081         if (fileObject == null)
1082         {
1083
1084           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1085                   fileName) ? DataSourceType.URL : DataSourceType.FILE;
1086           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1087                   currentFileFormat);
1088         }
1089         else
1090         {
1091           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1092                   DataSourceType.FILE, currentFileFormat);
1093         }
1094
1095         newframe.setBounds(bounds);
1096         if (featureSettings != null && featureSettings.isShowing())
1097         {
1098           final Rectangle fspos = featureSettings.frame.getBounds();
1099           // TODO: need a 'show feature settings' function that takes bounds -
1100           // need to refactor Desktop.addFrame
1101           newframe.featureSettings_actionPerformed(null);
1102           final FeatureSettings nfs = newframe.featureSettings;
1103           SwingUtilities.invokeLater(new Runnable()
1104           {
1105             @Override
1106             public void run()
1107             {
1108               nfs.frame.setBounds(fspos);
1109             }
1110           });
1111           this.featureSettings.close();
1112           this.featureSettings = null;
1113         }
1114         this.closeMenuItem_actionPerformed(true);
1115       }
1116     }
1117   }
1118
1119   @Override
1120   public void addFromText_actionPerformed(ActionEvent e)
1121   {
1122     Desktop.instance
1123             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1124   }
1125
1126   @Override
1127   public void addFromURL_actionPerformed(ActionEvent e)
1128   {
1129     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1130   }
1131
1132   @Override
1133   public void save_actionPerformed(ActionEvent e)
1134   {
1135     if (fileName == null || (currentFileFormat == null)
1136             || HttpUtils.startsWithHttpOrHttps(fileName))
1137     {
1138       saveAs_actionPerformed();
1139     }
1140     else
1141     {
1142       saveAlignment(fileName, currentFileFormat);
1143     }
1144   }
1145
1146   /**
1147    * Saves the alignment to a file with a name chosen by the user, if necessary
1148    * warning if a file would be overwritten
1149    */
1150   @Override
1151   public void saveAs_actionPerformed()
1152   {
1153     String format = currentFileFormat == null ? null
1154             : currentFileFormat.getName();
1155     JalviewFileChooser chooser = JalviewFileChooser
1156             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1157
1158     chooser.setFileView(new JalviewFileView());
1159     chooser.setDialogTitle(
1160             MessageManager.getString("label.save_alignment_to_file"));
1161     chooser.setToolTipText(MessageManager.getString("action.save"));
1162
1163     int value = chooser.showSaveDialog(this);
1164
1165     if (value != JalviewFileChooser.APPROVE_OPTION)
1166     {
1167       return;
1168     }
1169     currentFileFormat = chooser.getSelectedFormat();
1170     // todo is this (2005) test now obsolete - value is never null?
1171     while (currentFileFormat == null)
1172     {
1173       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1174               MessageManager
1175                       .getString("label.select_file_format_before_saving"),
1176               MessageManager.getString("label.file_format_not_specified"),
1177               JvOptionPane.WARNING_MESSAGE);
1178       currentFileFormat = chooser.getSelectedFormat();
1179       value = chooser.showSaveDialog(this);
1180       if (value != JalviewFileChooser.APPROVE_OPTION)
1181       {
1182         return;
1183       }
1184     }
1185
1186     fileName = chooser.getSelectedFile().getPath();
1187
1188     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1189     Cache.setProperty("LAST_DIRECTORY", fileName);
1190     saveAlignment(fileName, currentFileFormat);
1191   }
1192
1193   boolean lastSaveSuccessful = false;
1194
1195   FileFormatI lastFormatSaved;
1196
1197   String lastFilenameSaved;
1198
1199   /**
1200    * Raise a dialog or status message for the last call to saveAlignment.
1201    *
1202    * @return true if last call to saveAlignment(file, format) was successful.
1203    */
1204   public boolean isSaveAlignmentSuccessful()
1205   {
1206
1207     if (!lastSaveSuccessful)
1208     {
1209       if (!Platform.isHeadless())
1210       {
1211         JvOptionPane.showInternalMessageDialog(this, MessageManager
1212                 .formatMessage("label.couldnt_save_file", new Object[]
1213                 { lastFilenameSaved }),
1214                 MessageManager.getString("label.error_saving_file"),
1215                 JvOptionPane.WARNING_MESSAGE);
1216       }
1217       else
1218       {
1219         Console.error(MessageManager
1220                 .formatMessage("label.couldnt_save_file", new Object[]
1221                 { lastFilenameSaved }));
1222       }
1223     }
1224     else
1225     {
1226
1227       setStatus(MessageManager.formatMessage(
1228               "label.successfully_saved_to_file_in_format", new Object[]
1229               { lastFilenameSaved, lastFormatSaved }));
1230
1231     }
1232     return lastSaveSuccessful;
1233   }
1234
1235   /**
1236    * Saves the alignment to the specified file path, in the specified format,
1237    * which may be an alignment format, or Jalview project format. If the
1238    * alignment has hidden regions, or the format is one capable of including
1239    * non-sequence data (features, annotations, groups), then the user may be
1240    * prompted to specify what to include in the output.
1241    *
1242    * @param file
1243    * @param format
1244    */
1245   public void saveAlignment(String file, FileFormatI format)
1246   {
1247     lastSaveSuccessful = true;
1248     lastFilenameSaved = file;
1249     lastFormatSaved = format;
1250
1251     if (FileFormat.Jalview.equals(format))
1252     {
1253       String shortName = title;
1254       if (shortName.indexOf(File.separatorChar) > -1)
1255       {
1256         shortName = shortName
1257                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1258       }
1259       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1260               shortName);
1261
1262       statusBar.setText(MessageManager.formatMessage(
1263               "label.successfully_saved_to_file_in_format", new Object[]
1264               { file, format }));
1265
1266       return;
1267     }
1268
1269     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1270     Runnable cancelAction = new Runnable()
1271     {
1272       @Override
1273       public void run()
1274       {
1275         lastSaveSuccessful = false;
1276       }
1277     };
1278     Runnable outputAction = new Runnable()
1279     {
1280       @Override
1281       public void run()
1282       {
1283         // todo defer this to inside formatSequences (or later)
1284         AlignmentExportData exportData = viewport
1285                 .getAlignExportData(options);
1286         String output = new FormatAdapter(alignPanel, options)
1287                 .formatSequences(format, exportData.getAlignment(),
1288                         exportData.getOmitHidden(),
1289                         exportData.getStartEndPostions(),
1290                         viewport.getAlignment().getHiddenColumns());
1291         if (output == null)
1292         {
1293           lastSaveSuccessful = false;
1294         }
1295         else
1296         {
1297           // create backupfiles object and get new temp filename destination
1298           boolean doBackup = BackupFiles.getEnabled();
1299           BackupFiles backupfiles = null;
1300           if (doBackup)
1301           {
1302             Console.trace(
1303                     "ALIGNFRAME making backupfiles object for " + file);
1304             backupfiles = new BackupFiles(file);
1305           }
1306           try
1307           {
1308             String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1309                     : file;
1310             Console.trace("ALIGNFRAME setting PrintWriter");
1311             PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1312
1313             if (backupfiles != null)
1314             {
1315               Console.trace("ALIGNFRAME about to write to temp file "
1316                       + backupfiles.getTempFilePath());
1317             }
1318
1319             out.print(output);
1320             Console.trace("ALIGNFRAME about to close file");
1321             out.close();
1322             Console.trace("ALIGNFRAME closed file");
1323             AlignFrame.this.setTitle(file);
1324             statusBar.setText(MessageManager.formatMessage(
1325                     "label.successfully_saved_to_file_in_format",
1326                     new Object[]
1327                     { fileName, format.getName() }));
1328             lastSaveSuccessful = true;
1329           } catch (IOException e)
1330           {
1331             lastSaveSuccessful = false;
1332             Console.error(
1333                     "ALIGNFRAME Something happened writing the temp file");
1334             Console.error(e.getMessage());
1335             Console.debug(Cache.getStackTraceString(e));
1336           } catch (Exception ex)
1337           {
1338             lastSaveSuccessful = false;
1339             Console.error(
1340                     "ALIGNFRAME Something unexpected happened writing the temp file");
1341             Console.error(ex.getMessage());
1342             Console.debug(Cache.getStackTraceString(ex));
1343           }
1344
1345           if (doBackup)
1346           {
1347             backupfiles.setWriteSuccess(lastSaveSuccessful);
1348             Console.debug("ALIGNFRAME writing temp file was "
1349                     + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1350             // do the backup file roll and rename the temp file to actual file
1351             Console.trace(
1352                     "ALIGNFRAME about to rollBackupsAndRenameTempFile");
1353             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1354             Console.debug(
1355                     "ALIGNFRAME performed rollBackupsAndRenameTempFile "
1356                             + (lastSaveSuccessful ? "" : "un")
1357                             + "successfully");
1358           }
1359         }
1360       }
1361     };
1362
1363     /*
1364      * show dialog with export options if applicable; else just do it
1365      */
1366     if (AlignExportOptions.isNeeded(viewport, format))
1367     {
1368       AlignExportOptions choices = new AlignExportOptions(
1369               alignPanel.getAlignViewport(), format, options);
1370       choices.setResponseAction(0, outputAction);
1371       choices.setResponseAction(1, cancelAction);
1372       choices.showDialog();
1373     }
1374     else
1375     {
1376       outputAction.run();
1377     }
1378   }
1379
1380   /**
1381    * Outputs the alignment to textbox in the requested format, if necessary
1382    * first prompting the user for whether to include hidden regions or
1383    * non-sequence data
1384    *
1385    * @param fileFormatName
1386    */
1387   @Override
1388   protected void outputText_actionPerformed(String fileFormatName)
1389   {
1390     FileFormatI fileFormat = FileFormats.getInstance()
1391             .forName(fileFormatName);
1392     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1393     Runnable outputAction = new Runnable()
1394     {
1395       @Override
1396       public void run()
1397       {
1398         // todo defer this to inside formatSequences (or later)
1399         AlignmentExportData exportData = viewport
1400                 .getAlignExportData(options);
1401         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1402         cap.setForInput(null);
1403         try
1404         {
1405           FileFormatI format = fileFormat;
1406           cap.setText(new FormatAdapter(alignPanel, options)
1407                   .formatSequences(format, exportData.getAlignment(),
1408                           exportData.getOmitHidden(),
1409                           exportData.getStartEndPostions(),
1410                           viewport.getAlignment().getHiddenColumns()));
1411           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1412                   "label.alignment_output_command", new Object[]
1413                   { fileFormat.getName() }), 600, 500);
1414         } catch (OutOfMemoryError oom)
1415         {
1416           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1417                   oom);
1418           cap.dispose();
1419         }
1420       }
1421     };
1422
1423     /*
1424      * show dialog with export options if applicable; else just do it
1425      */
1426     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1427     {
1428       AlignExportOptions choices = new AlignExportOptions(
1429               alignPanel.getAlignViewport(), fileFormat, options);
1430       choices.setResponseAction(0, outputAction);
1431       choices.showDialog();
1432     }
1433     else
1434     {
1435       outputAction.run();
1436     }
1437   }
1438
1439   /**
1440    * DOCUMENT ME!
1441    *
1442    * @param e
1443    *          DOCUMENT ME!
1444    */
1445   @Override
1446   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1447   {
1448     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1449     htmlSVG.exportHTML(null);
1450   }
1451
1452   @Override
1453   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1454   {
1455     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1456     bjs.exportHTML(null);
1457   }
1458
1459   public void createImageMap(File file, String image)
1460   {
1461     alignPanel.makePNGImageMap(file, image);
1462   }
1463
1464   /**
1465    * Creates a PNG image of the alignment and writes it to the given file. If
1466    * the file is null, the user is prompted to choose a file.
1467    *
1468    * @param f
1469    */
1470   @Override
1471   public void createPNG(File f)
1472   {
1473     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1474   }
1475
1476   /**
1477    * Creates an EPS image of the alignment and writes it to the given file. If
1478    * the file is null, the user is prompted to choose a file.
1479    *
1480    * @param f
1481    */
1482   @Override
1483   public void createEPS(File f)
1484   {
1485     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1486   }
1487
1488   /**
1489    * Creates an SVG image of the alignment and writes it to the given file. If
1490    * the file is null, the user is prompted to choose a file.
1491    *
1492    * @param f
1493    */
1494   @Override
1495   public void createSVG(File f)
1496   {
1497     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1498   }
1499
1500   @Override
1501   public void pageSetup_actionPerformed(ActionEvent e)
1502   {
1503     PrinterJob printJob = PrinterJob.getPrinterJob();
1504     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1505   }
1506
1507   /**
1508    * DOCUMENT ME!
1509    *
1510    * @param e
1511    *          DOCUMENT ME!
1512    */
1513   @Override
1514   public void printMenuItem_actionPerformed(ActionEvent e)
1515   {
1516     // Putting in a thread avoids Swing painting problems
1517     PrintThread thread = new PrintThread(alignPanel);
1518     thread.start();
1519   }
1520
1521   @Override
1522   public void exportFeatures_actionPerformed(ActionEvent e)
1523   {
1524     new AnnotationExporter(alignPanel).exportFeatures();
1525   }
1526
1527   @Override
1528   public void exportAnnotations_actionPerformed(ActionEvent e)
1529   {
1530     new AnnotationExporter(alignPanel).exportAnnotations();
1531   }
1532
1533   @Override
1534   public void associatedData_actionPerformed(ActionEvent e)
1535   {
1536     final JalviewFileChooser chooser = new JalviewFileChooser(
1537             Cache.getProperty("LAST_DIRECTORY"));
1538     chooser.setFileView(new JalviewFileView());
1539     String tooltip = MessageManager
1540             .getString("label.load_jalview_annotations");
1541     chooser.setDialogTitle(tooltip);
1542     chooser.setToolTipText(tooltip);
1543     chooser.setResponseHandler(0, new Runnable()
1544     {
1545       @Override
1546       public void run()
1547       {
1548         String choice = chooser.getSelectedFile().getPath();
1549         Cache.setProperty("LAST_DIRECTORY", choice);
1550         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1551       }
1552     });
1553
1554     chooser.showOpenDialog(this);
1555   }
1556
1557   /**
1558    * Close the current view or all views in the alignment frame. If the frame
1559    * only contains one view then the alignment will be removed from memory.
1560    *
1561    * @param closeAllTabs
1562    */
1563   @Override
1564   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1565   {
1566     if (alignPanels != null && alignPanels.size() < 2)
1567     {
1568       closeAllTabs = true;
1569     }
1570
1571     try
1572     {
1573       if (alignPanels != null)
1574       {
1575         if (closeAllTabs)
1576         {
1577           if (this.isClosed())
1578           {
1579             // really close all the windows - otherwise wait till
1580             // setClosed(true) is called
1581             for (int i = 0; i < alignPanels.size(); i++)
1582             {
1583               AlignmentPanel ap = alignPanels.get(i);
1584               ap.closePanel();
1585             }
1586           }
1587         }
1588         else
1589         {
1590           closeView(alignPanel);
1591         }
1592       }
1593       if (closeAllTabs)
1594       {
1595         if (featureSettings != null && featureSettings.isOpen())
1596         {
1597           featureSettings.close();
1598           featureSettings = null;
1599         }
1600         /*
1601          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1602          * be called recursively, with the frame now in 'closed' state
1603          */
1604         this.setClosed(true);
1605       }
1606     } catch (Exception ex)
1607     {
1608       ex.printStackTrace();
1609     }
1610   }
1611
1612   /**
1613    * Close the specified panel and close up tabs appropriately.
1614    *
1615    * @param panelToClose
1616    */
1617   public void closeView(AlignmentPanel panelToClose)
1618   {
1619     int index = tabbedPane.getSelectedIndex();
1620     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1621     alignPanels.remove(panelToClose);
1622     panelToClose.closePanel();
1623     panelToClose = null;
1624
1625     tabbedPane.removeTabAt(closedindex);
1626     tabbedPane.validate();
1627
1628     if (index > closedindex || index == tabbedPane.getTabCount())
1629     {
1630       // modify currently selected tab index if necessary.
1631       index--;
1632     }
1633
1634     this.tabSelectionChanged(index);
1635   }
1636
1637   /**
1638    * DOCUMENT ME!
1639    */
1640   void updateEditMenuBar()
1641   {
1642
1643     if (viewport.getHistoryList().size() > 0)
1644     {
1645       undoMenuItem.setEnabled(true);
1646       CommandI command = viewport.getHistoryList().peek();
1647       undoMenuItem.setText(MessageManager
1648               .formatMessage("label.undo_command", new Object[]
1649               { command.getDescription() }));
1650     }
1651     else
1652     {
1653       undoMenuItem.setEnabled(false);
1654       undoMenuItem.setText(MessageManager.getString("action.undo"));
1655     }
1656
1657     if (viewport.getRedoList().size() > 0)
1658     {
1659       redoMenuItem.setEnabled(true);
1660
1661       CommandI command = viewport.getRedoList().peek();
1662       redoMenuItem.setText(MessageManager
1663               .formatMessage("label.redo_command", new Object[]
1664               { command.getDescription() }));
1665     }
1666     else
1667     {
1668       redoMenuItem.setEnabled(false);
1669       redoMenuItem.setText(MessageManager.getString("action.redo"));
1670     }
1671   }
1672
1673   @Override
1674   public void addHistoryItem(CommandI command)
1675   {
1676     if (command.getSize() > 0)
1677     {
1678       viewport.addToHistoryList(command);
1679       viewport.clearRedoList();
1680       updateEditMenuBar();
1681       viewport.updateHiddenColumns();
1682       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1683       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1684       // viewport.getColumnSelection()
1685       // .getHiddenColumns().size() > 0);
1686     }
1687   }
1688
1689   /**
1690    *
1691    * @return alignment objects for all views
1692    */
1693   AlignmentI[] getViewAlignments()
1694   {
1695     if (alignPanels != null)
1696     {
1697       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1698       int i = 0;
1699       for (AlignmentPanel ap : alignPanels)
1700       {
1701         als[i++] = ap.av.getAlignment();
1702       }
1703       return als;
1704     }
1705     if (viewport != null)
1706     {
1707       return new AlignmentI[] { viewport.getAlignment() };
1708     }
1709     return null;
1710   }
1711
1712   /**
1713    * DOCUMENT ME!
1714    *
1715    * @param e
1716    *          DOCUMENT ME!
1717    */
1718   @Override
1719   protected void undoMenuItem_actionPerformed(ActionEvent e)
1720   {
1721     if (viewport.getHistoryList().isEmpty())
1722     {
1723       return;
1724     }
1725     CommandI command = viewport.getHistoryList().pop();
1726     viewport.addToRedoList(command);
1727     command.undoCommand(getViewAlignments());
1728
1729     AlignmentViewport originalSource = getOriginatingSource(command);
1730     updateEditMenuBar();
1731
1732     if (originalSource != null)
1733     {
1734       if (originalSource != viewport)
1735       {
1736         Console.warn(
1737                 "Implementation worry: mismatch of viewport origin for undo");
1738       }
1739       originalSource.updateHiddenColumns();
1740       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1741       // null
1742       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1743       // viewport.getColumnSelection()
1744       // .getHiddenColumns().size() > 0);
1745       originalSource.firePropertyChange("alignment", null,
1746               originalSource.getAlignment().getSequences());
1747     }
1748   }
1749
1750   /**
1751    * DOCUMENT ME!
1752    *
1753    * @param e
1754    *          DOCUMENT ME!
1755    */
1756   @Override
1757   protected void redoMenuItem_actionPerformed(ActionEvent e)
1758   {
1759     if (viewport.getRedoList().size() < 1)
1760     {
1761       return;
1762     }
1763
1764     CommandI command = viewport.getRedoList().pop();
1765     viewport.addToHistoryList(command);
1766     command.doCommand(getViewAlignments());
1767
1768     AlignmentViewport originalSource = getOriginatingSource(command);
1769     updateEditMenuBar();
1770
1771     if (originalSource != null)
1772     {
1773
1774       if (originalSource != viewport)
1775       {
1776         Console.warn(
1777                 "Implementation worry: mismatch of viewport origin for redo");
1778       }
1779       originalSource.updateHiddenColumns();
1780       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1781       // null
1782       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1783       // viewport.getColumnSelection()
1784       // .getHiddenColumns().size() > 0);
1785       originalSource.firePropertyChange("alignment", null,
1786               originalSource.getAlignment().getSequences());
1787     }
1788   }
1789
1790   AlignmentViewport getOriginatingSource(CommandI command)
1791   {
1792     AlignmentViewport originalSource = null;
1793     // For sequence removal and addition, we need to fire
1794     // the property change event FROM the viewport where the
1795     // original alignment was altered
1796     AlignmentI al = null;
1797     if (command instanceof EditCommand)
1798     {
1799       EditCommand editCommand = (EditCommand) command;
1800       al = editCommand.getAlignment();
1801       List<Component> comps = PaintRefresher.components
1802               .get(viewport.getSequenceSetId());
1803
1804       for (Component comp : comps)
1805       {
1806         if (comp instanceof AlignmentPanel)
1807         {
1808           if (al == ((AlignmentPanel) comp).av.getAlignment())
1809           {
1810             originalSource = ((AlignmentPanel) comp).av;
1811             break;
1812           }
1813         }
1814       }
1815     }
1816
1817     if (originalSource == null)
1818     {
1819       // The original view is closed, we must validate
1820       // the current view against the closed view first
1821       if (al != null)
1822       {
1823         PaintRefresher.validateSequences(al, viewport.getAlignment());
1824       }
1825
1826       originalSource = viewport;
1827     }
1828
1829     return originalSource;
1830   }
1831
1832   /**
1833    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1834    * or the sequence under cursor in keyboard mode
1835    *
1836    * @param up
1837    *          or down (if !up)
1838    */
1839   public void moveSelectedSequences(boolean up)
1840   {
1841     SequenceGroup sg = viewport.getSelectionGroup();
1842
1843     if (sg == null)
1844     {
1845       if (viewport.cursorMode)
1846       {
1847         sg = new SequenceGroup();
1848         sg.addSequence(viewport.getAlignment().getSequenceAt(
1849                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1850       }
1851       else
1852       {
1853         return;
1854       }
1855     }
1856
1857     if (sg.getSize() < 1)
1858     {
1859       return;
1860     }
1861
1862     // TODO: JAL-3733 - add an event to the undo buffer for this !
1863
1864     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1865             viewport.getHiddenRepSequences(), up);
1866     alignPanel.paintAlignment(true, false);
1867   }
1868
1869   synchronized void slideSequences(boolean right, int size)
1870   {
1871     List<SequenceI> sg = new ArrayList<>();
1872     if (viewport.cursorMode)
1873     {
1874       sg.add(viewport.getAlignment()
1875               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1876     }
1877     else if (viewport.getSelectionGroup() != null
1878             && viewport.getSelectionGroup().getSize() != viewport
1879                     .getAlignment().getHeight())
1880     {
1881       sg = viewport.getSelectionGroup()
1882               .getSequences(viewport.getHiddenRepSequences());
1883     }
1884
1885     if (sg.size() < 1)
1886     {
1887       return;
1888     }
1889
1890     List<SequenceI> invertGroup = new ArrayList<>();
1891
1892     for (SequenceI seq : viewport.getAlignment().getSequences())
1893     {
1894       if (!sg.contains(seq))
1895       {
1896         invertGroup.add(seq);
1897       }
1898     }
1899
1900     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1901
1902     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1903     for (int i = 0; i < invertGroup.size(); i++)
1904     {
1905       seqs2[i] = invertGroup.get(i);
1906     }
1907
1908     SlideSequencesCommand ssc;
1909     if (right)
1910     {
1911       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1912               viewport.getGapCharacter());
1913     }
1914     else
1915     {
1916       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1917               viewport.getGapCharacter());
1918     }
1919
1920     int groupAdjustment = 0;
1921     if (ssc.getGapsInsertedBegin() && right)
1922     {
1923       if (viewport.cursorMode)
1924       {
1925         alignPanel.getSeqPanel().moveCursor(size, 0);
1926       }
1927       else
1928       {
1929         groupAdjustment = size;
1930       }
1931     }
1932     else if (!ssc.getGapsInsertedBegin() && !right)
1933     {
1934       if (viewport.cursorMode)
1935       {
1936         alignPanel.getSeqPanel().moveCursor(-size, 0);
1937       }
1938       else
1939       {
1940         groupAdjustment = -size;
1941       }
1942     }
1943
1944     if (groupAdjustment != 0)
1945     {
1946       viewport.getSelectionGroup().setStartRes(
1947               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1948       viewport.getSelectionGroup().setEndRes(
1949               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1950     }
1951
1952     /*
1953      * just extend the last slide command if compatible; but not if in
1954      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1955      */
1956     boolean appendHistoryItem = false;
1957     Deque<CommandI> historyList = viewport.getHistoryList();
1958     boolean inSplitFrame = getSplitViewContainer() != null;
1959     if (!inSplitFrame && historyList != null && historyList.size() > 0
1960             && historyList.peek() instanceof SlideSequencesCommand)
1961     {
1962       appendHistoryItem = ssc.appendSlideCommand(
1963               (SlideSequencesCommand) historyList.peek());
1964     }
1965
1966     if (!appendHistoryItem)
1967     {
1968       addHistoryItem(ssc);
1969     }
1970
1971     repaint();
1972   }
1973
1974   /**
1975    * DOCUMENT ME!
1976    *
1977    * @param e
1978    *          DOCUMENT ME!
1979    */
1980   @Override
1981   protected void copy_actionPerformed()
1982   {
1983     if (viewport.getSelectionGroup() == null)
1984     {
1985       return;
1986     }
1987     // TODO: preserve the ordering of displayed alignment annotation in any
1988     // internal paste (particularly sequence associated annotation)
1989     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1990     String[] omitHidden = null;
1991
1992     if (viewport.hasHiddenColumns())
1993     {
1994       omitHidden = viewport.getViewAsString(true);
1995     }
1996
1997     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1998             seqs, omitHidden, null);
1999
2000     StringSelection ss = new StringSelection(output);
2001
2002     try
2003     {
2004       jalview.gui.Desktop.internalCopy = true;
2005       // Its really worth setting the clipboard contents
2006       // to empty before setting the large StringSelection!!
2007       Toolkit.getDefaultToolkit().getSystemClipboard()
2008               .setContents(new StringSelection(""), null);
2009
2010       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2011               Desktop.instance);
2012     } catch (OutOfMemoryError er)
2013     {
2014       new OOMWarning("copying region", er);
2015       return;
2016     }
2017
2018     HiddenColumns hiddenColumns = null;
2019     if (viewport.hasHiddenColumns())
2020     {
2021       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2022       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2023
2024       // create new HiddenColumns object with copy of hidden regions
2025       // between startRes and endRes, offset by startRes
2026       hiddenColumns = new HiddenColumns(
2027               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2028               hiddenCutoff, hiddenOffset);
2029     }
2030
2031     Desktop.jalviewClipboard = new Object[] { seqs,
2032         viewport.getAlignment().getDataset(), hiddenColumns };
2033     setStatus(MessageManager.formatMessage(
2034             "label.copied_sequences_to_clipboard", new Object[]
2035             { Integer.valueOf(seqs.length).toString() }));
2036   }
2037
2038   /**
2039    * DOCUMENT ME!
2040    *
2041    * @param e
2042    *          DOCUMENT ME!
2043    */
2044   @Override
2045   protected void pasteNew_actionPerformed(ActionEvent e)
2046   {
2047     paste(true);
2048   }
2049
2050   /**
2051    * DOCUMENT ME!
2052    *
2053    * @param e
2054    *          DOCUMENT ME!
2055    */
2056   @Override
2057   protected void pasteThis_actionPerformed(ActionEvent e)
2058   {
2059     paste(false);
2060   }
2061
2062   /**
2063    * Paste contents of Jalview clipboard
2064    *
2065    * @param newAlignment
2066    *          true to paste to a new alignment, otherwise add to this.
2067    */
2068   void paste(boolean newAlignment)
2069   {
2070     boolean externalPaste = true;
2071     try
2072     {
2073       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2074       Transferable contents = c.getContents(this);
2075
2076       if (contents == null)
2077       {
2078         return;
2079       }
2080
2081       String str;
2082       FileFormatI format;
2083       try
2084       {
2085         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2086         if (str.length() < 1)
2087         {
2088           return;
2089         }
2090
2091         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2092
2093       } catch (OutOfMemoryError er)
2094       {
2095         new OOMWarning("Out of memory pasting sequences!!", er);
2096         return;
2097       }
2098
2099       SequenceI[] sequences;
2100       boolean annotationAdded = false;
2101       AlignmentI alignment = null;
2102
2103       if (Desktop.jalviewClipboard != null)
2104       {
2105         // The clipboard was filled from within Jalview, we must use the
2106         // sequences
2107         // And dataset from the copied alignment
2108         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2109         // be doubly sure that we create *new* sequence objects.
2110         sequences = new SequenceI[newseq.length];
2111         for (int i = 0; i < newseq.length; i++)
2112         {
2113           sequences[i] = new Sequence(newseq[i]);
2114         }
2115         alignment = new Alignment(sequences);
2116         externalPaste = false;
2117       }
2118       else
2119       {
2120         // parse the clipboard as an alignment.
2121         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2122                 format);
2123         sequences = alignment.getSequencesArray();
2124       }
2125
2126       int alwidth = 0;
2127       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2128       int fgroup = -1;
2129
2130       if (newAlignment)
2131       {
2132
2133         if (Desktop.jalviewClipboard != null)
2134         {
2135           // dataset is inherited
2136           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2137         }
2138         else
2139         {
2140           // new dataset is constructed
2141           alignment.setDataset(null);
2142         }
2143         alwidth = alignment.getWidth() + 1;
2144       }
2145       else
2146       {
2147         AlignmentI pastedal = alignment; // preserve pasted alignment object
2148         // Add pasted sequences and dataset into existing alignment.
2149         alignment = viewport.getAlignment();
2150         alwidth = alignment.getWidth() + 1;
2151         // decide if we need to import sequences from an existing dataset
2152         boolean importDs = Desktop.jalviewClipboard != null
2153                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2154         // importDs==true instructs us to copy over new dataset sequences from
2155         // an existing alignment
2156         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2157                                                                       // create
2158         // minimum dataset set
2159
2160         for (int i = 0; i < sequences.length; i++)
2161         {
2162           if (importDs)
2163           {
2164             newDs.addElement(null);
2165           }
2166           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2167           // paste
2168           if (importDs && ds != null)
2169           {
2170             if (!newDs.contains(ds))
2171             {
2172               newDs.setElementAt(ds, i);
2173               ds = new Sequence(ds);
2174               // update with new dataset sequence
2175               sequences[i].setDatasetSequence(ds);
2176             }
2177             else
2178             {
2179               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2180             }
2181           }
2182           else
2183           {
2184             // copy and derive new dataset sequence
2185             sequences[i] = sequences[i].deriveSequence();
2186             alignment.getDataset()
2187                     .addSequence(sequences[i].getDatasetSequence());
2188             // TODO: avoid creation of duplicate dataset sequences with a
2189             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2190           }
2191           alignment.addSequence(sequences[i]); // merges dataset
2192         }
2193         if (newDs != null)
2194         {
2195           newDs.clear(); // tidy up
2196         }
2197         if (alignment.getAlignmentAnnotation() != null)
2198         {
2199           for (AlignmentAnnotation alan : alignment
2200                   .getAlignmentAnnotation())
2201           {
2202             if (alan.graphGroup > fgroup)
2203             {
2204               fgroup = alan.graphGroup;
2205             }
2206           }
2207         }
2208         if (pastedal.getAlignmentAnnotation() != null)
2209         {
2210           // Add any annotation attached to alignment.
2211           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2212           for (int i = 0; i < alann.length; i++)
2213           {
2214             annotationAdded = true;
2215             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2216             {
2217               AlignmentAnnotation newann = new AlignmentAnnotation(
2218                       alann[i]);
2219               if (newann.graphGroup > -1)
2220               {
2221                 if (newGraphGroups.size() <= newann.graphGroup
2222                         || newGraphGroups.get(newann.graphGroup) == null)
2223                 {
2224                   for (int q = newGraphGroups
2225                           .size(); q <= newann.graphGroup; q++)
2226                   {
2227                     newGraphGroups.add(q, null);
2228                   }
2229                   newGraphGroups.set(newann.graphGroup,
2230                           Integer.valueOf(++fgroup));
2231                 }
2232                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2233                         .intValue();
2234               }
2235
2236               newann.padAnnotation(alwidth);
2237               alignment.addAnnotation(newann);
2238             }
2239           }
2240         }
2241       }
2242       if (!newAlignment)
2243       {
2244         // /////
2245         // ADD HISTORY ITEM
2246         //
2247         addHistoryItem(new EditCommand(
2248                 MessageManager.getString("label.add_sequences"),
2249                 Action.PASTE, sequences, 0, alignment.getWidth(),
2250                 alignment));
2251       }
2252       // Add any annotations attached to sequences
2253       for (int i = 0; i < sequences.length; i++)
2254       {
2255         if (sequences[i].getAnnotation() != null)
2256         {
2257           AlignmentAnnotation newann;
2258           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2259           {
2260             annotationAdded = true;
2261             newann = sequences[i].getAnnotation()[a];
2262             newann.adjustForAlignment();
2263             newann.padAnnotation(alwidth);
2264             if (newann.graphGroup > -1)
2265             {
2266               if (newann.graphGroup > -1)
2267               {
2268                 if (newGraphGroups.size() <= newann.graphGroup
2269                         || newGraphGroups.get(newann.graphGroup) == null)
2270                 {
2271                   for (int q = newGraphGroups
2272                           .size(); q <= newann.graphGroup; q++)
2273                   {
2274                     newGraphGroups.add(q, null);
2275                   }
2276                   newGraphGroups.set(newann.graphGroup,
2277                           Integer.valueOf(++fgroup));
2278                 }
2279                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2280                         .intValue();
2281               }
2282             }
2283             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2284             // was
2285             // duplicated
2286             // earlier
2287             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2288                     a);
2289           }
2290         }
2291       }
2292       if (!newAlignment)
2293       {
2294
2295         // propagate alignment changed.
2296         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2297         if (annotationAdded)
2298         {
2299           // Duplicate sequence annotation in all views.
2300           AlignmentI[] alview = this.getViewAlignments();
2301           for (int i = 0; i < sequences.length; i++)
2302           {
2303             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2304             if (sann == null)
2305             {
2306               continue;
2307             }
2308             for (int avnum = 0; avnum < alview.length; avnum++)
2309             {
2310               if (alview[avnum] != alignment)
2311               {
2312                 // duplicate in a view other than the one with input focus
2313                 int avwidth = alview[avnum].getWidth() + 1;
2314                 // this relies on sann being preserved after we
2315                 // modify the sequence's annotation array for each duplication
2316                 for (int a = 0; a < sann.length; a++)
2317                 {
2318                   AlignmentAnnotation newann = new AlignmentAnnotation(
2319                           sann[a]);
2320                   sequences[i].addAlignmentAnnotation(newann);
2321                   newann.padAnnotation(avwidth);
2322                   alview[avnum].addAnnotation(newann); // annotation was
2323                   // duplicated earlier
2324                   // TODO JAL-1145 graphGroups are not updated for sequence
2325                   // annotation added to several views. This may cause
2326                   // strangeness
2327                   alview[avnum].setAnnotationIndex(newann, a);
2328                 }
2329               }
2330             }
2331           }
2332           buildSortByAnnotationScoresMenu();
2333         }
2334         viewport.firePropertyChange("alignment", null,
2335                 alignment.getSequences());
2336         if (alignPanels != null)
2337         {
2338           for (AlignmentPanel ap : alignPanels)
2339           {
2340             ap.validateAnnotationDimensions(false);
2341           }
2342         }
2343         else
2344         {
2345           alignPanel.validateAnnotationDimensions(false);
2346         }
2347
2348       }
2349       else
2350       {
2351         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2352                 DEFAULT_HEIGHT);
2353         String newtitle = new String("Copied sequences");
2354
2355         if (Desktop.jalviewClipboard != null
2356                 && Desktop.jalviewClipboard[2] != null)
2357         {
2358           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2359           af.viewport.setHiddenColumns(hc);
2360         }
2361
2362         // >>>This is a fix for the moment, until a better solution is
2363         // found!!<<<
2364         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2365                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2366                         .getFeatureRenderer());
2367
2368         // TODO: maintain provenance of an alignment, rather than just make the
2369         // title a concatenation of operations.
2370         if (!externalPaste)
2371         {
2372           if (title.startsWith("Copied sequences"))
2373           {
2374             newtitle = title;
2375           }
2376           else
2377           {
2378             newtitle = newtitle.concat("- from " + title);
2379           }
2380         }
2381         else
2382         {
2383           newtitle = new String("Pasted sequences");
2384         }
2385
2386         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2387                 DEFAULT_HEIGHT);
2388
2389       }
2390
2391     } catch (Exception ex)
2392     {
2393       ex.printStackTrace();
2394       System.out.println("Exception whilst pasting: " + ex);
2395       // could be anything being pasted in here
2396     }
2397
2398   }
2399
2400   @Override
2401   protected void expand_newalign(ActionEvent e)
2402   {
2403     try
2404     {
2405       AlignmentI alignment = AlignmentUtils
2406               .expandContext(getViewport().getAlignment(), -1);
2407       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2408               DEFAULT_HEIGHT);
2409       String newtitle = new String("Flanking alignment");
2410
2411       if (Desktop.jalviewClipboard != null
2412               && Desktop.jalviewClipboard[2] != null)
2413       {
2414         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2415         af.viewport.setHiddenColumns(hc);
2416       }
2417
2418       // >>>This is a fix for the moment, until a better solution is
2419       // found!!<<<
2420       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2421               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2422                       .getFeatureRenderer());
2423
2424       // TODO: maintain provenance of an alignment, rather than just make the
2425       // title a concatenation of operations.
2426       {
2427         if (title.startsWith("Copied sequences"))
2428         {
2429           newtitle = title;
2430         }
2431         else
2432         {
2433           newtitle = newtitle.concat("- from " + title);
2434         }
2435       }
2436
2437       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2438
2439     } catch (Exception ex)
2440     {
2441       ex.printStackTrace();
2442       System.out.println("Exception whilst pasting: " + ex);
2443       // could be anything being pasted in here
2444     } catch (OutOfMemoryError oom)
2445     {
2446       new OOMWarning("Viewing flanking region of alignment", oom);
2447     }
2448   }
2449
2450   /**
2451    * Action Cut (delete and copy) the selected region
2452    */
2453   @Override
2454   protected void cut_actionPerformed()
2455   {
2456     copy_actionPerformed();
2457     delete_actionPerformed();
2458   }
2459
2460   /**
2461    * Performs menu option to Delete the currently selected region
2462    */
2463   @Override
2464   protected void delete_actionPerformed()
2465   {
2466
2467     SequenceGroup sg = viewport.getSelectionGroup();
2468     if (sg == null)
2469     {
2470       return;
2471     }
2472
2473     Runnable okAction = new Runnable()
2474     {
2475       @Override
2476       public void run()
2477       {
2478         SequenceI[] cut = sg.getSequences()
2479                 .toArray(new SequenceI[sg.getSize()]);
2480
2481         addHistoryItem(new EditCommand(
2482                 MessageManager.getString("label.cut_sequences"), Action.CUT,
2483                 cut, sg.getStartRes(),
2484                 sg.getEndRes() - sg.getStartRes() + 1,
2485                 viewport.getAlignment()));
2486
2487         viewport.setSelectionGroup(null);
2488         viewport.sendSelection();
2489         viewport.getAlignment().deleteGroup(sg);
2490
2491         viewport.firePropertyChange("alignment", null,
2492                 viewport.getAlignment().getSequences());
2493         if (viewport.getAlignment().getHeight() < 1)
2494         {
2495           try
2496           {
2497             AlignFrame.this.setClosed(true);
2498           } catch (Exception ex)
2499           {
2500           }
2501         }
2502       }
2503     };
2504
2505     /*
2506      * If the cut affects all sequences, prompt for confirmation
2507      */
2508     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2509             .getHeight();
2510     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2511             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2512     if (wholeHeight && wholeWidth)
2513     {
2514       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2515       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2516       Object[] options = new Object[] {
2517           MessageManager.getString("action.ok"),
2518           MessageManager.getString("action.cancel") };
2519       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2520               MessageManager.getString("label.delete_all"),
2521               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2522               options, options[0]);
2523     }
2524     else
2525     {
2526       okAction.run();
2527     }
2528   }
2529
2530   /**
2531    * DOCUMENT ME!
2532    *
2533    * @param e
2534    *          DOCUMENT ME!
2535    */
2536   @Override
2537   protected void deleteGroups_actionPerformed(ActionEvent e)
2538   {
2539     if (avc.deleteGroups())
2540     {
2541       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2542       alignPanel.updateAnnotation();
2543       alignPanel.paintAlignment(true, true);
2544     }
2545   }
2546
2547   /**
2548    * DOCUMENT ME!
2549    *
2550    * @param e
2551    *          DOCUMENT ME!
2552    */
2553   @Override
2554   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2555   {
2556     SequenceGroup sg = new SequenceGroup(
2557             viewport.getAlignment().getSequences());
2558
2559     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2560     viewport.setSelectionGroup(sg);
2561     viewport.isSelectionGroupChanged(true);
2562     viewport.sendSelection();
2563     // JAL-2034 - should delegate to
2564     // alignPanel to decide if overview needs
2565     // updating.
2566     alignPanel.paintAlignment(false, false);
2567     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2568   }
2569
2570   /**
2571    * DOCUMENT ME!
2572    *
2573    * @param e
2574    *          DOCUMENT ME!
2575    */
2576   @Override
2577   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2578   {
2579     if (viewport.cursorMode)
2580     {
2581       alignPanel.getSeqPanel().keyboardNo1 = null;
2582       alignPanel.getSeqPanel().keyboardNo2 = null;
2583     }
2584     viewport.setSelectionGroup(null);
2585     viewport.getColumnSelection().clear();
2586     viewport.setSearchResults(null);
2587     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2588     // JAL-2034 - should delegate to
2589     // alignPanel to decide if overview needs
2590     // updating.
2591     alignPanel.paintAlignment(false, false);
2592     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2593     viewport.sendSelection();
2594   }
2595
2596   /**
2597    * DOCUMENT ME!
2598    *
2599    * @param e
2600    *          DOCUMENT ME!
2601    */
2602   @Override
2603   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2604   {
2605     SequenceGroup sg = viewport.getSelectionGroup();
2606
2607     if (sg == null)
2608     {
2609       selectAllSequenceMenuItem_actionPerformed(null);
2610
2611       return;
2612     }
2613
2614     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2615     {
2616       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2617     }
2618     // JAL-2034 - should delegate to
2619     // alignPanel to decide if overview needs
2620     // updating.
2621
2622     alignPanel.paintAlignment(true, false);
2623     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2624     viewport.sendSelection();
2625   }
2626
2627   @Override
2628   public void invertColSel_actionPerformed(ActionEvent e)
2629   {
2630     viewport.invertColumnSelection();
2631     alignPanel.paintAlignment(true, false);
2632     viewport.sendSelection();
2633   }
2634
2635   /**
2636    * DOCUMENT ME!
2637    *
2638    * @param e
2639    *          DOCUMENT ME!
2640    */
2641   @Override
2642   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2643   {
2644     trimAlignment(true);
2645   }
2646
2647   /**
2648    * DOCUMENT ME!
2649    *
2650    * @param e
2651    *          DOCUMENT ME!
2652    */
2653   @Override
2654   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2655   {
2656     trimAlignment(false);
2657   }
2658
2659   void trimAlignment(boolean trimLeft)
2660   {
2661     ColumnSelection colSel = viewport.getColumnSelection();
2662     int column;
2663
2664     if (!colSel.isEmpty())
2665     {
2666       if (trimLeft)
2667       {
2668         column = colSel.getMin();
2669       }
2670       else
2671       {
2672         column = colSel.getMax();
2673       }
2674
2675       SequenceI[] seqs;
2676       if (viewport.getSelectionGroup() != null)
2677       {
2678         seqs = viewport.getSelectionGroup()
2679                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2680       }
2681       else
2682       {
2683         seqs = viewport.getAlignment().getSequencesArray();
2684       }
2685
2686       TrimRegionCommand trimRegion;
2687       if (trimLeft)
2688       {
2689         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2690                 column, viewport.getAlignment());
2691         viewport.getRanges().setStartRes(0);
2692       }
2693       else
2694       {
2695         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2696                 column, viewport.getAlignment());
2697       }
2698
2699       setStatus(MessageManager.formatMessage("label.removed_columns",
2700               new String[]
2701               { Integer.valueOf(trimRegion.getSize()).toString() }));
2702
2703       addHistoryItem(trimRegion);
2704
2705       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2706       {
2707         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2708                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2709         {
2710           viewport.getAlignment().deleteGroup(sg);
2711         }
2712       }
2713
2714       viewport.firePropertyChange("alignment", null,
2715               viewport.getAlignment().getSequences());
2716     }
2717   }
2718
2719   /**
2720    * DOCUMENT ME!
2721    *
2722    * @param e
2723    *          DOCUMENT ME!
2724    */
2725   @Override
2726   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2727   {
2728     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2729
2730     SequenceI[] seqs;
2731     if (viewport.getSelectionGroup() != null)
2732     {
2733       seqs = viewport.getSelectionGroup()
2734               .getSequencesAsArray(viewport.getHiddenRepSequences());
2735       start = viewport.getSelectionGroup().getStartRes();
2736       end = viewport.getSelectionGroup().getEndRes();
2737     }
2738     else
2739     {
2740       seqs = viewport.getAlignment().getSequencesArray();
2741     }
2742
2743     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2744             "Remove Gapped Columns", seqs, start, end,
2745             viewport.getAlignment());
2746
2747     addHistoryItem(removeGapCols);
2748
2749     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2750             new Object[]
2751             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2752
2753     // This is to maintain viewport position on first residue
2754     // of first sequence
2755     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2756     ViewportRanges ranges = viewport.getRanges();
2757     int startRes = seq.findPosition(ranges.getStartRes());
2758     // ShiftList shifts;
2759     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2760     // edit.alColumnChanges=shifts.getInverse();
2761     // if (viewport.hasHiddenColumns)
2762     // viewport.getColumnSelection().compensateForEdits(shifts);
2763     ranges.setStartRes(seq.findIndex(startRes) - 1);
2764     viewport.firePropertyChange("alignment", null,
2765             viewport.getAlignment().getSequences());
2766
2767   }
2768
2769   /**
2770    * DOCUMENT ME!
2771    *
2772    * @param e
2773    *          DOCUMENT ME!
2774    */
2775   @Override
2776   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2777   {
2778     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2779
2780     SequenceI[] seqs;
2781     if (viewport.getSelectionGroup() != null)
2782     {
2783       seqs = viewport.getSelectionGroup()
2784               .getSequencesAsArray(viewport.getHiddenRepSequences());
2785       start = viewport.getSelectionGroup().getStartRes();
2786       end = viewport.getSelectionGroup().getEndRes();
2787     }
2788     else
2789     {
2790       seqs = viewport.getAlignment().getSequencesArray();
2791     }
2792
2793     // This is to maintain viewport position on first residue
2794     // of first sequence
2795     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2796     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2797
2798     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2799             viewport.getAlignment()));
2800
2801     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2802
2803     viewport.firePropertyChange("alignment", null,
2804             viewport.getAlignment().getSequences());
2805
2806   }
2807
2808   /**
2809    * DOCUMENT ME!
2810    *
2811    * @param e
2812    *          DOCUMENT ME!
2813    */
2814   @Override
2815   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2816   {
2817     viewport.setPadGaps(padGapsMenuitem.isSelected());
2818     viewport.firePropertyChange("alignment", null,
2819             viewport.getAlignment().getSequences());
2820   }
2821
2822   /**
2823    * Opens a Finder dialog
2824    *
2825    * @param e
2826    */
2827   @Override
2828   public void findMenuItem_actionPerformed(ActionEvent e)
2829   {
2830     new Finder(alignPanel, false, null);
2831   }
2832
2833   /**
2834    * Create a new view of the current alignment.
2835    */
2836   @Override
2837   public void newView_actionPerformed(ActionEvent e)
2838   {
2839     newView(null, true);
2840   }
2841
2842   /**
2843    * Creates and shows a new view of the current alignment.
2844    *
2845    * @param viewTitle
2846    *          title of newly created view; if null, one will be generated
2847    * @param copyAnnotation
2848    *          if true then duplicate all annnotation, groups and settings
2849    * @return new alignment panel, already displayed.
2850    */
2851   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2852   {
2853     /*
2854      * Create a new AlignmentPanel (with its own, new Viewport)
2855      */
2856     AlignmentPanel newap = new jalview.project.Jalview2XML()
2857             .copyAlignPanel(alignPanel);
2858     if (!copyAnnotation)
2859     {
2860       /*
2861        * remove all groups and annotation except for the automatic stuff
2862        */
2863       newap.av.getAlignment().deleteAllGroups();
2864       newap.av.getAlignment().deleteAllAnnotations(false);
2865     }
2866
2867     newap.av.setGatherViewsHere(false);
2868
2869     if (viewport.getViewName() == null)
2870     {
2871       viewport.setViewName(
2872               MessageManager.getString("label.view_name_original"));
2873     }
2874
2875     /*
2876      * Views share the same edits undo and redo stacks
2877      */
2878     newap.av.setHistoryList(viewport.getHistoryList());
2879     newap.av.setRedoList(viewport.getRedoList());
2880
2881     /*
2882      * copy any visualisation settings that are not saved in the project
2883      */
2884     newap.av.setColourAppliesToAllGroups(
2885             viewport.getColourAppliesToAllGroups());
2886
2887     /*
2888      * Views share the same mappings; need to deregister any new mappings
2889      * created by copyAlignPanel, and register the new reference to the shared
2890      * mappings
2891      */
2892     newap.av.replaceMappings(viewport.getAlignment());
2893
2894     /*
2895      * start up cDNA consensus (if applicable) now mappings are in place
2896      */
2897     if (newap.av.initComplementConsensus())
2898     {
2899       newap.refresh(true); // adjust layout of annotations
2900     }
2901
2902     newap.av.setViewName(getNewViewName(viewTitle));
2903
2904     addAlignmentPanel(newap, true);
2905     newap.alignmentChanged();
2906
2907     if (alignPanels.size() == 2)
2908     {
2909       viewport.setGatherViewsHere(true);
2910     }
2911     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2912     return newap;
2913   }
2914
2915   /**
2916    * Make a new name for the view, ensuring it is unique within the current
2917    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2918    * these now use viewId. Unique view names are still desirable for usability.)
2919    *
2920    * @param viewTitle
2921    * @return
2922    */
2923   protected String getNewViewName(String viewTitle)
2924   {
2925     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2926     boolean addFirstIndex = false;
2927     if (viewTitle == null || viewTitle.trim().length() == 0)
2928     {
2929       viewTitle = MessageManager.getString("action.view");
2930       addFirstIndex = true;
2931     }
2932     else
2933     {
2934       index = 1;// we count from 1 if given a specific name
2935     }
2936     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2937
2938     List<Component> comps = PaintRefresher.components
2939             .get(viewport.getSequenceSetId());
2940
2941     List<String> existingNames = getExistingViewNames(comps);
2942
2943     while (existingNames.contains(newViewName))
2944     {
2945       newViewName = viewTitle + " " + (++index);
2946     }
2947     return newViewName;
2948   }
2949
2950   /**
2951    * Returns a list of distinct view names found in the given list of
2952    * components. View names are held on the viewport of an AlignmentPanel.
2953    *
2954    * @param comps
2955    * @return
2956    */
2957   protected List<String> getExistingViewNames(List<Component> comps)
2958   {
2959     List<String> existingNames = new ArrayList<>();
2960     for (Component comp : comps)
2961     {
2962       if (comp instanceof AlignmentPanel)
2963       {
2964         AlignmentPanel ap = (AlignmentPanel) comp;
2965         if (!existingNames.contains(ap.av.getViewName()))
2966         {
2967           existingNames.add(ap.av.getViewName());
2968         }
2969       }
2970     }
2971     return existingNames;
2972   }
2973
2974   /**
2975    * Explode tabbed views into separate windows.
2976    */
2977   @Override
2978   public void expandViews_actionPerformed(ActionEvent e)
2979   {
2980     Desktop.explodeViews(this);
2981   }
2982
2983   /**
2984    * Gather views in separate windows back into a tabbed presentation.
2985    */
2986   @Override
2987   public void gatherViews_actionPerformed(ActionEvent e)
2988   {
2989     Desktop.instance.gatherViews(this);
2990   }
2991
2992   /**
2993    * DOCUMENT ME!
2994    *
2995    * @param e
2996    *          DOCUMENT ME!
2997    */
2998   @Override
2999   public void font_actionPerformed(ActionEvent e)
3000   {
3001     new FontChooser(alignPanel);
3002   }
3003
3004   /**
3005    * DOCUMENT ME!
3006    *
3007    * @param e
3008    *          DOCUMENT ME!
3009    */
3010   @Override
3011   protected void seqLimit_actionPerformed(ActionEvent e)
3012   {
3013     viewport.setShowJVSuffix(seqLimits.isSelected());
3014
3015     alignPanel.getIdPanel().getIdCanvas()
3016             .setPreferredSize(alignPanel.calculateIdWidth());
3017     alignPanel.paintAlignment(true, false);
3018   }
3019
3020   @Override
3021   public void idRightAlign_actionPerformed(ActionEvent e)
3022   {
3023     viewport.setRightAlignIds(idRightAlign.isSelected());
3024     alignPanel.paintAlignment(false, false);
3025   }
3026
3027   @Override
3028   public void centreColumnLabels_actionPerformed(ActionEvent e)
3029   {
3030     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3031     alignPanel.paintAlignment(false, false);
3032   }
3033
3034   /*
3035    * (non-Javadoc)
3036    *
3037    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3038    */
3039   @Override
3040   protected void followHighlight_actionPerformed()
3041   {
3042     /*
3043      * Set the 'follow' flag on the Viewport (and scroll to position if now
3044      * true).
3045      */
3046     final boolean state = this.followHighlightMenuItem.getState();
3047     viewport.setFollowHighlight(state);
3048     if (state)
3049     {
3050       alignPanel.scrollToPosition(viewport.getSearchResults());
3051     }
3052   }
3053
3054   /**
3055    * DOCUMENT ME!
3056    *
3057    * @param e
3058    *          DOCUMENT ME!
3059    */
3060   @Override
3061   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3062   {
3063     viewport.setColourText(colourTextMenuItem.isSelected());
3064     alignPanel.paintAlignment(false, false);
3065   }
3066
3067   /**
3068    * DOCUMENT ME!
3069    *
3070    * @param e
3071    *          DOCUMENT ME!
3072    */
3073   @Override
3074   public void wrapMenuItem_actionPerformed(ActionEvent e)
3075   {
3076     scaleAbove.setVisible(wrapMenuItem.isSelected());
3077     scaleLeft.setVisible(wrapMenuItem.isSelected());
3078     scaleRight.setVisible(wrapMenuItem.isSelected());
3079     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3080     alignPanel.updateLayout();
3081   }
3082
3083   @Override
3084   public void showAllSeqs_actionPerformed(ActionEvent e)
3085   {
3086     viewport.showAllHiddenSeqs();
3087   }
3088
3089   @Override
3090   public void showAllColumns_actionPerformed(ActionEvent e)
3091   {
3092     viewport.showAllHiddenColumns();
3093     alignPanel.paintAlignment(true, true);
3094     viewport.sendSelection();
3095   }
3096
3097   @Override
3098   public void hideSelSequences_actionPerformed(ActionEvent e)
3099   {
3100     viewport.hideAllSelectedSeqs();
3101   }
3102
3103   /**
3104    * called by key handler and the hide all/show all menu items
3105    *
3106    * @param toggleSeqs
3107    * @param toggleCols
3108    */
3109   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3110   {
3111
3112     boolean hide = false;
3113     SequenceGroup sg = viewport.getSelectionGroup();
3114     if (!toggleSeqs && !toggleCols)
3115     {
3116       // Hide everything by the current selection - this is a hack - we do the
3117       // invert and then hide
3118       // first check that there will be visible columns after the invert.
3119       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3120               && sg.getStartRes() <= sg.getEndRes()))
3121       {
3122         // now invert the sequence set, if required - empty selection implies
3123         // that no hiding is required.
3124         if (sg != null)
3125         {
3126           invertSequenceMenuItem_actionPerformed(null);
3127           sg = viewport.getSelectionGroup();
3128           toggleSeqs = true;
3129
3130         }
3131         viewport.expandColSelection(sg, true);
3132         // finally invert the column selection and get the new sequence
3133         // selection.
3134         invertColSel_actionPerformed(null);
3135         toggleCols = true;
3136       }
3137     }
3138
3139     if (toggleSeqs)
3140     {
3141       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3142       {
3143         hideSelSequences_actionPerformed(null);
3144         hide = true;
3145       }
3146       else if (!(toggleCols && viewport.hasSelectedColumns()))
3147       {
3148         showAllSeqs_actionPerformed(null);
3149       }
3150     }
3151
3152     if (toggleCols)
3153     {
3154       if (viewport.hasSelectedColumns())
3155       {
3156         hideSelColumns_actionPerformed(null);
3157         if (!toggleSeqs)
3158         {
3159           viewport.setSelectionGroup(sg);
3160         }
3161       }
3162       else if (!hide)
3163       {
3164         showAllColumns_actionPerformed(null);
3165       }
3166     }
3167   }
3168
3169   /*
3170    * (non-Javadoc)
3171    *
3172    * @see
3173    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3174    * event.ActionEvent)
3175    */
3176   @Override
3177   public void hideAllButSelection_actionPerformed(ActionEvent e)
3178   {
3179     toggleHiddenRegions(false, false);
3180     viewport.sendSelection();
3181   }
3182
3183   /*
3184    * (non-Javadoc)
3185    *
3186    * @see
3187    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3188    * .ActionEvent)
3189    */
3190   @Override
3191   public void hideAllSelection_actionPerformed(ActionEvent e)
3192   {
3193     SequenceGroup sg = viewport.getSelectionGroup();
3194     viewport.expandColSelection(sg, false);
3195     viewport.hideAllSelectedSeqs();
3196     viewport.hideSelectedColumns();
3197     alignPanel.updateLayout();
3198     alignPanel.paintAlignment(true, true);
3199     viewport.sendSelection();
3200   }
3201
3202   /*
3203    * (non-Javadoc)
3204    *
3205    * @see
3206    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3207    * ActionEvent)
3208    */
3209   @Override
3210   public void showAllhidden_actionPerformed(ActionEvent e)
3211   {
3212     viewport.showAllHiddenColumns();
3213     viewport.showAllHiddenSeqs();
3214     alignPanel.paintAlignment(true, true);
3215     viewport.sendSelection();
3216   }
3217
3218   @Override
3219   public void hideSelColumns_actionPerformed(ActionEvent e)
3220   {
3221     viewport.hideSelectedColumns();
3222     alignPanel.updateLayout();
3223     alignPanel.paintAlignment(true, true);
3224     viewport.sendSelection();
3225   }
3226
3227   @Override
3228   public void hiddenMarkers_actionPerformed(ActionEvent e)
3229   {
3230     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3231     repaint();
3232   }
3233
3234   /**
3235    * DOCUMENT ME!
3236    *
3237    * @param e
3238    *          DOCUMENT ME!
3239    */
3240   @Override
3241   protected void scaleAbove_actionPerformed(ActionEvent e)
3242   {
3243     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3244     alignPanel.updateLayout();
3245     alignPanel.paintAlignment(true, false);
3246   }
3247
3248   /**
3249    * DOCUMENT ME!
3250    *
3251    * @param e
3252    *          DOCUMENT ME!
3253    */
3254   @Override
3255   protected void scaleLeft_actionPerformed(ActionEvent e)
3256   {
3257     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3258     alignPanel.updateLayout();
3259     alignPanel.paintAlignment(true, false);
3260   }
3261
3262   /**
3263    * DOCUMENT ME!
3264    *
3265    * @param e
3266    *          DOCUMENT ME!
3267    */
3268   @Override
3269   protected void scaleRight_actionPerformed(ActionEvent e)
3270   {
3271     viewport.setScaleRightWrapped(scaleRight.isSelected());
3272     alignPanel.updateLayout();
3273     alignPanel.paintAlignment(true, false);
3274   }
3275
3276   /**
3277    * DOCUMENT ME!
3278    *
3279    * @param e
3280    *          DOCUMENT ME!
3281    */
3282   @Override
3283   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3284   {
3285     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3286     alignPanel.paintAlignment(false, false);
3287   }
3288
3289   /**
3290    * DOCUMENT ME!
3291    *
3292    * @param e
3293    *          DOCUMENT ME!
3294    */
3295   @Override
3296   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3297   {
3298     viewport.setShowText(viewTextMenuItem.isSelected());
3299     alignPanel.paintAlignment(false, false);
3300   }
3301
3302   /**
3303    * DOCUMENT ME!
3304    *
3305    * @param e
3306    *          DOCUMENT ME!
3307    */
3308   @Override
3309   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3310   {
3311     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3312     alignPanel.paintAlignment(false, false);
3313   }
3314
3315   public FeatureSettings featureSettings;
3316
3317   @Override
3318   public FeatureSettingsControllerI getFeatureSettingsUI()
3319   {
3320     return featureSettings;
3321   }
3322
3323   @Override
3324   public void featureSettings_actionPerformed(ActionEvent e)
3325   {
3326     showFeatureSettingsUI();
3327   }
3328
3329   @Override
3330   public FeatureSettingsControllerI showFeatureSettingsUI()
3331   {
3332     if (featureSettings != null)
3333     {
3334       featureSettings.closeOldSettings();
3335       featureSettings = null;
3336     }
3337     if (!showSeqFeatures.isSelected())
3338     {
3339       // make sure features are actually displayed
3340       showSeqFeatures.setSelected(true);
3341       showSeqFeatures_actionPerformed(null);
3342     }
3343     featureSettings = new FeatureSettings(this);
3344     return featureSettings;
3345   }
3346
3347   /**
3348    * Set or clear 'Show Sequence Features'
3349    *
3350    * @param evt
3351    *          DOCUMENT ME!
3352    */
3353   @Override
3354   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3355   {
3356     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3357     alignPanel.paintAlignment(true, true);
3358   }
3359
3360   /**
3361    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3362    * the annotations panel as a whole.
3363    *
3364    * The options to show/hide all annotations should be enabled when the panel
3365    * is shown, and disabled when the panel is hidden.
3366    *
3367    * @param e
3368    */
3369   @Override
3370   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3371   {
3372     final boolean setVisible = annotationPanelMenuItem.isSelected();
3373     viewport.setShowAnnotation(setVisible);
3374     this.showAllSeqAnnotations.setEnabled(setVisible);
3375     this.hideAllSeqAnnotations.setEnabled(setVisible);
3376     this.showAllAlAnnotations.setEnabled(setVisible);
3377     this.hideAllAlAnnotations.setEnabled(setVisible);
3378     alignPanel.updateLayout();
3379   }
3380
3381   @Override
3382   public void alignmentProperties()
3383   {
3384     JComponent pane;
3385     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3386
3387             .formatAsHtml();
3388     String content = MessageManager.formatMessage("label.html_content",
3389             new Object[]
3390             { contents.toString() });
3391     contents = null;
3392
3393     if (Platform.isJS())
3394     {
3395       JLabel textLabel = new JLabel();
3396       textLabel.setText(content);
3397       textLabel.setBackground(Color.WHITE);
3398
3399       pane = new JPanel(new BorderLayout());
3400       ((JPanel) pane).setOpaque(true);
3401       pane.setBackground(Color.WHITE);
3402       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3403     }
3404     else
3405     /**
3406      * Java only
3407      *
3408      * @j2sIgnore
3409      */
3410     {
3411       JEditorPane editPane = new JEditorPane("text/html", "");
3412       editPane.setEditable(false);
3413       editPane.setText(content);
3414       pane = editPane;
3415     }
3416
3417     JInternalFrame frame = new JInternalFrame();
3418
3419     frame.getContentPane().add(new JScrollPane(pane));
3420
3421     Desktop.addInternalFrame(frame, MessageManager
3422             .formatMessage("label.alignment_properties", new Object[]
3423             { getTitle() }), 500, 400);
3424   }
3425
3426   /**
3427    * DOCUMENT ME!
3428    *
3429    * @param e
3430    *          DOCUMENT ME!
3431    */
3432   @Override
3433   public void overviewMenuItem_actionPerformed(ActionEvent e)
3434   {
3435     if (alignPanel.overviewPanel != null)
3436     {
3437       return;
3438     }
3439
3440     JInternalFrame frame = new JInternalFrame();
3441     final OverviewPanel overview = new OverviewPanel(alignPanel);
3442     frame.setContentPane(overview);
3443     Desktop.addInternalFrame(frame, MessageManager
3444             .formatMessage("label.overview_params", new Object[]
3445             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3446             true, true);
3447     frame.pack();
3448     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3449     frame.addInternalFrameListener(
3450             new javax.swing.event.InternalFrameAdapter()
3451             {
3452               @Override
3453               public void internalFrameClosed(
3454                       javax.swing.event.InternalFrameEvent evt)
3455               {
3456                 overview.dispose();
3457                 alignPanel.setOverviewPanel(null);
3458               }
3459             });
3460     if (getKeyListeners().length > 0)
3461     {
3462       frame.addKeyListener(getKeyListeners()[0]);
3463     }
3464
3465     alignPanel.setOverviewPanel(overview);
3466   }
3467
3468   @Override
3469   public void textColour_actionPerformed()
3470   {
3471     new TextColourChooser().chooseColour(alignPanel, null);
3472   }
3473
3474   /*
3475    * public void covariationColour_actionPerformed() {
3476    * changeColour(new
3477    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3478    * ()[0])); }
3479    */
3480   @Override
3481   public void annotationColour_actionPerformed()
3482   {
3483     new AnnotationColourChooser(viewport, alignPanel);
3484   }
3485
3486   @Override
3487   public void annotationColumn_actionPerformed(ActionEvent e)
3488   {
3489     new AnnotationColumnChooser(viewport, alignPanel);
3490   }
3491
3492   /**
3493    * Action on the user checking or unchecking the option to apply the selected
3494    * colour scheme to all groups. If unchecked, groups may have their own
3495    * independent colour schemes.
3496    *
3497    * @param selected
3498    */
3499   @Override
3500   public void applyToAllGroups_actionPerformed(boolean selected)
3501   {
3502     viewport.setColourAppliesToAllGroups(selected);
3503   }
3504
3505   /**
3506    * Action on user selecting a colour from the colour menu
3507    *
3508    * @param name
3509    *          the name (not the menu item label!) of the colour scheme
3510    */
3511   @Override
3512   public void changeColour_actionPerformed(String name)
3513   {
3514     /*
3515      * 'User Defined' opens a panel to configure or load a
3516      * user-defined colour scheme
3517      */
3518     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3519     {
3520       new UserDefinedColours(alignPanel);
3521       return;
3522     }
3523
3524     /*
3525      * otherwise set the chosen colour scheme (or null for 'None')
3526      */
3527     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3528             viewport, viewport.getAlignment(),
3529             viewport.getHiddenRepSequences());
3530     changeColour(cs);
3531   }
3532
3533   /**
3534    * Actions on setting or changing the alignment colour scheme
3535    *
3536    * @param cs
3537    */
3538   @Override
3539   public void changeColour(ColourSchemeI cs)
3540   {
3541     // TODO: pull up to controller method
3542     ColourMenuHelper.setColourSelected(colourMenu, cs);
3543
3544     viewport.setGlobalColourScheme(cs);
3545
3546     alignPanel.paintAlignment(true, true);
3547   }
3548
3549   /**
3550    * Show the PID threshold slider panel
3551    */
3552   @Override
3553   protected void modifyPID_actionPerformed()
3554   {
3555     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3556             alignPanel.getViewName());
3557     SliderPanel.showPIDSlider();
3558   }
3559
3560   /**
3561    * Show the Conservation slider panel
3562    */
3563   @Override
3564   protected void modifyConservation_actionPerformed()
3565   {
3566     SliderPanel.setConservationSlider(alignPanel,
3567             viewport.getResidueShading(), alignPanel.getViewName());
3568     SliderPanel.showConservationSlider();
3569   }
3570
3571   /**
3572    * Action on selecting or deselecting (Colour) By Conservation
3573    */
3574   @Override
3575   public void conservationMenuItem_actionPerformed(boolean selected)
3576   {
3577     modifyConservation.setEnabled(selected);
3578     viewport.setConservationSelected(selected);
3579     viewport.getResidueShading().setConservationApplied(selected);
3580
3581     changeColour(viewport.getGlobalColourScheme());
3582     if (selected)
3583     {
3584       modifyConservation_actionPerformed();
3585     }
3586     else
3587     {
3588       SliderPanel.hideConservationSlider();
3589     }
3590   }
3591
3592   /**
3593    * Action on selecting or deselecting (Colour) Above PID Threshold
3594    */
3595   @Override
3596   public void abovePIDThreshold_actionPerformed(boolean selected)
3597   {
3598     modifyPID.setEnabled(selected);
3599     viewport.setAbovePIDThreshold(selected);
3600     if (!selected)
3601     {
3602       viewport.getResidueShading().setThreshold(0,
3603               viewport.isIgnoreGapsConsensus());
3604     }
3605
3606     changeColour(viewport.getGlobalColourScheme());
3607     if (selected)
3608     {
3609       modifyPID_actionPerformed();
3610     }
3611     else
3612     {
3613       SliderPanel.hidePIDSlider();
3614     }
3615   }
3616
3617   /**
3618    * DOCUMENT ME!
3619    *
3620    * @param e
3621    *          DOCUMENT ME!
3622    */
3623   @Override
3624   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3625   {
3626     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3627     AlignmentSorter.sortByPID(viewport.getAlignment(),
3628             viewport.getAlignment().getSequenceAt(0));
3629     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3630             viewport.getAlignment()));
3631     alignPanel.paintAlignment(true, false);
3632   }
3633
3634   /**
3635    * DOCUMENT ME!
3636    *
3637    * @param e
3638    *          DOCUMENT ME!
3639    */
3640   @Override
3641   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3642   {
3643     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3644     AlignmentSorter.sortByID(viewport.getAlignment());
3645     addHistoryItem(
3646             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3647     alignPanel.paintAlignment(true, false);
3648   }
3649
3650   /**
3651    * DOCUMENT ME!
3652    *
3653    * @param e
3654    *          DOCUMENT ME!
3655    */
3656   @Override
3657   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3658   {
3659     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3660     AlignmentSorter.sortByLength(viewport.getAlignment());
3661     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3662             viewport.getAlignment()));
3663     alignPanel.paintAlignment(true, false);
3664   }
3665
3666   /**
3667    * DOCUMENT ME!
3668    *
3669    * @param e
3670    *          DOCUMENT ME!
3671    */
3672   @Override
3673   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3674   {
3675     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3676     AlignmentSorter.sortByGroup(viewport.getAlignment());
3677     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3678             viewport.getAlignment()));
3679
3680     alignPanel.paintAlignment(true, false);
3681   }
3682
3683   /**
3684    * DOCUMENT ME!
3685    *
3686    * @param e
3687    *          DOCUMENT ME!
3688    */
3689   @Override
3690   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3691   {
3692     new RedundancyPanel(alignPanel, this);
3693   }
3694
3695   /**
3696    * DOCUMENT ME!
3697    *
3698    * @param e
3699    *          DOCUMENT ME!
3700    */
3701   @Override
3702   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3703   {
3704     if ((viewport.getSelectionGroup() == null)
3705             || (viewport.getSelectionGroup().getSize() < 2))
3706     {
3707       JvOptionPane.showInternalMessageDialog(this,
3708               MessageManager.getString(
3709                       "label.you_must_select_least_two_sequences"),
3710               MessageManager.getString("label.invalid_selection"),
3711               JvOptionPane.WARNING_MESSAGE);
3712     }
3713     else
3714     {
3715       JInternalFrame frame = new JInternalFrame();
3716       frame.setContentPane(new PairwiseAlignPanel(viewport));
3717       Desktop.addInternalFrame(frame,
3718               MessageManager.getString("action.pairwise_alignment"), 600,
3719               500);
3720     }
3721   }
3722
3723   @Override
3724   public void autoCalculate_actionPerformed(ActionEvent e)
3725   {
3726     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3727     if (viewport.autoCalculateConsensus)
3728     {
3729       viewport.firePropertyChange("alignment", null,
3730               viewport.getAlignment().getSequences());
3731     }
3732   }
3733
3734   @Override
3735   public void sortByTreeOption_actionPerformed(ActionEvent e)
3736   {
3737     viewport.sortByTree = sortByTree.isSelected();
3738   }
3739
3740   @Override
3741   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3742   {
3743     viewport.followSelection = listenToViewSelections.isSelected();
3744   }
3745
3746   /**
3747    * Constructs a tree panel and adds it to the desktop
3748    *
3749    * @param type
3750    *          tree type (NJ or AV)
3751    * @param modelName
3752    *          name of score model used to compute the tree
3753    * @param options
3754    *          parameters for the distance or similarity calculation
3755    */
3756   void newTreePanel(String type, String modelName,
3757           SimilarityParamsI options)
3758   {
3759     String frameTitle = "";
3760     TreePanel tp;
3761
3762     boolean onSelection = false;
3763     if (viewport.getSelectionGroup() != null
3764             && viewport.getSelectionGroup().getSize() > 0)
3765     {
3766       SequenceGroup sg = viewport.getSelectionGroup();
3767
3768       /* Decide if the selection is a column region */
3769       for (SequenceI _s : sg.getSequences())
3770       {
3771         if (_s.getLength() < sg.getEndRes())
3772         {
3773           JvOptionPane.showMessageDialog(Desktop.desktop,
3774                   MessageManager.getString(
3775                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3776                   MessageManager.getString(
3777                           "label.sequences_selection_not_aligned"),
3778                   JvOptionPane.WARNING_MESSAGE);
3779
3780           return;
3781         }
3782       }
3783       onSelection = true;
3784     }
3785     else
3786     {
3787       if (viewport.getAlignment().getHeight() < 2)
3788       {
3789         return;
3790       }
3791     }
3792
3793     tp = new TreePanel(alignPanel, type, modelName, options);
3794     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3795
3796     frameTitle += " from ";
3797
3798     if (viewport.getViewName() != null)
3799     {
3800       frameTitle += viewport.getViewName() + " of ";
3801     }
3802
3803     frameTitle += this.title;
3804
3805     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3806   }
3807
3808   /**
3809    * DOCUMENT ME!
3810    *
3811    * @param title
3812    *          DOCUMENT ME!
3813    * @param order
3814    *          DOCUMENT ME!
3815    */
3816   public void addSortByOrderMenuItem(String title,
3817           final AlignmentOrder order)
3818   {
3819     final JMenuItem item = new JMenuItem(MessageManager
3820             .formatMessage("action.by_title_param", new Object[]
3821             { title }));
3822     sort.add(item);
3823     item.addActionListener(new java.awt.event.ActionListener()
3824     {
3825       @Override
3826       public void actionPerformed(ActionEvent e)
3827       {
3828         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3829
3830         // TODO: JBPNote - have to map order entries to curent SequenceI
3831         // pointers
3832         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3833
3834         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3835                 viewport.getAlignment()));
3836
3837         alignPanel.paintAlignment(true, false);
3838       }
3839     });
3840   }
3841
3842   /**
3843    * Add a new sort by annotation score menu item
3844    *
3845    * @param sort
3846    *          the menu to add the option to
3847    * @param scoreLabel
3848    *          the label used to retrieve scores for each sequence on the
3849    *          alignment
3850    */
3851   public void addSortByAnnotScoreMenuItem(JMenu sort,
3852           final String scoreLabel)
3853   {
3854     final JMenuItem item = new JMenuItem(scoreLabel);
3855     sort.add(item);
3856     item.addActionListener(new java.awt.event.ActionListener()
3857     {
3858       @Override
3859       public void actionPerformed(ActionEvent e)
3860       {
3861         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3862         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3863                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3864         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3865                 viewport.getAlignment()));
3866         alignPanel.paintAlignment(true, false);
3867       }
3868     });
3869   }
3870
3871   /**
3872    * last hash for alignment's annotation array - used to minimise cost of
3873    * rebuild.
3874    */
3875   protected int _annotationScoreVectorHash;
3876
3877   /**
3878    * search the alignment and rebuild the sort by annotation score submenu the
3879    * last alignment annotation vector hash is stored to minimize cost of
3880    * rebuilding in subsequence calls.
3881    *
3882    */
3883   @Override
3884   public void buildSortByAnnotationScoresMenu()
3885   {
3886     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3887     {
3888       return;
3889     }
3890
3891     if (viewport.getAlignment().getAlignmentAnnotation()
3892             .hashCode() != _annotationScoreVectorHash)
3893     {
3894       sortByAnnotScore.removeAll();
3895       // almost certainly a quicker way to do this - but we keep it simple
3896       Hashtable<String, String> scoreSorts = new Hashtable<>();
3897       AlignmentAnnotation aann[];
3898       for (SequenceI sqa : viewport.getAlignment().getSequences())
3899       {
3900         aann = sqa.getAnnotation();
3901         for (int i = 0; aann != null && i < aann.length; i++)
3902         {
3903           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3904           {
3905             scoreSorts.put(aann[i].label, aann[i].label);
3906           }
3907         }
3908       }
3909       Enumeration<String> labels = scoreSorts.keys();
3910       while (labels.hasMoreElements())
3911       {
3912         addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
3913       }
3914       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3915       scoreSorts.clear();
3916
3917       _annotationScoreVectorHash = viewport.getAlignment()
3918               .getAlignmentAnnotation().hashCode();
3919     }
3920   }
3921
3922   /**
3923    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3924    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3925    * call. Listeners are added to remove the menu item when the treePanel is
3926    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3927    * modified.
3928    */
3929   @Override
3930   public void buildTreeSortMenu()
3931   {
3932     sortByTreeMenu.removeAll();
3933
3934     List<Component> comps = PaintRefresher.components
3935             .get(viewport.getSequenceSetId());
3936     List<TreePanel> treePanels = new ArrayList<>();
3937     for (Component comp : comps)
3938     {
3939       if (comp instanceof TreePanel)
3940       {
3941         treePanels.add((TreePanel) comp);
3942       }
3943     }
3944
3945     if (treePanels.size() < 1)
3946     {
3947       sortByTreeMenu.setVisible(false);
3948       return;
3949     }
3950
3951     sortByTreeMenu.setVisible(true);
3952
3953     for (final TreePanel tp : treePanels)
3954     {
3955       final JMenuItem item = new JMenuItem(tp.getTitle());
3956       item.addActionListener(new java.awt.event.ActionListener()
3957       {
3958         @Override
3959         public void actionPerformed(ActionEvent e)
3960         {
3961           tp.sortByTree_actionPerformed();
3962           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3963
3964         }
3965       });
3966
3967       sortByTreeMenu.add(item);
3968     }
3969   }
3970
3971   public boolean sortBy(AlignmentOrder alorder, String undoname)
3972   {
3973     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3974     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3975     if (undoname != null)
3976     {
3977       addHistoryItem(new OrderCommand(undoname, oldOrder,
3978               viewport.getAlignment()));
3979     }
3980     alignPanel.paintAlignment(true, false);
3981     return true;
3982   }
3983
3984   /**
3985    * Work out whether the whole set of sequences or just the selected set will
3986    * be submitted for multiple alignment.
3987    *
3988    */
3989   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3990   {
3991     // Now, check we have enough sequences
3992     AlignmentView msa = null;
3993
3994     if ((viewport.getSelectionGroup() != null)
3995             && (viewport.getSelectionGroup().getSize() > 1))
3996     {
3997       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3998       // some common interface!
3999       /*
4000        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4001        * SequenceI[sz = seqs.getSize(false)];
4002        *
4003        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4004        * seqs.getSequenceAt(i); }
4005        */
4006       msa = viewport.getAlignmentView(true);
4007     }
4008     else if (viewport.getSelectionGroup() != null
4009             && viewport.getSelectionGroup().getSize() == 1)
4010     {
4011       int option = JvOptionPane.showConfirmDialog(this,
4012               MessageManager.getString("warn.oneseq_msainput_selection"),
4013               MessageManager.getString("label.invalid_selection"),
4014               JvOptionPane.OK_CANCEL_OPTION);
4015       if (option == JvOptionPane.OK_OPTION)
4016       {
4017         msa = viewport.getAlignmentView(false);
4018       }
4019     }
4020     else
4021     {
4022       msa = viewport.getAlignmentView(false);
4023     }
4024     return msa;
4025   }
4026
4027   /**
4028    * Decides what is submitted to a secondary structure prediction service: the
4029    * first sequence in the alignment, or in the current selection, or, if the
4030    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4031    * region or the whole alignment. (where the first sequence in the set is the
4032    * one that the prediction will be for).
4033    */
4034   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4035   {
4036     AlignmentView seqs = null;
4037
4038     if ((viewport.getSelectionGroup() != null)
4039             && (viewport.getSelectionGroup().getSize() > 0))
4040     {
4041       seqs = viewport.getAlignmentView(true);
4042     }
4043     else
4044     {
4045       seqs = viewport.getAlignmentView(false);
4046     }
4047     // limit sequences - JBPNote in future - could spawn multiple prediction
4048     // jobs
4049     // TODO: viewport.getAlignment().isAligned is a global state - the local
4050     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4051     if (!viewport.getAlignment().isAligned(false))
4052     {
4053       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4054       // TODO: if seqs.getSequences().length>1 then should really have warned
4055       // user!
4056
4057     }
4058     return seqs;
4059   }
4060
4061   /**
4062    * DOCUMENT ME!
4063    *
4064    * @param e
4065    *          DOCUMENT ME!
4066    */
4067   @Override
4068   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4069   {
4070     // Pick the tree file
4071     JalviewFileChooser chooser = new JalviewFileChooser(
4072             Cache.getProperty("LAST_DIRECTORY"));
4073     chooser.setFileView(new JalviewFileView());
4074     chooser.setDialogTitle(
4075             MessageManager.getString("label.select_newick_like_tree_file"));
4076     chooser.setToolTipText(
4077             MessageManager.getString("label.load_tree_file"));
4078
4079     chooser.setResponseHandler(0, new Runnable()
4080     {
4081       @Override
4082       public void run()
4083       {
4084         String filePath = chooser.getSelectedFile().getPath();
4085         Cache.setProperty("LAST_DIRECTORY", filePath);
4086         NewickFile fin = null;
4087         try
4088         {
4089           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4090                   DataSourceType.FILE));
4091           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4092         } catch (Exception ex)
4093         {
4094           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4095                   MessageManager
4096                           .getString("label.problem_reading_tree_file"),
4097                   JvOptionPane.WARNING_MESSAGE);
4098           ex.printStackTrace();
4099         }
4100         if (fin != null && fin.hasWarningMessage())
4101         {
4102           JvOptionPane.showMessageDialog(Desktop.desktop,
4103                   fin.getWarningMessage(),
4104                   MessageManager.getString(
4105                           "label.possible_problem_with_tree_file"),
4106                   JvOptionPane.WARNING_MESSAGE);
4107         }
4108       }
4109     });
4110     chooser.showOpenDialog(this);
4111   }
4112
4113   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4114   {
4115     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4116   }
4117
4118   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4119           int h, int x, int y)
4120   {
4121     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4122   }
4123
4124   /**
4125    * Add a treeviewer for the tree extracted from a Newick file object to the
4126    * current alignment view
4127    *
4128    * @param nf
4129    *          the tree
4130    * @param title
4131    *          tree viewer title
4132    * @param input
4133    *          Associated alignment input data (or null)
4134    * @param w
4135    *          width
4136    * @param h
4137    *          height
4138    * @param x
4139    *          position
4140    * @param y
4141    *          position
4142    * @return TreePanel handle
4143    */
4144   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4145           AlignmentView input, int w, int h, int x, int y)
4146   {
4147     TreePanel tp = null;
4148
4149     try
4150     {
4151       nf.parse();
4152
4153       if (nf.getTree() != null)
4154       {
4155         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4156
4157         tp.setSize(w, h);
4158
4159         if (x > 0 && y > 0)
4160         {
4161           tp.setLocation(x, y);
4162         }
4163
4164         Desktop.addInternalFrame(tp, treeTitle, w, h);
4165       }
4166     } catch (Exception ex)
4167     {
4168       ex.printStackTrace();
4169     }
4170
4171     return tp;
4172   }
4173
4174   private boolean buildingMenu = false;
4175
4176   /**
4177    * Generates menu items and listener event actions for web service clients
4178    *
4179    */
4180   public void BuildWebServiceMenu()
4181   {
4182     while (buildingMenu)
4183     {
4184       try
4185       {
4186         System.err.println("Waiting for building menu to finish.");
4187         Thread.sleep(10);
4188       } catch (Exception e)
4189       {
4190       }
4191     }
4192     final AlignFrame me = this;
4193     buildingMenu = true;
4194     new Thread(new Runnable()
4195     {
4196       @Override
4197       public void run()
4198       {
4199         final List<JMenuItem> legacyItems = new ArrayList<>();
4200         try
4201         {
4202           // System.err.println("Building ws menu again "
4203           // + Thread.currentThread());
4204           // TODO: add support for context dependent disabling of services based
4205           // on
4206           // alignment and current selection
4207           // TODO: add additional serviceHandle parameter to specify abstract
4208           // handler
4209           // class independently of AbstractName
4210           // TODO: add in rediscovery GUI function to restart discoverer
4211           // TODO: group services by location as well as function and/or
4212           // introduce
4213           // object broker mechanism.
4214           final Vector<JMenu> wsmenu = new Vector<>();
4215           final IProgressIndicator af = me;
4216
4217           /*
4218            * do not i18n these strings - they are hard-coded in class
4219            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4220            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4221            */
4222           final JMenu msawsmenu = new JMenu("Alignment");
4223           final JMenu secstrmenu = new JMenu(
4224                   "Secondary Structure Prediction");
4225           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4226           final JMenu analymenu = new JMenu("Analysis");
4227           final JMenu dismenu = new JMenu("Protein Disorder");
4228           // JAL-940 - only show secondary structure prediction services from
4229           // the legacy server
4230           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4231               // &&
4232           Discoverer.services != null && (Discoverer.services.size() > 0))
4233           {
4234             // TODO: refactor to allow list of AbstractName/Handler bindings to
4235             // be
4236             // stored or retrieved from elsewhere
4237             // No MSAWS used any more:
4238             // Vector msaws = null; // (Vector)
4239             // Discoverer.services.get("MsaWS");
4240             Vector<ServiceHandle> secstrpr = Discoverer.services
4241                     .get("SecStrPred");
4242             if (secstrpr != null)
4243             {
4244               // Add any secondary structure prediction services
4245               for (int i = 0, j = secstrpr.size(); i < j; i++)
4246               {
4247                 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4248                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4249                         .getServiceClient(sh);
4250                 int p = secstrmenu.getItemCount();
4251                 impl.attachWSMenuEntry(secstrmenu, me);
4252                 int q = secstrmenu.getItemCount();
4253                 for (int litm = p; litm < q; litm++)
4254                 {
4255                   legacyItems.add(secstrmenu.getItem(litm));
4256                 }
4257               }
4258             }
4259           }
4260
4261           // Add all submenus in the order they should appear on the web
4262           // services menu
4263           wsmenu.add(msawsmenu);
4264           wsmenu.add(secstrmenu);
4265           wsmenu.add(dismenu);
4266           wsmenu.add(analymenu);
4267           // No search services yet
4268           // wsmenu.add(seqsrchmenu);
4269
4270           javax.swing.SwingUtilities.invokeLater(new Runnable()
4271           {
4272             @Override
4273             public void run()
4274             {
4275               try
4276               {
4277                 webService.removeAll();
4278                 // first, add discovered services onto the webservices menu
4279                 if (wsmenu.size() > 0)
4280                 {
4281                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4282                   {
4283                     webService.add(wsmenu.get(i));
4284                   }
4285                 }
4286                 else
4287                 {
4288                   webService.add(me.webServiceNoServices);
4289                 }
4290                 // TODO: move into separate menu builder class.
4291                 {
4292                   // logic for 2.11.1.4 is
4293                   // always look to see if there is a discover. if there isn't
4294                   // we can't show any Jws2 services
4295                   // if there are services available, show them - regardless of
4296                   // the 'show JWS2 preference'
4297                   // if the discoverer is running then say so
4298                   // otherwise offer to trigger discovery if 'show JWS2' is not
4299                   // enabled
4300                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4301                   if (jws2servs != null)
4302                   {
4303                     if (jws2servs.hasServices())
4304                     {
4305                       jws2servs.attachWSMenuEntry(webService, me);
4306                       for (Jws2Instance sv : jws2servs.getServices())
4307                       {
4308                         if (sv.description.toLowerCase(Locale.ROOT)
4309                                 .contains("jpred"))
4310                         {
4311                           for (JMenuItem jmi : legacyItems)
4312                           {
4313                             jmi.setVisible(false);
4314                           }
4315                         }
4316                       }
4317                     }
4318
4319                     if (jws2servs.isRunning())
4320                     {
4321                       JMenuItem tm = new JMenuItem(
4322                               "Still discovering JABA Services");
4323                       tm.setEnabled(false);
4324                       webService.add(tm);
4325                     }
4326                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4327                     {
4328                       JMenuItem enableJws2 = new JMenuItem(
4329                               "Discover Web Services");
4330                       enableJws2.setToolTipText(
4331                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4332                       enableJws2.setEnabled(true);
4333                       enableJws2.addActionListener(new ActionListener()
4334                       {
4335
4336                         @Override
4337                         public void actionPerformed(ActionEvent e)
4338                         {
4339                           // start service discoverer, but ignore preference
4340                           Desktop.instance.startServiceDiscovery(false,
4341                                   true);
4342                         }
4343                       });
4344                       webService.add(enableJws2);
4345                     }
4346                   }
4347                 }
4348                 build_urlServiceMenu(me.webService);
4349                 build_fetchdbmenu(webService);
4350                 for (JMenu item : wsmenu)
4351                 {
4352                   if (item.getItemCount() == 0)
4353                   {
4354                     item.setEnabled(false);
4355                   }
4356                   else
4357                   {
4358                     item.setEnabled(true);
4359                   }
4360                 }
4361               } catch (Exception e)
4362               {
4363                 Console.debug(
4364                         "Exception during web service menu building process.",
4365                         e);
4366               }
4367             }
4368           });
4369         } catch (Exception e)
4370         {
4371         }
4372         buildingMenu = false;
4373       }
4374     }).start();
4375
4376   }
4377
4378   /**
4379    * construct any groupURL type service menu entries.
4380    *
4381    * @param webService
4382    */
4383   protected void build_urlServiceMenu(JMenu webService)
4384   {
4385     // TODO: remove this code when 2.7 is released
4386     // DEBUG - alignmentView
4387     /*
4388      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4389      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4390      *
4391      * @Override public void actionPerformed(ActionEvent e) {
4392      * jalview.datamodel.AlignmentView
4393      * .testSelectionViews(af.viewport.getAlignment(),
4394      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4395      *
4396      * }); webService.add(testAlView);
4397      */
4398     // TODO: refactor to RestClient discoverer and merge menu entries for
4399     // rest-style services with other types of analysis/calculation service
4400     // SHmmr test client - still being implemented.
4401     // DEBUG - alignmentView
4402
4403     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4404             .getRestClients())
4405     {
4406       client.attachWSMenuEntry(
4407               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4408               this);
4409     }
4410   }
4411
4412   /**
4413    * Searches the alignment sequences for xRefs and builds the Show
4414    * Cross-References menu (formerly called Show Products), with database
4415    * sources for which cross-references are found (protein sources for a
4416    * nucleotide alignment and vice versa)
4417    *
4418    * @return true if Show Cross-references menu should be enabled
4419    */
4420   public boolean canShowProducts()
4421   {
4422     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4423     AlignmentI dataset = viewport.getAlignment().getDataset();
4424
4425     showProducts.removeAll();
4426     final boolean dna = viewport.getAlignment().isNucleotide();
4427
4428     if (seqs == null || seqs.length == 0)
4429     {
4430       // nothing to see here.
4431       return false;
4432     }
4433
4434     boolean showp = false;
4435     try
4436     {
4437       List<String> ptypes = new CrossRef(seqs, dataset)
4438               .findXrefSourcesForSequences(dna);
4439
4440       for (final String source : ptypes)
4441       {
4442         showp = true;
4443         final AlignFrame af = this;
4444         JMenuItem xtype = new JMenuItem(source);
4445         xtype.addActionListener(new ActionListener()
4446         {
4447           @Override
4448           public void actionPerformed(ActionEvent e)
4449           {
4450             showProductsFor(af.viewport.getSequenceSelection(), dna,
4451                     source);
4452           }
4453         });
4454         showProducts.add(xtype);
4455       }
4456       showProducts.setVisible(showp);
4457       showProducts.setEnabled(showp);
4458     } catch (Exception e)
4459     {
4460       Console.warn(
4461               "canShowProducts threw an exception - please report to help@jalview.org",
4462               e);
4463       return false;
4464     }
4465     return showp;
4466   }
4467
4468   /**
4469    * Finds and displays cross-references for the selected sequences (protein
4470    * products for nucleotide sequences, dna coding sequences for peptides).
4471    *
4472    * @param sel
4473    *          the sequences to show cross-references for
4474    * @param dna
4475    *          true if from a nucleotide alignment (so showing proteins)
4476    * @param source
4477    *          the database to show cross-references for
4478    */
4479   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4480           final String source)
4481   {
4482     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4483             .start();
4484   }
4485
4486   /**
4487    * Construct and display a new frame containing the translation of this
4488    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4489    */
4490   @Override
4491   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4492   {
4493     AlignmentI al = null;
4494     try
4495     {
4496       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4497
4498       al = dna.translateCdna(codeTable);
4499     } catch (Exception ex)
4500     {
4501       Console.error("Exception during translation. Please report this !",
4502               ex);
4503       final String msg = MessageManager.getString(
4504               "label.error_when_translating_sequences_submit_bug_report");
4505       final String errorTitle = MessageManager
4506               .getString("label.implementation_error")
4507               + MessageManager.getString("label.translation_failed");
4508       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4509               JvOptionPane.ERROR_MESSAGE);
4510       return;
4511     }
4512     if (al == null || al.getHeight() == 0)
4513     {
4514       final String msg = MessageManager.getString(
4515               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4516       final String errorTitle = MessageManager
4517               .getString("label.translation_failed");
4518       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4519               JvOptionPane.WARNING_MESSAGE);
4520     }
4521     else
4522     {
4523       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4524       af.setFileFormat(this.currentFileFormat);
4525       final String newTitle = MessageManager
4526               .formatMessage("label.translation_of_params", new Object[]
4527               { this.getTitle(), codeTable.getId() });
4528       af.setTitle(newTitle);
4529       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4530       {
4531         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4532         viewport.openSplitFrame(af, new Alignment(seqs));
4533       }
4534       else
4535       {
4536         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4537                 DEFAULT_HEIGHT);
4538       }
4539     }
4540   }
4541
4542   /**
4543    * Set the file format
4544    *
4545    * @param format
4546    */
4547   public void setFileFormat(FileFormatI format)
4548   {
4549     this.currentFileFormat = format;
4550   }
4551
4552   /**
4553    * Try to load a features file onto the alignment.
4554    *
4555    * @param file
4556    *          contents or path to retrieve file or a File object
4557    * @param sourceType
4558    *          access mode of file (see jalview.io.AlignFile)
4559    * @return true if features file was parsed correctly.
4560    */
4561   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4562   {
4563     // BH 2018
4564     return avc.parseFeaturesFile(file, sourceType,
4565             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4566
4567   }
4568
4569   @Override
4570   public void refreshFeatureUI(boolean enableIfNecessary)
4571   {
4572     // note - currently this is only still here rather than in the controller
4573     // because of the featureSettings hard reference that is yet to be
4574     // abstracted
4575     if (enableIfNecessary)
4576     {
4577       viewport.setShowSequenceFeatures(true);
4578       showSeqFeatures.setSelected(true);
4579     }
4580
4581   }
4582
4583   @Override
4584   public void dragEnter(DropTargetDragEvent evt)
4585   {
4586   }
4587
4588   @Override
4589   public void dragExit(DropTargetEvent evt)
4590   {
4591   }
4592
4593   @Override
4594   public void dragOver(DropTargetDragEvent evt)
4595   {
4596   }
4597
4598   @Override
4599   public void dropActionChanged(DropTargetDragEvent evt)
4600   {
4601   }
4602
4603   @Override
4604   public void drop(DropTargetDropEvent evt)
4605   {
4606     // JAL-1552 - acceptDrop required before getTransferable call for
4607     // Java's Transferable for native dnd
4608     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4609     Transferable t = evt.getTransferable();
4610
4611     final AlignFrame thisaf = this;
4612     final List<Object> files = new ArrayList<>();
4613     List<DataSourceType> protocols = new ArrayList<>();
4614
4615     try
4616     {
4617       Desktop.transferFromDropTarget(files, protocols, evt, t);
4618     } catch (Exception e)
4619     {
4620       e.printStackTrace();
4621     }
4622     if (files != null)
4623     {
4624       new Thread(new Runnable()
4625       {
4626         @Override
4627         public void run()
4628         {
4629           try
4630           {
4631             // check to see if any of these files have names matching sequences
4632             // in
4633             // the alignment
4634             SequenceIdMatcher idm = new SequenceIdMatcher(
4635                     viewport.getAlignment().getSequencesArray());
4636             /**
4637              * Object[] { String,SequenceI}
4638              */
4639             ArrayList<Object[]> filesmatched = new ArrayList<>();
4640             ArrayList<Object> filesnotmatched = new ArrayList<>();
4641             for (int i = 0; i < files.size(); i++)
4642             {
4643               // BH 2018
4644               Object file = files.get(i);
4645               String fileName = file.toString();
4646               String pdbfn = "";
4647               DataSourceType protocol = (file instanceof File
4648                       ? DataSourceType.FILE
4649                       : FormatAdapter.checkProtocol(fileName));
4650               if (protocol == DataSourceType.FILE)
4651               {
4652                 File fl;
4653                 if (file instanceof File)
4654                 {
4655                   fl = (File) file;
4656                   Platform.cacheFileData(fl);
4657                 }
4658                 else
4659                 {
4660                   fl = new File(fileName);
4661                 }
4662                 pdbfn = fl.getName();
4663               }
4664               else if (protocol == DataSourceType.URL)
4665               {
4666                 URL url = new URL(fileName);
4667                 pdbfn = url.getFile();
4668               }
4669               if (pdbfn.length() > 0)
4670               {
4671                 // attempt to find a match in the alignment
4672                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4673                 int l = 0, c = pdbfn.indexOf(".");
4674                 while (mtch == null && c != -1)
4675                 {
4676                   do
4677                   {
4678                     l = c;
4679                   } while ((c = pdbfn.indexOf(".", l)) > l);
4680                   if (l > -1)
4681                   {
4682                     pdbfn = pdbfn.substring(0, l);
4683                   }
4684                   mtch = idm.findAllIdMatches(pdbfn);
4685                 }
4686                 if (mtch != null)
4687                 {
4688                   FileFormatI type;
4689                   try
4690                   {
4691                     type = new IdentifyFile().identify(file, protocol);
4692                   } catch (Exception ex)
4693                   {
4694                     type = null;
4695                   }
4696                   if (type != null && type.isStructureFile())
4697                   {
4698                     filesmatched.add(new Object[] { file, protocol, mtch });
4699                     continue;
4700                   }
4701                 }
4702                 // File wasn't named like one of the sequences or wasn't a PDB
4703                 // file.
4704                 filesnotmatched.add(file);
4705               }
4706             }
4707             int assocfiles = 0;
4708             if (filesmatched.size() > 0)
4709             {
4710               boolean autoAssociate = Cache
4711                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4712               if (!autoAssociate)
4713               {
4714                 String msg = MessageManager.formatMessage(
4715                         "label.automatically_associate_structure_files_with_sequences_same_name",
4716                         new Object[]
4717                         { Integer.valueOf(filesmatched.size())
4718                                 .toString() });
4719                 String ttl = MessageManager.getString(
4720                         "label.automatically_associate_structure_files_by_name");
4721                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4722                         ttl, JvOptionPane.YES_NO_OPTION);
4723                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4724               }
4725               if (autoAssociate)
4726               {
4727                 for (Object[] fm : filesmatched)
4728                 {
4729                   // try and associate
4730                   // TODO: may want to set a standard ID naming formalism for
4731                   // associating PDB files which have no IDs.
4732                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4733                   {
4734                     PDBEntry pe = new AssociatePdbFileWithSeq()
4735                             .associatePdbWithSeq(fm[0].toString(),
4736                                     (DataSourceType) fm[1], toassoc, false,
4737                                     Desktop.instance);
4738                     if (pe != null)
4739                     {
4740                       System.err.println("Associated file : "
4741                               + (fm[0].toString()) + " with "
4742                               + toassoc.getDisplayId(true));
4743                       assocfiles++;
4744                     }
4745                   }
4746                   // TODO: do we need to update overview ? only if features are
4747                   // shown I guess
4748                   alignPanel.paintAlignment(true, false);
4749                 }
4750               }
4751               else
4752               {
4753                 /*
4754                  * add declined structures as sequences
4755                  */
4756                 for (Object[] o : filesmatched)
4757                 {
4758                   filesnotmatched.add(o[0]);
4759                 }
4760               }
4761             }
4762             if (filesnotmatched.size() > 0)
4763             {
4764               if (assocfiles > 0 && (Cache.getDefault(
4765                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4766                       || JvOptionPane.showConfirmDialog(thisaf,
4767                               "<html>" + MessageManager.formatMessage(
4768                                       "label.ignore_unmatched_dropped_files_info",
4769                                       new Object[]
4770                                       { Integer.valueOf(
4771                                               filesnotmatched.size())
4772                                               .toString() })
4773                                       + "</html>",
4774                               MessageManager.getString(
4775                                       "label.ignore_unmatched_dropped_files"),
4776                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4777               {
4778                 return;
4779               }
4780               for (Object fn : filesnotmatched)
4781               {
4782                 loadJalviewDataFile(fn, null, null, null);
4783               }
4784
4785             }
4786           } catch (Exception ex)
4787           {
4788             ex.printStackTrace();
4789           }
4790         }
4791       }).start();
4792     }
4793   }
4794
4795   /**
4796    * Attempt to load a "dropped" file or URL string, by testing in turn for
4797    * <ul>
4798    * <li>an Annotation file</li>
4799    * <li>a JNet file</li>
4800    * <li>a features file</li>
4801    * <li>else try to interpret as an alignment file</li>
4802    * </ul>
4803    *
4804    * @param file
4805    *          either a filename or a URL string.
4806    */
4807   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4808           FileFormatI format, SequenceI assocSeq)
4809   {
4810     // BH 2018 was String file
4811     try
4812     {
4813       if (sourceType == null)
4814       {
4815         sourceType = FormatAdapter.checkProtocol(file);
4816       }
4817       // if the file isn't identified, or not positively identified as some
4818       // other filetype (PFAM is default unidentified alignment file type) then
4819       // try to parse as annotation.
4820       boolean isAnnotation = (format == null
4821               || FileFormat.Pfam.equals(format))
4822                       ? new AnnotationFile().annotateAlignmentView(viewport,
4823                               file, sourceType)
4824                       : false;
4825
4826       if (!isAnnotation)
4827       {
4828         // first see if its a T-COFFEE score file
4829         TCoffeeScoreFile tcf = null;
4830         try
4831         {
4832           tcf = new TCoffeeScoreFile(file, sourceType);
4833           if (tcf.isValid())
4834           {
4835             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4836             {
4837               buildColourMenu();
4838               changeColour(
4839                       new TCoffeeColourScheme(viewport.getAlignment()));
4840               isAnnotation = true;
4841               setStatus(MessageManager.getString(
4842                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4843             }
4844             else
4845             {
4846               // some problem - if no warning its probable that the ID matching
4847               // process didn't work
4848               JvOptionPane.showMessageDialog(Desktop.desktop,
4849                       tcf.getWarningMessage() == null
4850                               ? MessageManager.getString(
4851                                       "label.check_file_matches_sequence_ids_alignment")
4852                               : tcf.getWarningMessage(),
4853                       MessageManager.getString(
4854                               "label.problem_reading_tcoffee_score_file"),
4855                       JvOptionPane.WARNING_MESSAGE);
4856             }
4857           }
4858           else
4859           {
4860             tcf = null;
4861           }
4862         } catch (Exception x)
4863         {
4864           Console.debug(
4865                   "Exception when processing data source as T-COFFEE score file",
4866                   x);
4867           tcf = null;
4868         }
4869         if (tcf == null)
4870         {
4871           // try to see if its a JNet 'concise' style annotation file *before*
4872           // we
4873           // try to parse it as a features file
4874           if (format == null)
4875           {
4876             format = new IdentifyFile().identify(file, sourceType);
4877           }
4878           if (FileFormat.ScoreMatrix == format)
4879           {
4880             ScoreMatrixFile sm = new ScoreMatrixFile(
4881                     new FileParse(file, sourceType));
4882             sm.parse();
4883             // todo: i18n this message
4884             setStatus(MessageManager.formatMessage(
4885                     "label.successfully_loaded_matrix",
4886                     sm.getMatrixName()));
4887           }
4888           else if (FileFormat.Jnet.equals(format))
4889           {
4890             JPredFile predictions = new JPredFile(file, sourceType);
4891             new JnetAnnotationMaker();
4892             JnetAnnotationMaker.add_annotation(predictions,
4893                     viewport.getAlignment(), 0, false);
4894             viewport.getAlignment().setupJPredAlignment();
4895             isAnnotation = true;
4896           }
4897           // else if (IdentifyFile.FeaturesFile.equals(format))
4898           else if (FileFormat.Features.equals(format))
4899           {
4900             if (parseFeaturesFile(file, sourceType))
4901             {
4902               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4903               if (splitFrame != null)
4904               {
4905                 splitFrame.repaint();
4906               }
4907               else
4908               {
4909                 alignPanel.paintAlignment(true, true);
4910               }
4911             }
4912           }
4913           else
4914           {
4915             new FileLoader().LoadFile(viewport, file, sourceType, format);
4916           }
4917         }
4918       }
4919       if (isAnnotation)
4920       {
4921
4922         alignPanel.adjustAnnotationHeight();
4923         viewport.updateSequenceIdColours();
4924         buildSortByAnnotationScoresMenu();
4925         alignPanel.paintAlignment(true, true);
4926       }
4927     } catch (Exception ex)
4928     {
4929       ex.printStackTrace();
4930     } catch (OutOfMemoryError oom)
4931     {
4932       try
4933       {
4934         System.gc();
4935       } catch (Exception x)
4936       {
4937       }
4938       new OOMWarning(
4939               "loading data "
4940                       + (sourceType != null
4941                               ? (sourceType == DataSourceType.PASTE
4942                                       ? "from clipboard."
4943                                       : "using " + sourceType + " from "
4944                                               + file)
4945                               : ".")
4946                       + (format != null
4947                               ? "(parsing as '" + format + "' file)"
4948                               : ""),
4949               oom, Desktop.desktop);
4950     }
4951   }
4952
4953   /**
4954    * Method invoked by the ChangeListener on the tabbed pane, in other words
4955    * when a different tabbed pane is selected by the user or programmatically.
4956    */
4957   @Override
4958   public void tabSelectionChanged(int index)
4959   {
4960     if (index > -1)
4961     {
4962       alignPanel = alignPanels.get(index);
4963       viewport = alignPanel.av;
4964       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4965       setMenusFromViewport(viewport);
4966       if (featureSettings != null && featureSettings.isOpen()
4967               && featureSettings.fr.getViewport() != viewport)
4968       {
4969         if (viewport.isShowSequenceFeatures())
4970         {
4971           // refresh the featureSettings to reflect UI change
4972           showFeatureSettingsUI();
4973         }
4974         else
4975         {
4976           // close feature settings for this view.
4977           featureSettings.close();
4978         }
4979       }
4980
4981     }
4982
4983     /*
4984      * 'focus' any colour slider that is open to the selected viewport
4985      */
4986     if (viewport.getConservationSelected())
4987     {
4988       SliderPanel.setConservationSlider(alignPanel,
4989               viewport.getResidueShading(), alignPanel.getViewName());
4990     }
4991     else
4992     {
4993       SliderPanel.hideConservationSlider();
4994     }
4995     if (viewport.getAbovePIDThreshold())
4996     {
4997       SliderPanel.setPIDSliderSource(alignPanel,
4998               viewport.getResidueShading(), alignPanel.getViewName());
4999     }
5000     else
5001     {
5002       SliderPanel.hidePIDSlider();
5003     }
5004
5005     /*
5006      * If there is a frame linked to this one in a SplitPane, switch it to the
5007      * same view tab index. No infinite recursion of calls should happen, since
5008      * tabSelectionChanged() should not get invoked on setting the selected
5009      * index to an unchanged value. Guard against setting an invalid index
5010      * before the new view peer tab has been created.
5011      */
5012     final AlignViewportI peer = viewport.getCodingComplement();
5013     if (peer != null)
5014     {
5015       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5016               .getAlignPanel().alignFrame;
5017       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5018       {
5019         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5020       }
5021     }
5022   }
5023
5024   /**
5025    * On right mouse click on view tab, prompt for and set new view name.
5026    */
5027   @Override
5028   public void tabbedPane_mousePressed(MouseEvent e)
5029   {
5030     if (e.isPopupTrigger())
5031     {
5032       String msg = MessageManager.getString("label.enter_view_name");
5033       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5034       String reply = JvOptionPane.showInputDialog(msg, ttl);
5035
5036       if (reply != null)
5037       {
5038         viewport.setViewName(reply);
5039         // TODO warn if reply is in getExistingViewNames()?
5040         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5041       }
5042     }
5043   }
5044
5045   public AlignViewport getCurrentView()
5046   {
5047     return viewport;
5048   }
5049
5050   /**
5051    * Open the dialog for regex description parsing.
5052    */
5053   @Override
5054   protected void extractScores_actionPerformed(ActionEvent e)
5055   {
5056     ParseProperties pp = new jalview.analysis.ParseProperties(
5057             viewport.getAlignment());
5058     // TODO: verify regex and introduce GUI dialog for version 2.5
5059     // if (pp.getScoresFromDescription("col", "score column ",
5060     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5061     // true)>0)
5062     if (pp.getScoresFromDescription("description column",
5063             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5064     {
5065       buildSortByAnnotationScoresMenu();
5066     }
5067   }
5068
5069   /*
5070    * (non-Javadoc)
5071    *
5072    * @see
5073    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5074    * )
5075    */
5076   @Override
5077   protected void showDbRefs_actionPerformed(ActionEvent e)
5078   {
5079     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5080   }
5081
5082   /*
5083    * (non-Javadoc)
5084    *
5085    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5086    * ActionEvent)
5087    */
5088   @Override
5089   protected void showNpFeats_actionPerformed(ActionEvent e)
5090   {
5091     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5092   }
5093
5094   /**
5095    * find the viewport amongst the tabs in this alignment frame and close that
5096    * tab
5097    *
5098    * @param av
5099    */
5100   public boolean closeView(AlignViewportI av)
5101   {
5102     if (viewport == av)
5103     {
5104       this.closeMenuItem_actionPerformed(false);
5105       return true;
5106     }
5107     Component[] comp = tabbedPane.getComponents();
5108     for (int i = 0; comp != null && i < comp.length; i++)
5109     {
5110       if (comp[i] instanceof AlignmentPanel)
5111       {
5112         if (((AlignmentPanel) comp[i]).av == av)
5113         {
5114           // close the view.
5115           closeView((AlignmentPanel) comp[i]);
5116           return true;
5117         }
5118       }
5119     }
5120     return false;
5121   }
5122
5123   protected void build_fetchdbmenu(JMenu webService)
5124   {
5125     // Temporary hack - DBRef Fetcher always top level ws entry.
5126     // TODO We probably want to store a sequence database checklist in
5127     // preferences and have checkboxes.. rather than individual sources selected
5128     // here
5129     final JMenu rfetch = new JMenu(
5130             MessageManager.getString("action.fetch_db_references"));
5131     rfetch.setToolTipText(MessageManager.getString(
5132             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5133     webService.add(rfetch);
5134
5135     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5136             MessageManager.getString("option.trim_retrieved_seqs"));
5137     trimrs.setToolTipText(
5138             MessageManager.getString("label.trim_retrieved_sequences"));
5139     trimrs.setSelected(
5140             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5141     trimrs.addActionListener(new ActionListener()
5142     {
5143       @Override
5144       public void actionPerformed(ActionEvent e)
5145       {
5146         trimrs.setSelected(trimrs.isSelected());
5147         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5148                 Boolean.valueOf(trimrs.isSelected()).toString());
5149       }
5150     });
5151     rfetch.add(trimrs);
5152     JMenuItem fetchr = new JMenuItem(
5153             MessageManager.getString("label.standard_databases"));
5154     fetchr.setToolTipText(
5155             MessageManager.getString("label.fetch_embl_uniprot"));
5156     fetchr.addActionListener(new ActionListener()
5157     {
5158
5159       @Override
5160       public void actionPerformed(ActionEvent e)
5161       {
5162         new Thread(new Runnable()
5163         {
5164           @Override
5165           public void run()
5166           {
5167             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5168                     .getAlignment().isNucleotide();
5169             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5170                     alignPanel.av.getSequenceSelection(),
5171                     alignPanel.alignFrame, null,
5172                     alignPanel.alignFrame.featureSettings, isNucleotide);
5173             dbRefFetcher.addListener(new FetchFinishedListenerI()
5174             {
5175               @Override
5176               public void finished()
5177               {
5178
5179                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5180                         .getFeatureSettingsModels())
5181                 {
5182
5183                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5184                 }
5185                 AlignFrame.this.setMenusForViewport();
5186               }
5187             });
5188             dbRefFetcher.fetchDBRefs(false);
5189           }
5190         }).start();
5191
5192       }
5193
5194     });
5195     rfetch.add(fetchr);
5196     new Thread(new Runnable()
5197     {
5198       @Override
5199       public void run()
5200       {
5201         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5202                 .getSequenceFetcherSingleton();
5203         javax.swing.SwingUtilities.invokeLater(new Runnable()
5204         {
5205           @Override
5206           public void run()
5207           {
5208             String[] dbclasses = sf.getNonAlignmentSources();
5209             List<DbSourceProxy> otherdb;
5210             JMenu dfetch = new JMenu();
5211             JMenu ifetch = new JMenu();
5212             JMenuItem fetchr = null;
5213             int comp = 0, icomp = 0, mcomp = 15;
5214             String mname = null;
5215             int dbi = 0;
5216             for (String dbclass : dbclasses)
5217             {
5218               otherdb = sf.getSourceProxy(dbclass);
5219               // add a single entry for this class, or submenu allowing 'fetch
5220               // all' or pick one
5221               if (otherdb == null || otherdb.size() < 1)
5222               {
5223                 continue;
5224               }
5225               if (mname == null)
5226               {
5227                 mname = "From " + dbclass;
5228               }
5229               if (otherdb.size() == 1)
5230               {
5231                 final DbSourceProxy[] dassource = otherdb
5232                         .toArray(new DbSourceProxy[0]);
5233                 DbSourceProxy src = otherdb.get(0);
5234                 fetchr = new JMenuItem(src.getDbSource());
5235                 fetchr.addActionListener(new ActionListener()
5236                 {
5237
5238                   @Override
5239                   public void actionPerformed(ActionEvent e)
5240                   {
5241                     new Thread(new Runnable()
5242                     {
5243
5244                       @Override
5245                       public void run()
5246                       {
5247                         boolean isNucleotide = alignPanel.alignFrame
5248                                 .getViewport().getAlignment()
5249                                 .isNucleotide();
5250                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5251                                 alignPanel.av.getSequenceSelection(),
5252                                 alignPanel.alignFrame, dassource,
5253                                 alignPanel.alignFrame.featureSettings,
5254                                 isNucleotide);
5255                         dbRefFetcher
5256                                 .addListener(new FetchFinishedListenerI()
5257                                 {
5258                                   @Override
5259                                   public void finished()
5260                                   {
5261                                     FeatureSettingsModelI srcSettings = dassource[0]
5262                                             .getFeatureColourScheme();
5263                                     alignPanel.av.mergeFeaturesStyle(
5264                                             srcSettings);
5265                                     AlignFrame.this.setMenusForViewport();
5266                                   }
5267                                 });
5268                         dbRefFetcher.fetchDBRefs(false);
5269                       }
5270                     }).start();
5271                   }
5272
5273                 });
5274                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5275                         MessageManager.formatMessage(
5276                                 "label.fetch_retrieve_from", new Object[]
5277                                 { src.getDbName() })));
5278                 dfetch.add(fetchr);
5279                 comp++;
5280               }
5281               else
5282               {
5283                 final DbSourceProxy[] dassource = otherdb
5284                         .toArray(new DbSourceProxy[0]);
5285                 // fetch all entry
5286                 DbSourceProxy src = otherdb.get(0);
5287                 fetchr = new JMenuItem(MessageManager
5288                         .formatMessage("label.fetch_all_param", new Object[]
5289                         { src.getDbSource() }));
5290                 fetchr.addActionListener(new ActionListener()
5291                 {
5292                   @Override
5293                   public void actionPerformed(ActionEvent e)
5294                   {
5295                     new Thread(new Runnable()
5296                     {
5297
5298                       @Override
5299                       public void run()
5300                       {
5301                         boolean isNucleotide = alignPanel.alignFrame
5302                                 .getViewport().getAlignment()
5303                                 .isNucleotide();
5304                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5305                                 alignPanel.av.getSequenceSelection(),
5306                                 alignPanel.alignFrame, dassource,
5307                                 alignPanel.alignFrame.featureSettings,
5308                                 isNucleotide);
5309                         dbRefFetcher
5310                                 .addListener(new FetchFinishedListenerI()
5311                                 {
5312                                   @Override
5313                                   public void finished()
5314                                   {
5315                                     AlignFrame.this.setMenusForViewport();
5316                                   }
5317                                 });
5318                         dbRefFetcher.fetchDBRefs(false);
5319                       }
5320                     }).start();
5321                   }
5322                 });
5323
5324                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5325                         MessageManager.formatMessage(
5326                                 "label.fetch_retrieve_from_all_sources",
5327                                 new Object[]
5328                                 { Integer.valueOf(otherdb.size())
5329                                         .toString(),
5330                                     src.getDbSource(), src.getDbName() })));
5331                 dfetch.add(fetchr);
5332                 comp++;
5333                 // and then build the rest of the individual menus
5334                 ifetch = new JMenu(MessageManager.formatMessage(
5335                         "label.source_from_db_source", new Object[]
5336                         { src.getDbSource() }));
5337                 icomp = 0;
5338                 String imname = null;
5339                 int i = 0;
5340                 for (DbSourceProxy sproxy : otherdb)
5341                 {
5342                   String dbname = sproxy.getDbName();
5343                   String sname = dbname.length() > 5
5344                           ? dbname.substring(0, 5) + "..."
5345                           : dbname;
5346                   String msname = dbname.length() > 10
5347                           ? dbname.substring(0, 10) + "..."
5348                           : dbname;
5349                   if (imname == null)
5350                   {
5351                     imname = MessageManager
5352                             .formatMessage("label.from_msname", new Object[]
5353                             { sname });
5354                   }
5355                   fetchr = new JMenuItem(msname);
5356                   final DbSourceProxy[] dassrc = { sproxy };
5357                   fetchr.addActionListener(new ActionListener()
5358                   {
5359
5360                     @Override
5361                     public void actionPerformed(ActionEvent e)
5362                     {
5363                       new Thread(new Runnable()
5364                       {
5365
5366                         @Override
5367                         public void run()
5368                         {
5369                           boolean isNucleotide = alignPanel.alignFrame
5370                                   .getViewport().getAlignment()
5371                                   .isNucleotide();
5372                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5373                                   alignPanel.av.getSequenceSelection(),
5374                                   alignPanel.alignFrame, dassrc,
5375                                   alignPanel.alignFrame.featureSettings,
5376                                   isNucleotide);
5377                           dbRefFetcher
5378                                   .addListener(new FetchFinishedListenerI()
5379                                   {
5380                                     @Override
5381                                     public void finished()
5382                                     {
5383                                       AlignFrame.this.setMenusForViewport();
5384                                     }
5385                                   });
5386                           dbRefFetcher.fetchDBRefs(false);
5387                         }
5388                       }).start();
5389                     }
5390
5391                   });
5392                   fetchr.setToolTipText(
5393                           "<html>" + MessageManager.formatMessage(
5394                                   "label.fetch_retrieve_from", new Object[]
5395                                   { dbname }));
5396                   ifetch.add(fetchr);
5397                   ++i;
5398                   if (++icomp >= mcomp || i == (otherdb.size()))
5399                   {
5400                     ifetch.setText(MessageManager.formatMessage(
5401                             "label.source_to_target", imname, sname));
5402                     dfetch.add(ifetch);
5403                     ifetch = new JMenu();
5404                     imname = null;
5405                     icomp = 0;
5406                     comp++;
5407                   }
5408                 }
5409               }
5410               ++dbi;
5411               if (comp >= mcomp || dbi >= (dbclasses.length))
5412               {
5413                 dfetch.setText(MessageManager.formatMessage(
5414                         "label.source_to_target", mname, dbclass));
5415                 rfetch.add(dfetch);
5416                 dfetch = new JMenu();
5417                 mname = null;
5418                 comp = 0;
5419               }
5420             }
5421           }
5422         });
5423       }
5424     }).start();
5425
5426   }
5427
5428   /**
5429    * Left justify the whole alignment.
5430    */
5431   @Override
5432   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5433   {
5434     AlignmentI al = viewport.getAlignment();
5435     al.justify(false);
5436     viewport.firePropertyChange("alignment", null, al);
5437   }
5438
5439   /**
5440    * Right justify the whole alignment.
5441    */
5442   @Override
5443   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5444   {
5445     AlignmentI al = viewport.getAlignment();
5446     al.justify(true);
5447     viewport.firePropertyChange("alignment", null, al);
5448   }
5449
5450   @Override
5451   public void setShowSeqFeatures(boolean b)
5452   {
5453     showSeqFeatures.setSelected(b);
5454     viewport.setShowSequenceFeatures(b);
5455   }
5456
5457   /*
5458    * (non-Javadoc)
5459    *
5460    * @see
5461    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5462    * awt.event.ActionEvent)
5463    */
5464   @Override
5465   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5466   {
5467     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5468     alignPanel.paintAlignment(false, false);
5469   }
5470
5471   /*
5472    * (non-Javadoc)
5473    *
5474    * @see
5475    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5476    * .ActionEvent)
5477    */
5478   @Override
5479   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5480   {
5481     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5482     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5483
5484   }
5485
5486   /*
5487    * (non-Javadoc)
5488    *
5489    * @see
5490    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5491    * .event.ActionEvent)
5492    */
5493   @Override
5494   protected void showGroupConservation_actionPerformed(ActionEvent e)
5495   {
5496     viewport.setShowGroupConservation(showGroupConservation.getState());
5497     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5498   }
5499
5500   /*
5501    * (non-Javadoc)
5502    *
5503    * @see
5504    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5505    * .event.ActionEvent)
5506    */
5507   @Override
5508   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5509   {
5510     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5511     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5512   }
5513
5514   /*
5515    * (non-Javadoc)
5516    *
5517    * @see
5518    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5519    * .event.ActionEvent)
5520    */
5521   @Override
5522   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5523   {
5524     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5525     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5526   }
5527
5528   @Override
5529   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5530   {
5531     showSequenceLogo.setState(true);
5532     viewport.setShowSequenceLogo(true);
5533     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5534     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5535   }
5536
5537   @Override
5538   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5539   {
5540     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5541   }
5542
5543   /*
5544    * (non-Javadoc)
5545    *
5546    * @see
5547    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5548    * .event.ActionEvent)
5549    */
5550   @Override
5551   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5552   {
5553     if (avc.makeGroupsFromSelection())
5554     {
5555       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5556       alignPanel.updateAnnotation();
5557       alignPanel.paintAlignment(true,
5558               viewport.needToUpdateStructureViews());
5559     }
5560   }
5561
5562   public void clearAlignmentSeqRep()
5563   {
5564     // TODO refactor alignmentseqrep to controller
5565     if (viewport.getAlignment().hasSeqrep())
5566     {
5567       viewport.getAlignment().setSeqrep(null);
5568       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5569       alignPanel.updateAnnotation();
5570       alignPanel.paintAlignment(true, true);
5571     }
5572   }
5573
5574   @Override
5575   protected void createGroup_actionPerformed(ActionEvent e)
5576   {
5577     if (avc.createGroup())
5578     {
5579       if (applyAutoAnnotationSettings.isSelected())
5580       {
5581         alignPanel.updateAnnotation(true, false);
5582       }
5583       alignPanel.alignmentChanged();
5584     }
5585   }
5586
5587   @Override
5588   protected void unGroup_actionPerformed(ActionEvent e)
5589   {
5590     if (avc.unGroup())
5591     {
5592       alignPanel.alignmentChanged();
5593     }
5594   }
5595
5596   /**
5597    * make the given alignmentPanel the currently selected tab
5598    *
5599    * @param alignmentPanel
5600    */
5601   public void setDisplayedView(AlignmentPanel alignmentPanel)
5602   {
5603     if (!viewport.getSequenceSetId()
5604             .equals(alignmentPanel.av.getSequenceSetId()))
5605     {
5606       throw new Error(MessageManager.getString(
5607               "error.implementation_error_cannot_show_view_alignment_frame"));
5608     }
5609     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5610             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5611     {
5612       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5613     }
5614   }
5615
5616   /**
5617    * Action on selection of menu options to Show or Hide annotations.
5618    *
5619    * @param visible
5620    * @param forSequences
5621    *          update sequence-related annotations
5622    * @param forAlignment
5623    *          update non-sequence-related annotations
5624    */
5625   @Override
5626   protected void setAnnotationsVisibility(boolean visible,
5627           boolean forSequences, boolean forAlignment)
5628   {
5629     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5630             .getAlignmentAnnotation();
5631     if (anns == null)
5632     {
5633       return;
5634     }
5635     for (AlignmentAnnotation aa : anns)
5636     {
5637       /*
5638        * don't display non-positional annotations on an alignment
5639        */
5640       if (aa.annotations == null)
5641       {
5642         continue;
5643       }
5644       boolean apply = (aa.sequenceRef == null && forAlignment)
5645               || (aa.sequenceRef != null && forSequences);
5646       if (apply)
5647       {
5648         aa.visible = visible;
5649       }
5650     }
5651     alignPanel.validateAnnotationDimensions(true);
5652     alignPanel.alignmentChanged();
5653   }
5654
5655   /**
5656    * Store selected annotation sort order for the view and repaint.
5657    */
5658   @Override
5659   protected void sortAnnotations_actionPerformed()
5660   {
5661     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5662     this.alignPanel.av
5663             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5664     alignPanel.paintAlignment(false, false);
5665   }
5666
5667   /**
5668    *
5669    * @return alignment panels in this alignment frame
5670    */
5671   public List<? extends AlignmentViewPanel> getAlignPanels()
5672   {
5673     // alignPanels is never null
5674     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5675     return alignPanels;
5676   }
5677
5678   /**
5679    * Open a new alignment window, with the cDNA associated with this (protein)
5680    * alignment, aligned as is the protein.
5681    */
5682   protected void viewAsCdna_actionPerformed()
5683   {
5684     // TODO no longer a menu action - refactor as required
5685     final AlignmentI alignment = getViewport().getAlignment();
5686     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5687     if (mappings == null)
5688     {
5689       return;
5690     }
5691     List<SequenceI> cdnaSeqs = new ArrayList<>();
5692     for (SequenceI aaSeq : alignment.getSequences())
5693     {
5694       for (AlignedCodonFrame acf : mappings)
5695       {
5696         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5697         if (dnaSeq != null)
5698         {
5699           /*
5700            * There is a cDNA mapping for this protein sequence - add to new
5701            * alignment. It will share the same dataset sequence as other mapped
5702            * cDNA (no new mappings need to be created).
5703            */
5704           final Sequence newSeq = new Sequence(dnaSeq);
5705           newSeq.setDatasetSequence(dnaSeq);
5706           cdnaSeqs.add(newSeq);
5707         }
5708       }
5709     }
5710     if (cdnaSeqs.size() == 0)
5711     {
5712       // show a warning dialog no mapped cDNA
5713       return;
5714     }
5715     AlignmentI cdna = new Alignment(
5716             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5717     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5718             AlignFrame.DEFAULT_HEIGHT);
5719     cdna.alignAs(alignment);
5720     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5721             + this.title;
5722     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5723             AlignFrame.DEFAULT_HEIGHT);
5724   }
5725
5726   /**
5727    * Set visibility of dna/protein complement view (available when shown in a
5728    * split frame).
5729    *
5730    * @param show
5731    */
5732   @Override
5733   protected void showComplement_actionPerformed(boolean show)
5734   {
5735     SplitContainerI sf = getSplitViewContainer();
5736     if (sf != null)
5737     {
5738       sf.setComplementVisible(this, show);
5739     }
5740   }
5741
5742   /**
5743    * Generate the reverse (optionally complemented) of the selected sequences,
5744    * and add them to the alignment
5745    */
5746   @Override
5747   protected void showReverse_actionPerformed(boolean complement)
5748   {
5749     AlignmentI al = null;
5750     try
5751     {
5752       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5753       al = dna.reverseCdna(complement);
5754       viewport.addAlignment(al, "");
5755       addHistoryItem(new EditCommand(
5756               MessageManager.getString("label.add_sequences"), Action.PASTE,
5757               al.getSequencesArray(), 0, al.getWidth(),
5758               viewport.getAlignment()));
5759     } catch (Exception ex)
5760     {
5761       System.err.println(ex.getMessage());
5762       return;
5763     }
5764   }
5765
5766   /**
5767    * Try to run a script in the Groovy console, having first ensured that this
5768    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5769    * be targeted at this alignment.
5770    */
5771   @Override
5772   protected void runGroovy_actionPerformed()
5773   {
5774     Jalview.setCurrentAlignFrame(this);
5775     groovy.ui.Console console = Desktop.getGroovyConsole();
5776     if (console != null)
5777     {
5778       try
5779       {
5780         console.runScript();
5781       } catch (Exception ex)
5782       {
5783         System.err.println((ex.toString()));
5784         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5785                 MessageManager.getString("label.couldnt_run_groovy_script"),
5786                 MessageManager.getString("label.groovy_support_failed"),
5787                 JvOptionPane.ERROR_MESSAGE);
5788       }
5789     }
5790     else
5791     {
5792       System.err.println("Can't run Groovy script as console not found");
5793     }
5794   }
5795
5796   /**
5797    * Hides columns containing (or not containing) a specified feature, provided
5798    * that would not leave all columns hidden
5799    *
5800    * @param featureType
5801    * @param columnsContaining
5802    * @return
5803    */
5804   public boolean hideFeatureColumns(String featureType,
5805           boolean columnsContaining)
5806   {
5807     boolean notForHiding = avc.markColumnsContainingFeatures(
5808             columnsContaining, false, false, featureType);
5809     if (notForHiding)
5810     {
5811       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5812               false, featureType))
5813       {
5814         getViewport().hideSelectedColumns();
5815         return true;
5816       }
5817     }
5818     return false;
5819   }
5820
5821   @Override
5822   protected void selectHighlightedColumns_actionPerformed(
5823           ActionEvent actionEvent)
5824   {
5825     // include key modifier check in case user selects from menu
5826     avc.markHighlightedColumns(
5827             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5828             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5829                     | ActionEvent.CTRL_MASK)) != 0);
5830   }
5831
5832   /**
5833    * Rebuilds the Colour menu, including any user-defined colours which have
5834    * been loaded either on startup or during the session
5835    */
5836   public void buildColourMenu()
5837   {
5838     colourMenu.removeAll();
5839
5840     colourMenu.add(applyToAllGroups);
5841     colourMenu.add(textColour);
5842     colourMenu.addSeparator();
5843
5844     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5845             viewport.getAlignment(), false);
5846
5847     colourMenu.add(annotationColour);
5848     bg.add(annotationColour);
5849     colourMenu.addSeparator();
5850     colourMenu.add(conservationMenuItem);
5851     colourMenu.add(modifyConservation);
5852     colourMenu.add(abovePIDThreshold);
5853     colourMenu.add(modifyPID);
5854
5855     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5856     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5857   }
5858
5859   /**
5860    * Open a dialog (if not already open) that allows the user to select and
5861    * calculate PCA or Tree analysis
5862    */
5863   protected void openTreePcaDialog()
5864   {
5865     if (alignPanel.getCalculationDialog() == null)
5866     {
5867       new CalculationChooser(AlignFrame.this);
5868     }
5869   }
5870
5871   @Override
5872   protected void loadVcf_actionPerformed()
5873   {
5874     JalviewFileChooser chooser = new JalviewFileChooser(
5875             Cache.getProperty("LAST_DIRECTORY"));
5876     chooser.setFileView(new JalviewFileView());
5877     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5878     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5879     final AlignFrame us = this;
5880     chooser.setResponseHandler(0, new Runnable()
5881     {
5882       @Override
5883       public void run()
5884       {
5885         String choice = chooser.getSelectedFile().getPath();
5886         Cache.setProperty("LAST_DIRECTORY", choice);
5887         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5888         new VCFLoader(choice).loadVCF(seqs, us);
5889       }
5890     });
5891     chooser.showOpenDialog(null);
5892
5893   }
5894
5895   private Rectangle lastFeatureSettingsBounds = null;
5896
5897   @Override
5898   public void setFeatureSettingsGeometry(Rectangle bounds)
5899   {
5900     lastFeatureSettingsBounds = bounds;
5901   }
5902
5903   @Override
5904   public Rectangle getFeatureSettingsGeometry()
5905   {
5906     return lastFeatureSettingsBounds;
5907   }
5908 }
5909
5910 class PrintThread extends Thread
5911 {
5912   AlignmentPanel ap;
5913
5914   public PrintThread(AlignmentPanel ap)
5915   {
5916     this.ap = ap;
5917   }
5918
5919   static PageFormat pf;
5920
5921   @Override
5922   public void run()
5923   {
5924     PrinterJob printJob = PrinterJob.getPrinterJob();
5925
5926     if (pf != null)
5927     {
5928       printJob.setPrintable(ap, pf);
5929     }
5930     else
5931     {
5932       printJob.setPrintable(ap);
5933     }
5934
5935     if (printJob.printDialog())
5936     {
5937       try
5938       {
5939         printJob.print();
5940       } catch (Exception PrintException)
5941       {
5942         PrintException.printStackTrace();
5943       }
5944     }
5945   }
5946 }