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