src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenMarkovModel;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.hmmer.HMMERCommands;
  67 import jalview.io.AlignmentProperties;
  68 import jalview.io.AnnotationFile;
  69 import jalview.io.BioJsHTMLOutput;
  70 import jalview.io.DataSourceType;
  71 import jalview.io.FileFormat;
  72 import jalview.io.FileFormatI;
  73 import jalview.io.FileFormats;
  74 import jalview.io.FileLoader;
  75 import jalview.io.FileParse;
  76 import jalview.io.FormatAdapter;
  77 import jalview.io.HMMFile;
  78 import jalview.io.HtmlSvgOutput;
  79 import jalview.io.IdentifyFile;
  80 import jalview.io.JPredFile;
  81 import jalview.io.JalviewFileChooser;
  82 import jalview.io.JalviewFileView;
  83 import jalview.io.JnetAnnotationMaker;
  84 import jalview.io.NewickFile;
  85 import jalview.io.ScoreMatrixFile;
  86 import jalview.io.TCoffeeScoreFile;
  87 import jalview.jbgui.GAlignFrame;
  88 import jalview.schemes.ColourSchemeI;
  89 import jalview.schemes.ColourSchemes;
  90 import jalview.schemes.ResidueColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.util.MessageManager;
  93 import jalview.viewmodel.AlignmentViewport;
  94 import jalview.viewmodel.ViewportRanges;
  95 import jalview.workers.InformationThread;
  96 import jalview.ws.DBRefFetcher;
  97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  98 import jalview.ws.jws1.Discoverer;
  99 import jalview.ws.jws2.Jws2Discoverer;
 100 import jalview.ws.jws2.jabaws2.Jws2Instance;
 101 import jalview.ws.seqfetcher.DbSourceProxy;
 102
 103 import java.awt.BorderLayout;
 104 import java.awt.Component;
 105 import java.awt.Rectangle;
 106 import java.awt.Toolkit;
 107 import java.awt.datatransfer.Clipboard;
 108 import java.awt.datatransfer.DataFlavor;
 109 import java.awt.datatransfer.StringSelection;
 110 import java.awt.datatransfer.Transferable;
 111 import java.awt.dnd.DnDConstants;
 112 import java.awt.dnd.DropTargetDragEvent;
 113 import java.awt.dnd.DropTargetDropEvent;
 114 import java.awt.dnd.DropTargetEvent;
 115 import java.awt.dnd.DropTargetListener;
 116 import java.awt.event.ActionEvent;
 117 import java.awt.event.ActionListener;
 118 import java.awt.event.FocusAdapter;
 119 import java.awt.event.FocusEvent;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseEvent;
 125 import java.awt.print.PageFormat;
 126 import java.awt.print.PrinterJob;
 127 import java.beans.PropertyChangeEvent;
 128 import java.io.File;
 129 import java.io.FileWriter;
 130 import java.io.IOException;
 131 import java.io.PrintWriter;
 132 import java.net.URL;
 133 import java.util.ArrayList;
 134 import java.util.Arrays;
 135 import java.util.Deque;
 136 import java.util.Enumeration;
 137 import java.util.HashMap;
 138 import java.util.Hashtable;
 139 import java.util.List;
 140 import java.util.Map;
 141 import java.util.Vector;
 142
 143 import javax.swing.JCheckBoxMenuItem;
 144 import javax.swing.JEditorPane;
 145 import javax.swing.JInternalFrame;
 146 import javax.swing.JLayeredPane;
 147 import javax.swing.JMenu;
 148 import javax.swing.JMenuItem;
 149 import javax.swing.JScrollPane;
 150 import javax.swing.SwingUtilities;
 151
 152 /**
 153  * DOCUMENT ME!
 154  *
 155  * @author $author$
 156  * @version $Revision$
 157  */
 158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 159         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 160 {
 161
 162   Map<String, Float> distribution = new HashMap<>(); // temporary
 163
 164   public static final int DEFAULT_WIDTH = 700;
 165
 166   public static final int DEFAULT_HEIGHT = 500;
 167
 168   boolean autoAlignNewSequences;
 169
 170   boolean recurring;
 171
 172   /*
 173    * The currently displayed panel (selected tabbed view if more than one)
 174    */
 175   public AlignmentPanel alignPanel;
 176
 177   AlignViewport viewport;
 178
 179   ViewportRanges vpRanges;
 180
 181   public AlignViewControllerI avc;
 182
 183   List<AlignmentPanel> alignPanels = new ArrayList<>();
 184
 185   /**
 186    * Last format used to load or save alignments in this window
 187    */
 188   FileFormatI currentFileFormat = null;
 189
 190   /**
 191    * Current filename for this alignment
 192    */
 193   String fileName = null;
 194
 195
 196   /**
 197    * Creates a new AlignFrame object with specific width and height.
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    */
 203   public AlignFrame(AlignmentI al, int width, int height)
 204   {
 205     this(al, null, width, height);
 206   }
 207
 208   /**
 209    * Creates a new AlignFrame object with specific width, height and
 210    * sequenceSetId
 211    *
 212    * @param al
 213    * @param width
 214    * @param height
 215    * @param sequenceSetId
 216    */
 217   public AlignFrame(AlignmentI al, int width, int height,
 218           String sequenceSetId)
 219   {
 220     this(al, null, width, height, sequenceSetId);
 221   }
 222
 223   /**
 224    * Creates a new AlignFrame object with specific width, height and
 225    * sequenceSetId
 226    *
 227    * @param al
 228    * @param width
 229    * @param height
 230    * @param sequenceSetId
 231    * @param viewId
 232    */
 233   public AlignFrame(AlignmentI al, int width, int height,
 234           String sequenceSetId, String viewId)
 235   {
 236     this(al, null, width, height, sequenceSetId, viewId);
 237   }
 238
 239   /**
 240    * new alignment window with hidden columns
 241    *
 242    * @param al
 243    *          AlignmentI
 244    * @param hiddenColumns
 245    *          ColumnSelection or null
 246    * @param width
 247    *          Width of alignment frame
 248    * @param height
 249    *          height of frame.
 250    */
 251   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 252           int width, int height)
 253   {
 254     this(al, hiddenColumns, width, height, null);
 255   }
 256
 257   /**
 258    * Create alignment frame for al with hiddenColumns, a specific width and
 259    * height, and specific sequenceId
 260    *
 261    * @param al
 262    * @param hiddenColumns
 263    * @param width
 264    * @param height
 265    * @param sequenceSetId
 266    *          (may be null)
 267    */
 268   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 269           int width, int height, String sequenceSetId)
 270   {
 271     this(al, hiddenColumns, width, height, sequenceSetId, null);
 272   }
 273
 274   /**
 275    * Create alignment frame for al with hiddenColumns, a specific width and
 276    * height, and specific sequenceId
 277    *
 278    * @param al
 279    * @param hiddenColumns
 280    * @param width
 281    * @param height
 282    * @param sequenceSetId
 283    *          (may be null)
 284    * @param viewId
 285    *          (may be null)
 286    */
 287   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 288           int width, int height, String sequenceSetId, String viewId)
 289   {
 290     setSize(width, height);
 291
 292     if (al.getDataset() == null)
 293     {
 294       al.setDataset(null);
 295     }
 296
 297     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 298
 299     alignPanel = new AlignmentPanel(this, viewport);
 300
 301     addAlignmentPanel(alignPanel, true);
 302     init();
 303   }
 304
 305   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 306           HiddenColumns hiddenColumns, int width, int height)
 307   {
 308     setSize(width, height);
 309
 310     if (al.getDataset() == null)
 311     {
 312       al.setDataset(null);
 313     }
 314
 315     viewport = new AlignViewport(al, hiddenColumns);
 316
 317     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 318     {
 319       viewport.hideSequence(hiddenSeqs);
 320     }
 321     alignPanel = new AlignmentPanel(this, viewport);
 322     addAlignmentPanel(alignPanel, true);
 323     init();
 324   }
 325
 326   /**
 327    * Make a new AlignFrame from existing alignmentPanels
 328    *
 329    * @param ap
 330    *          AlignmentPanel
 331    * @param av
 332    *          AlignViewport
 333    */
 334   public AlignFrame(AlignmentPanel ap)
 335   {
 336     viewport = ap.av;
 337     alignPanel = ap;
 338     addAlignmentPanel(ap, false);
 339     init();
 340   }
 341
 342   /**
 343    * initalise the alignframe from the underlying viewport data and the
 344    * configurations
 345    */
 346   void init()
 347   {
 348     if (!Jalview.isHeadlessMode())
 349     {
 350       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 351     }
 352
 353     vpRanges = viewport.getRanges();
 354     avc = new jalview.controller.AlignViewController(this, viewport,
 355             alignPanel);
 356     if (viewport.getAlignmentConservationAnnotation() == null)
 357     {
 358       // BLOSUM62Colour.setEnabled(false);
 359       conservationMenuItem.setEnabled(false);
 360       modifyConservation.setEnabled(false);
 361       // PIDColour.setEnabled(false);
 362       // abovePIDThreshold.setEnabled(false);
 363       // modifyPID.setEnabled(false);
 364     }
 365
 366     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 367             "No sort");
 368
 369     if (sortby.equals("Id"))
 370     {
 371       sortIDMenuItem_actionPerformed(null);
 372     }
 373     else if (sortby.equals("Pairwise Identity"))
 374     {
 375       sortPairwiseMenuItem_actionPerformed(null);
 376     }
 377
 378     this.alignPanel.av
 379             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 380
 381     setMenusFromViewport(viewport);
 382     buildSortByAnnotationScoresMenu();
 383     calculateTree.addActionListener(new ActionListener()
 384     {
 385
 386       @Override
 387       public void actionPerformed(ActionEvent e)
 388       {
 389         openTreePcaDialog();
 390       }
 391     });
 392     buildColourMenu();
 393     buildHMMERMenu();
 394
 395     if (Desktop.desktop != null)
 396     {
 397       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 398       addServiceListeners();
 399       setGUINucleotide();
 400     }
 401
 402     if (viewport.getWrapAlignment())
 403     {
 404       wrapMenuItem_actionPerformed(null);
 405     }
 406
 407     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 408     {
 409       this.overviewMenuItem_actionPerformed(null);
 410     }
 411
 412     addKeyListener();
 413
 414     final List<AlignmentPanel> selviews = new ArrayList<>();
 415     final List<AlignmentPanel> origview = new ArrayList<>();
 416     final String menuLabel = MessageManager
 417             .getString("label.copy_format_from");
 418     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 419             new ViewSetProvider()
 420             {
 421
 422               @Override
 423               public AlignmentPanel[] getAllAlignmentPanels()
 424               {
 425                 origview.clear();
 426                 origview.add(alignPanel);
 427                 // make an array of all alignment panels except for this one
 428                 List<AlignmentPanel> aps = new ArrayList<>(
 429                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 430                 aps.remove(AlignFrame.this.alignPanel);
 431                 return aps.toArray(new AlignmentPanel[aps.size()]);
 432               }
 433             }, selviews, new ItemListener()
 434             {
 435
 436               @Override
 437               public void itemStateChanged(ItemEvent e)
 438               {
 439                 if (origview.size() > 0)
 440                 {
 441                   final AlignmentPanel ap = origview.get(0);
 442
 443                   /*
 444                    * Copy the ViewStyle of the selected panel to 'this one'.
 445                    * Don't change value of 'scaleProteinAsCdna' unless copying
 446                    * from a SplitFrame.
 447                    */
 448                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 449                           .getViewStyle();
 450                   boolean fromSplitFrame = selviews.get(0)
 451                           .getAlignViewport().getCodingComplement() != null;
 452                   if (!fromSplitFrame)
 453                   {
 454                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 455                             .getViewStyle().isScaleProteinAsCdna());
 456                   }
 457                   ap.getAlignViewport().setViewStyle(vs);
 458
 459                   /*
 460                    * Also rescale ViewStyle of SplitFrame complement if there is
 461                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 462                    * the whole ViewStyle (allow cDNA protein to have different
 463                    * fonts)
 464                    */
 465                   AlignViewportI complement = ap.getAlignViewport()
 466                           .getCodingComplement();
 467                   if (complement != null && vs.isScaleProteinAsCdna())
 468                   {
 469                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 470                     ((SplitFrame) af.getSplitViewContainer())
 471                             .adjustLayout();
 472                     af.setMenusForViewport();
 473                   }
 474
 475                   ap.updateLayout();
 476                   ap.setSelected(true);
 477                   ap.alignFrame.setMenusForViewport();
 478
 479                 }
 480               }
 481             });
 482     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 483             .indexOf("devel") > -1
 484             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 485                     .indexOf("test") > -1)
 486     {
 487       formatMenu.add(vsel);
 488     }
 489     addFocusListener(new FocusAdapter()
 490     {
 491       @Override
 492       public void focusGained(FocusEvent e)
 493       {
 494         Jalview.setCurrentAlignFrame(AlignFrame.this);
 495       }
 496     });
 497
 498   }
 499
 500   private void buildHMMERMenu()
 501   {
 502     hmmerMenu.removeAll();
 503
 504     hmmerMenu.add(autoAlignSeqs);
 505     hmmerMenu.addSeparator();
 506
 507     hmmerMenu.add(hmmAlign);
 508     hmmerMenu.add(hmmBuild);
 509     hmmerMenu.add(hmmSearch);
 510
 511   }
 512
 513   /**
 514    * Change the filename and format for the alignment, and enable the 'reload'
 515    * button functionality.
 516    *
 517    * @param file
 518    *          valid filename
 519    * @param format
 520    *          format of file
 521    */
 522   public void setFileName(String file, FileFormatI format)
 523   {
 524     fileName = file;
 525     setFileFormat(format);
 526     reload.setEnabled(true);
 527   }
 528
 529   /**
 530    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 531    * events
 532    */
 533   void addKeyListener()
 534   {
 535     addKeyListener(new KeyAdapter()
 536     {
 537       @Override
 538       public void keyPressed(KeyEvent evt)
 539       {
 540         if (viewport.cursorMode
 541                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 542                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 543                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 544                 && Character.isDigit(evt.getKeyChar()))
 545         {
 546           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 547         }
 548
 549         switch (evt.getKeyCode())
 550         {
 551
 552         case 27: // escape key
 553           deselectAllSequenceMenuItem_actionPerformed(null);
 554
 555           break;
 556
 557         case KeyEvent.VK_DOWN:
 558           if (evt.isAltDown() || !viewport.cursorMode)
 559           {
 560             moveSelectedSequences(false);
 561           }
 562           if (viewport.cursorMode)
 563           {
 564             alignPanel.getSeqPanel().moveCursor(0, 1);
 565           }
 566           break;
 567
 568         case KeyEvent.VK_UP:
 569           if (evt.isAltDown() || !viewport.cursorMode)
 570           {
 571             moveSelectedSequences(true);
 572           }
 573           if (viewport.cursorMode)
 574           {
 575             alignPanel.getSeqPanel().moveCursor(0, -1);
 576           }
 577
 578           break;
 579
 580         case KeyEvent.VK_LEFT:
 581           if (evt.isAltDown() || !viewport.cursorMode)
 582           {
 583             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 584           }
 585           else
 586           {
 587             alignPanel.getSeqPanel().moveCursor(-1, 0);
 588           }
 589
 590           break;
 591
 592         case KeyEvent.VK_RIGHT:
 593           if (evt.isAltDown() || !viewport.cursorMode)
 594           {
 595             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 596           }
 597           else
 598           {
 599             alignPanel.getSeqPanel().moveCursor(1, 0);
 600           }
 601           break;
 602
 603         case KeyEvent.VK_SPACE:
 604           if (viewport.cursorMode)
 605           {
 606             alignPanel.getSeqPanel().insertGapAtCursor(
 607                     evt.isControlDown() || evt.isShiftDown()
 608                             || evt.isAltDown());
 609           }
 610           break;
 611
 612         // case KeyEvent.VK_A:
 613         // if (viewport.cursorMode)
 614         // {
 615         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 616         // //System.out.println("A");
 617         // }
 618         // break;
 619         /*
 620          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 621          * System.out.println("closing bracket"); } break;
 622          */
 623         case KeyEvent.VK_DELETE:
 624         case KeyEvent.VK_BACK_SPACE:
 625           if (!viewport.cursorMode)
 626           {
 627             cut_actionPerformed(null);
 628           }
 629           else
 630           {
 631             alignPanel.getSeqPanel().deleteGapAtCursor(
 632                     evt.isControlDown() || evt.isShiftDown()
 633                             || evt.isAltDown());
 634           }
 635
 636           break;
 637
 638         case KeyEvent.VK_S:
 639           if (viewport.cursorMode)
 640           {
 641             alignPanel.getSeqPanel().setCursorRow();
 642           }
 643           break;
 644         case KeyEvent.VK_C:
 645           if (viewport.cursorMode && !evt.isControlDown())
 646           {
 647             alignPanel.getSeqPanel().setCursorColumn();
 648           }
 649           break;
 650         case KeyEvent.VK_P:
 651           if (viewport.cursorMode)
 652           {
 653             alignPanel.getSeqPanel().setCursorPosition();
 654           }
 655           break;
 656
 657         case KeyEvent.VK_ENTER:
 658         case KeyEvent.VK_COMMA:
 659           if (viewport.cursorMode)
 660           {
 661             alignPanel.getSeqPanel().setCursorRowAndColumn();
 662           }
 663           break;
 664
 665         case KeyEvent.VK_Q:
 666           if (viewport.cursorMode)
 667           {
 668             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 669           }
 670           break;
 671         case KeyEvent.VK_M:
 672           if (viewport.cursorMode)
 673           {
 674             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 675           }
 676           break;
 677
 678         case KeyEvent.VK_F2:
 679           viewport.cursorMode = !viewport.cursorMode;
 680           statusBar.setText(MessageManager.formatMessage(
 681                   "label.keyboard_editing_mode",
 682                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 683           if (viewport.cursorMode)
 684           {
 685             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 686                     .getStartRes();
 687             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 688                     .getStartSeq();
 689           }
 690           alignPanel.getSeqPanel().seqCanvas.repaint();
 691           break;
 692
 693         case KeyEvent.VK_F1:
 694           try
 695           {
 696             Help.showHelpWindow();
 697           } catch (Exception ex)
 698           {
 699             ex.printStackTrace();
 700           }
 701           break;
 702         case KeyEvent.VK_H:
 703         {
 704           boolean toggleSeqs = !evt.isControlDown();
 705           boolean toggleCols = !evt.isShiftDown();
 706           toggleHiddenRegions(toggleSeqs, toggleCols);
 707           break;
 708         }
 709         case KeyEvent.VK_B:
 710         {
 711           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 712           boolean modifyExisting = true; // always modify, don't clear
 713                                          // evt.isShiftDown();
 714           boolean invertHighlighted = evt.isAltDown();
 715           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 716                   toggleSel);
 717           break;
 718         }
 719         case KeyEvent.VK_PAGE_UP:
 720           if (viewport.getWrapAlignment())
 721           {
 722             vpRanges.scrollUp(true);
 723           }
 724           else
 725           {
 726             vpRanges.pageUp();
 727           }
 728           break;
 729         case KeyEvent.VK_PAGE_DOWN:
 730           if (viewport.getWrapAlignment())
 731           {
 732             vpRanges.scrollUp(false);
 733           }
 734           else
 735           {
 736             vpRanges.pageDown();
 737           }
 738           break;
 739         }
 740       }
 741
 742       @Override
 743       public void keyReleased(KeyEvent evt)
 744       {
 745         switch (evt.getKeyCode())
 746         {
 747         case KeyEvent.VK_LEFT:
 748           if (evt.isAltDown() || !viewport.cursorMode)
 749           {
 750             viewport.firePropertyChange("alignment", null, viewport
 751                     .getAlignment().getSequences());
 752           }
 753           break;
 754
 755         case KeyEvent.VK_RIGHT:
 756           if (evt.isAltDown() || !viewport.cursorMode)
 757           {
 758             viewport.firePropertyChange("alignment", null, viewport
 759                     .getAlignment().getSequences());
 760           }
 761           break;
 762         }
 763       }
 764     });
 765   }
 766
 767   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 768   {
 769     ap.alignFrame = this;
 770     avc = new jalview.controller.AlignViewController(this, viewport,
 771             alignPanel);
 772
 773     alignPanels.add(ap);
 774
 775     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 776
 777     int aSize = alignPanels.size();
 778
 779     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 780
 781     if (aSize == 1 && ap.av.viewName == null)
 782     {
 783       this.getContentPane().add(ap, BorderLayout.CENTER);
 784     }
 785     else
 786     {
 787       if (aSize == 2)
 788       {
 789         setInitialTabVisible();
 790       }
 791
 792       expandViews.setEnabled(true);
 793       gatherViews.setEnabled(true);
 794       tabbedPane.addTab(ap.av.viewName, ap);
 795
 796       ap.setVisible(false);
 797     }
 798
 799     if (newPanel)
 800     {
 801       if (ap.av.isPadGaps())
 802       {
 803         ap.av.getAlignment().padGaps();
 804       }
 805       ap.av.updateConservation(ap);
 806       ap.av.updateConsensus(ap);
 807       ap.av.updateStrucConsensus(ap);
 808       ap.av.updateInformation(ap);
 809     }
 810   }
 811
 812   public void setInitialTabVisible()
 813   {
 814     expandViews.setEnabled(true);
 815     gatherViews.setEnabled(true);
 816     tabbedPane.setVisible(true);
 817     AlignmentPanel first = alignPanels.get(0);
 818     tabbedPane.addTab(first.av.viewName, first);
 819     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 820   }
 821
 822   public AlignViewport getViewport()
 823   {
 824     return viewport;
 825   }
 826
 827   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 828   private void addServiceListeners()
 829   {
 830     final java.beans.PropertyChangeListener thisListener;
 831     Desktop.instance.addJalviewPropertyChangeListener("services",
 832             thisListener = new java.beans.PropertyChangeListener()
 833             {
 834               @Override
 835               public void propertyChange(PropertyChangeEvent evt)
 836               {
 837                 // // System.out.println("Discoverer property change.");
 838                 // if (evt.getPropertyName().equals("services"))
 839                 {
 840                   SwingUtilities.invokeLater(new Runnable()
 841                   {
 842
 843                     @Override
 844                     public void run()
 845                     {
 846                       System.err
 847                               .println("Rebuild WS Menu for service change");
 848                       BuildWebServiceMenu();
 849                     }
 850
 851                   });
 852                 }
 853               }
 854             });
 855     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 856     {
 857       @Override
 858       public void internalFrameClosed(
 859               javax.swing.event.InternalFrameEvent evt)
 860       {
 861         // System.out.println("deregistering discoverer listener");
 862         Desktop.instance.removeJalviewPropertyChangeListener("services",
 863                 thisListener);
 864         closeMenuItem_actionPerformed(true);
 865       };
 866     });
 867     // Finally, build the menu once to get current service state
 868     new Thread(new Runnable()
 869     {
 870       @Override
 871       public void run()
 872       {
 873         BuildWebServiceMenu();
 874       }
 875     }).start();
 876   }
 877
 878   /**
 879    * Configure menu items that vary according to whether the alignment is
 880    * nucleotide or protein
 881    */
 882   public void setGUINucleotide()
 883   {
 884     AlignmentI al = getViewport().getAlignment();
 885     boolean nucleotide = al.isNucleotide();
 886
 887     showTranslation.setVisible(nucleotide);
 888     showReverse.setVisible(nucleotide);
 889     showReverseComplement.setVisible(nucleotide);
 890     conservationMenuItem.setEnabled(!nucleotide);
 891     modifyConservation.setEnabled(!nucleotide
 892             && conservationMenuItem.isSelected());
 893     showGroupConservation.setEnabled(!nucleotide);
 894
 895     showComplementMenuItem.setText(nucleotide ? MessageManager
 896             .getString("label.protein") : MessageManager
 897             .getString("label.nucleotide"));
 898   }
 899
 900   /**
 901    * set up menus for the current viewport. This may be called after any
 902    * operation that affects the data in the current view (selection changed,
 903    * etc) to update the menus to reflect the new state.
 904    */
 905   @Override
 906   public void setMenusForViewport()
 907   {
 908     setMenusFromViewport(viewport);
 909   }
 910
 911   /**
 912    * Need to call this method when tabs are selected for multiple views, or when
 913    * loading from Jalview2XML.java
 914    *
 915    * @param av
 916    *          AlignViewport
 917    */
 918   void setMenusFromViewport(AlignViewport av)
 919   {
 920     padGapsMenuitem.setSelected(av.isPadGaps());
 921     colourTextMenuItem.setSelected(av.isShowColourText());
 922     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 923     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 924     conservationMenuItem.setSelected(av.getConservationSelected());
 925     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 926     seqLimits.setSelected(av.getShowJVSuffix());
 927     idRightAlign.setSelected(av.isRightAlignIds());
 928     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 929     renderGapsMenuItem.setSelected(av.isRenderGaps());
 930     wrapMenuItem.setSelected(av.getWrapAlignment());
 931     scaleAbove.setVisible(av.getWrapAlignment());
 932     scaleLeft.setVisible(av.getWrapAlignment());
 933     scaleRight.setVisible(av.getWrapAlignment());
 934     annotationPanelMenuItem.setState(av.isShowAnnotation());
 935     /*
 936      * Show/hide annotations only enabled if annotation panel is shown
 937      */
 938     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 939     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 940     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 941     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 942     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 943     viewTextMenuItem.setSelected(av.getShowText());
 944     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 945     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 946     showGroupConservation.setSelected(av.isShowGroupConservation());
 947     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 948     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 949     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 950     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 951     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 952     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 953
 954     ColourMenuHelper.setColourSelected(colourMenu,
 955             av.getGlobalColourScheme());
 956
 957     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 958     hiddenMarkers.setState(av.getShowHiddenMarkers());
 959     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 960     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 961     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 962     autoCalculate.setSelected(av.autoCalculateConsensus);
 963     sortByTree.setSelected(av.sortByTree);
 964     listenToViewSelections.setSelected(av.followSelection);
 965
 966     showProducts.setEnabled(canShowProducts());
 967     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 968
 969     updateEditMenuBar();
 970   }
 971
 972   /**
 973    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 974    *
 975    * @param b
 976    */
 977   public void setGroovyEnabled(boolean b)
 978   {
 979     runGroovy.setEnabled(b);
 980   }
 981
 982   private IProgressIndicator progressBar;
 983
 984   /*
 985    * (non-Javadoc)
 986    *
 987    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 988    */
 989   @Override
 990   public void setProgressBar(String message, long id)
 991   {
 992     progressBar.setProgressBar(message, id);
 993   }
 994
 995   @Override
 996   public void registerHandler(final long id,
 997           final IProgressIndicatorHandler handler)
 998   {
 999     progressBar.registerHandler(id, handler);
1000   }
1001
1002   /**
1003    *
1004    * @return true if any progress bars are still active
1005    */
1006   @Override
1007   public boolean operationInProgress()
1008   {
1009     return progressBar.operationInProgress();
1010   }
1011
1012   @Override
1013   public void setStatus(String text)
1014   {
1015     statusBar.setText(text);
1016   }
1017
1018   /*
1019    * Added so Castor Mapping file can obtain Jalview Version
1020    */
1021   public String getVersion()
1022   {
1023     return jalview.bin.Cache.getProperty("VERSION");
1024   }
1025
1026   public FeatureRenderer getFeatureRenderer()
1027   {
1028     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1029   }
1030
1031   @Override
1032   public void fetchSequence_actionPerformed(ActionEvent e)
1033   {
1034     new jalview.gui.SequenceFetcher(this);
1035   }
1036
1037   @Override
1038   public void addFromFile_actionPerformed(ActionEvent e)
1039   {
1040     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1041   }
1042
1043   @Override
1044   public void hmmBuild_actionPerformed(ActionEvent e)
1045           throws IOException, InterruptedException
1046   {
1047
1048     HMMERCommands.hmmBuild(this);
1049     alignPanel.repaint();
1050
1051   }
1052
1053   @Override
1054   public void hmmAlign_actionPerformed(ActionEvent e)
1055           throws IOException, InterruptedException
1056   {
1057     SequenceI seq = getViewport().getAlignment()
1058             .getHMMConsensusSequences(false).get(0);
1059     HMMERCommands.hmmAlign(this, true, seq.getHMM());
1060     alignPanel.repaint();
1061   }
1062
1063   @Override
1064   public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
1065   {
1066     autoAlignNewSequences = autoAlignSeqs;
1067     alignPanel.repaint();
1068   }
1069
1070   @Override
1071   public void hmmSearch_actionPerformed(ActionEvent e)
1072   {
1073     alignPanel.repaint();
1074   }
1075
1076   @Override
1077   public void reload_actionPerformed(ActionEvent e)
1078   {
1079     if (fileName != null)
1080     {
1081       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1082       // originating file's format
1083       // TODO: work out how to recover feature settings for correct view(s) when
1084       // file is reloaded.
1085       if (FileFormat.Jalview.equals(currentFileFormat))
1086       {
1087         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1088         for (int i = 0; i < frames.length; i++)
1089         {
1090           if (frames[i] instanceof AlignFrame && frames[i] != this
1091                   && ((AlignFrame) frames[i]).fileName != null
1092                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1093           {
1094             try
1095             {
1096               frames[i].setSelected(true);
1097               Desktop.instance.closeAssociatedWindows();
1098             } catch (java.beans.PropertyVetoException ex)
1099             {
1100             }
1101           }
1102
1103         }
1104         Desktop.instance.closeAssociatedWindows();
1105
1106         FileLoader loader = new FileLoader();
1107         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1108                 : DataSourceType.FILE;
1109         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1110       }
1111       else
1112       {
1113         Rectangle bounds = this.getBounds();
1114
1115         FileLoader loader = new FileLoader();
1116         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1117                 : DataSourceType.FILE;
1118         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1119                 protocol, currentFileFormat);
1120
1121         newframe.setBounds(bounds);
1122         if (featureSettings != null && featureSettings.isShowing())
1123         {
1124           final Rectangle fspos = featureSettings.frame.getBounds();
1125           // TODO: need a 'show feature settings' function that takes bounds -
1126           // need to refactor Desktop.addFrame
1127           newframe.featureSettings_actionPerformed(null);
1128           final FeatureSettings nfs = newframe.featureSettings;
1129           SwingUtilities.invokeLater(new Runnable()
1130           {
1131             @Override
1132             public void run()
1133             {
1134               nfs.frame.setBounds(fspos);
1135             }
1136           });
1137           this.featureSettings.close();
1138           this.featureSettings = null;
1139         }
1140         this.closeMenuItem_actionPerformed(true);
1141       }
1142     }
1143   }
1144
1145   @Override
1146   public void addFromText_actionPerformed(ActionEvent e)
1147   {
1148     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1149             .getAlignPanel());
1150   }
1151
1152   @Override
1153   public void addFromURL_actionPerformed(ActionEvent e)
1154   {
1155     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1156   }
1157
1158   @Override
1159   public void save_actionPerformed(ActionEvent e)
1160   {
1161     if (fileName == null || (currentFileFormat == null)
1162             || fileName.startsWith("http"))
1163     {
1164       saveAs_actionPerformed(null);
1165     }
1166     else
1167     {
1168       saveAlignment(fileName, currentFileFormat);
1169     }
1170   }
1171
1172   /**
1173    * DOCUMENT ME!
1174    *
1175    * @param e
1176    *          DOCUMENT ME!
1177    */
1178   @Override
1179   public void saveAs_actionPerformed(ActionEvent e)
1180   {
1181     String format = currentFileFormat == null ? null : currentFileFormat
1182             .getName();
1183     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1184             Cache.getProperty("LAST_DIRECTORY"), format);
1185
1186     chooser.setFileView(new JalviewFileView());
1187     chooser.setDialogTitle(MessageManager
1188             .getString("label.save_alignment_to_file"));
1189     chooser.setToolTipText(MessageManager.getString("action.save"));
1190
1191     int value = chooser.showSaveDialog(this);
1192
1193     if (value == JalviewFileChooser.APPROVE_OPTION)
1194     {
1195       currentFileFormat = chooser.getSelectedFormat();
1196       while (currentFileFormat == null)
1197       {
1198         JvOptionPane
1199                 .showInternalMessageDialog(
1200                         Desktop.desktop,
1201                         MessageManager
1202                                 .getString("label.select_file_format_before_saving"),
1203                         MessageManager
1204                                 .getString("label.file_format_not_specified"),
1205                         JvOptionPane.WARNING_MESSAGE);
1206         currentFileFormat = chooser.getSelectedFormat();
1207         value = chooser.showSaveDialog(this);
1208         if (value != JalviewFileChooser.APPROVE_OPTION)
1209         {
1210           return;
1211         }
1212       }
1213
1214       fileName = chooser.getSelectedFile().getPath();
1215
1216       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1217
1218       Cache.setProperty("LAST_DIRECTORY", fileName);
1219       saveAlignment(fileName, currentFileFormat);
1220     }
1221   }
1222
1223   public boolean saveAlignment(String file, FileFormatI format)
1224   {
1225     boolean success = true;
1226
1227     if (FileFormat.Jalview.equals(format))
1228     {
1229       String shortName = title;
1230
1231       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1232       {
1233         shortName = shortName.substring(shortName
1234                 .lastIndexOf(java.io.File.separatorChar) + 1);
1235       }
1236
1237       success = new Jalview2XML().saveAlignment(this, file, shortName);
1238
1239       statusBar.setText(MessageManager.formatMessage(
1240               "label.successfully_saved_to_file_in_format", new Object[] {
1241                   fileName, format }));
1242
1243     }
1244     else
1245     {
1246       AlignmentExportData exportData = getAlignmentForExport(format,
1247               viewport, null);
1248       if (exportData.getSettings().isCancelled())
1249       {
1250         return false;
1251       }
1252       FormatAdapter f = new FormatAdapter(alignPanel,
1253               exportData.getSettings());
1254       String output = f.formatSequences(
1255               format,
1256               exportData.getAlignment(), // class cast exceptions will
1257               // occur in the distant future
1258               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1259               f.getCacheSuffixDefault(format), viewport.getAlignment()
1260                       .getHiddenColumns());
1261
1262       if (output == null)
1263       {
1264         success = false;
1265       }
1266       else
1267       {
1268         try
1269         {
1270           PrintWriter out = new PrintWriter(new FileWriter(file));
1271
1272           out.print(output);
1273           out.close();
1274           this.setTitle(file);
1275           statusBar.setText(MessageManager.formatMessage(
1276                   "label.successfully_saved_to_file_in_format",
1277                   new Object[] { fileName, format.getName() }));
1278         } catch (Exception ex)
1279         {
1280           success = false;
1281           ex.printStackTrace();
1282         }
1283       }
1284     }
1285
1286     if (!success)
1287     {
1288       JvOptionPane.showInternalMessageDialog(this, MessageManager
1289               .formatMessage("label.couldnt_save_file",
1290                       new Object[] { fileName }), MessageManager
1291               .getString("label.error_saving_file"),
1292               JvOptionPane.WARNING_MESSAGE);
1293     }
1294
1295     return success;
1296   }
1297
1298   private void warningMessage(String warning, String title)
1299   {
1300     if (new jalview.util.Platform().isHeadless())
1301     {
1302       System.err.println("Warning: " + title + "\nWarning: " + warning);
1303
1304     }
1305     else
1306     {
1307       JvOptionPane.showInternalMessageDialog(this, warning, title,
1308               JvOptionPane.WARNING_MESSAGE);
1309     }
1310     return;
1311   }
1312
1313   /**
1314    * DOCUMENT ME!
1315    *
1316    * @param e
1317    *          DOCUMENT ME!
1318    */
1319   @Override
1320   protected void outputText_actionPerformed(ActionEvent e)
1321   {
1322     FileFormatI fileFormat = FileFormats.getInstance().forName(
1323             e.getActionCommand());
1324     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1325             viewport, null);
1326     if (exportData.getSettings().isCancelled())
1327     {
1328       return;
1329     }
1330     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1331     cap.setForInput(null);
1332     try
1333     {
1334       FileFormatI format = fileFormat;
1335       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1336               .formatSequences(format, exportData.getAlignment(),
1337                       exportData.getOmitHidden(),
1338  exportData
1339                               .getStartEndPostions(), viewport
1340                               .getAlignment().getHiddenColumns()));
1341       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1342               "label.alignment_output_command",
1343               new Object[] { e.getActionCommand() }), 600, 500);
1344     } catch (OutOfMemoryError oom)
1345     {
1346       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1347       cap.dispose();
1348     }
1349
1350   }
1351
1352   public static AlignmentExportData getAlignmentForExport(
1353           FileFormatI format, AlignViewportI viewport,
1354           AlignExportSettingI exportSettings)
1355   {
1356     AlignmentI alignmentToExport = null;
1357     AlignExportSettingI settings = exportSettings;
1358     String[] omitHidden = null;
1359
1360     HiddenSequences hiddenSeqs = viewport.getAlignment()
1361             .getHiddenSequences();
1362
1363     alignmentToExport = viewport.getAlignment();
1364
1365     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1366     if (settings == null)
1367     {
1368       settings = new AlignExportSettings(hasHiddenSeqs,
1369               viewport.hasHiddenColumns(), format);
1370     }
1371     // settings.isExportAnnotations();
1372
1373     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1374     {
1375       omitHidden = viewport.getViewAsString(false,
1376               settings.isExportHiddenSequences());
1377     }
1378
1379     int[] alignmentStartEnd = new int[2];
1380     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1381     {
1382       alignmentToExport = hiddenSeqs.getFullAlignment();
1383     }
1384     else
1385     {
1386       alignmentToExport = viewport.getAlignment();
1387     }
1388     alignmentStartEnd = alignmentToExport
1389             .getVisibleStartAndEndIndex(viewport.getAlignment()
1390                     .getHiddenColumns()
1391                     .getHiddenRegions());
1392     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1393             omitHidden, alignmentStartEnd, settings);
1394     return ed;
1395   }
1396
1397   /**
1398    * DOCUMENT ME!
1399    *
1400    * @param e
1401    *          DOCUMENT ME!
1402    */
1403   @Override
1404   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1405   {
1406     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1407     htmlSVG.exportHTML(null);
1408   }
1409
1410   @Override
1411   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1412   {
1413     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1414     bjs.exportHTML(null);
1415   }
1416
1417   public void createImageMap(File file, String image)
1418   {
1419     alignPanel.makePNGImageMap(file, image);
1420   }
1421
1422   /**
1423    * DOCUMENT ME!
1424    *
1425    * @param e
1426    *          DOCUMENT ME!
1427    */
1428   @Override
1429   public void createPNG(File f)
1430   {
1431     alignPanel.makePNG(f);
1432   }
1433
1434   /**
1435    * DOCUMENT ME!
1436    *
1437    * @param e
1438    *          DOCUMENT ME!
1439    */
1440   @Override
1441   public void createEPS(File f)
1442   {
1443     alignPanel.makeEPS(f);
1444   }
1445
1446   @Override
1447   public void createSVG(File f)
1448   {
1449     alignPanel.makeSVG(f);
1450   }
1451
1452   @Override
1453   public void pageSetup_actionPerformed(ActionEvent e)
1454   {
1455     PrinterJob printJob = PrinterJob.getPrinterJob();
1456     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1457   }
1458
1459   /**
1460    * DOCUMENT ME!
1461    *
1462    * @param e
1463    *          DOCUMENT ME!
1464    */
1465   @Override
1466   public void printMenuItem_actionPerformed(ActionEvent e)
1467   {
1468     // Putting in a thread avoids Swing painting problems
1469     PrintThread thread = new PrintThread(alignPanel);
1470     thread.start();
1471   }
1472
1473   @Override
1474   public void exportFeatures_actionPerformed(ActionEvent e)
1475   {
1476     new AnnotationExporter().exportFeatures(alignPanel);
1477   }
1478
1479   @Override
1480   public void exportAnnotations_actionPerformed(ActionEvent e)
1481   {
1482     new AnnotationExporter().exportAnnotations(alignPanel);
1483   }
1484
1485   @Override
1486   public void associatedData_actionPerformed(ActionEvent e)
1487           throws IOException, InterruptedException
1488   {
1489     // Pick the tree file
1490     JalviewFileChooser chooser = new JalviewFileChooser(
1491             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1492     chooser.setFileView(new JalviewFileView());
1493     chooser.setDialogTitle(MessageManager
1494             .getString("label.load_jalview_annotations"));
1495     chooser.setToolTipText(MessageManager
1496             .getString("label.load_jalview_annotations"));
1497
1498     int value = chooser.showOpenDialog(null);
1499
1500     if (value == JalviewFileChooser.APPROVE_OPTION)
1501     {
1502       String choice = chooser.getSelectedFile().getPath();
1503       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1504       loadJalviewDataFile(choice, null, null, null);
1505     }
1506
1507   }
1508
1509   /**
1510    * Close the current view or all views in the alignment frame. If the frame
1511    * only contains one view then the alignment will be removed from memory.
1512    *
1513    * @param closeAllTabs
1514    */
1515   @Override
1516   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1517   {
1518     if (alignPanels != null && alignPanels.size() < 2)
1519     {
1520       closeAllTabs = true;
1521     }
1522
1523     try
1524     {
1525       if (alignPanels != null)
1526       {
1527         if (closeAllTabs)
1528         {
1529           if (this.isClosed())
1530           {
1531             // really close all the windows - otherwise wait till
1532             // setClosed(true) is called
1533             for (int i = 0; i < alignPanels.size(); i++)
1534             {
1535               AlignmentPanel ap = alignPanels.get(i);
1536               ap.closePanel();
1537             }
1538           }
1539         }
1540         else
1541         {
1542           closeView(alignPanel);
1543         }
1544       }
1545
1546       if (closeAllTabs)
1547       {
1548         /*
1549          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1550          * be called recursively, with the frame now in 'closed' state
1551          */
1552         this.setClosed(true);
1553       }
1554     } catch (Exception ex)
1555     {
1556       ex.printStackTrace();
1557     }
1558   }
1559
1560   /**
1561    * Close the specified panel and close up tabs appropriately.
1562    *
1563    * @param panelToClose
1564    */
1565   public void closeView(AlignmentPanel panelToClose)
1566   {
1567     int index = tabbedPane.getSelectedIndex();
1568     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1569     alignPanels.remove(panelToClose);
1570     panelToClose.closePanel();
1571     panelToClose = null;
1572
1573     tabbedPane.removeTabAt(closedindex);
1574     tabbedPane.validate();
1575
1576     if (index > closedindex || index == tabbedPane.getTabCount())
1577     {
1578       // modify currently selected tab index if necessary.
1579       index--;
1580     }
1581
1582     this.tabSelectionChanged(index);
1583   }
1584
1585   /**
1586    * DOCUMENT ME!
1587    */
1588   void updateEditMenuBar()
1589   {
1590
1591     if (viewport.getHistoryList().size() > 0)
1592     {
1593       undoMenuItem.setEnabled(true);
1594       CommandI command = viewport.getHistoryList().peek();
1595       undoMenuItem.setText(MessageManager.formatMessage(
1596               "label.undo_command",
1597               new Object[] { command.getDescription() }));
1598     }
1599     else
1600     {
1601       undoMenuItem.setEnabled(false);
1602       undoMenuItem.setText(MessageManager.getString("action.undo"));
1603     }
1604
1605     if (viewport.getRedoList().size() > 0)
1606     {
1607       redoMenuItem.setEnabled(true);
1608
1609       CommandI command = viewport.getRedoList().peek();
1610       redoMenuItem.setText(MessageManager.formatMessage(
1611               "label.redo_command",
1612               new Object[] { command.getDescription() }));
1613     }
1614     else
1615     {
1616       redoMenuItem.setEnabled(false);
1617       redoMenuItem.setText(MessageManager.getString("action.redo"));
1618     }
1619   }
1620
1621   @Override
1622   public void addHistoryItem(CommandI command)
1623   {
1624     if (command.getSize() > 0)
1625     {
1626       viewport.addToHistoryList(command);
1627       viewport.clearRedoList();
1628       updateEditMenuBar();
1629       viewport.updateHiddenColumns();
1630       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1631       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1632       // viewport.getColumnSelection()
1633       // .getHiddenColumns().size() > 0);
1634     }
1635   }
1636
1637   /**
1638    *
1639    * @return alignment objects for all views
1640    */
1641   AlignmentI[] getViewAlignments()
1642   {
1643     if (alignPanels != null)
1644     {
1645       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1646       int i = 0;
1647       for (AlignmentPanel ap : alignPanels)
1648       {
1649         als[i++] = ap.av.getAlignment();
1650       }
1651       return als;
1652     }
1653     if (viewport != null)
1654     {
1655       return new AlignmentI[] { viewport.getAlignment() };
1656     }
1657     return null;
1658   }
1659
1660   /**
1661    * DOCUMENT ME!
1662    *
1663    * @param e
1664    *          DOCUMENT ME!
1665    */
1666   @Override
1667   protected void undoMenuItem_actionPerformed(ActionEvent e)
1668   {
1669     if (viewport.getHistoryList().isEmpty())
1670     {
1671       return;
1672     }
1673     CommandI command = viewport.getHistoryList().pop();
1674     viewport.addToRedoList(command);
1675     command.undoCommand(getViewAlignments());
1676
1677     AlignmentViewport originalSource = getOriginatingSource(command);
1678     updateEditMenuBar();
1679
1680     if (originalSource != null)
1681     {
1682       if (originalSource != viewport)
1683       {
1684         Cache.log
1685                 .warn("Implementation worry: mismatch of viewport origin for undo");
1686       }
1687       originalSource.updateHiddenColumns();
1688       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1689       // null
1690       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1691       // viewport.getColumnSelection()
1692       // .getHiddenColumns().size() > 0);
1693       originalSource.firePropertyChange("alignment", null, originalSource
1694               .getAlignment().getSequences());
1695     }
1696   }
1697
1698   /**
1699    * DOCUMENT ME!
1700    *
1701    * @param e
1702    *          DOCUMENT ME!
1703    */
1704   @Override
1705   protected void redoMenuItem_actionPerformed(ActionEvent e)
1706   {
1707     if (viewport.getRedoList().size() < 1)
1708     {
1709       return;
1710     }
1711
1712     CommandI command = viewport.getRedoList().pop();
1713     viewport.addToHistoryList(command);
1714     command.doCommand(getViewAlignments());
1715
1716     AlignmentViewport originalSource = getOriginatingSource(command);
1717     updateEditMenuBar();
1718
1719     if (originalSource != null)
1720     {
1721
1722       if (originalSource != viewport)
1723       {
1724         Cache.log
1725                 .warn("Implementation worry: mismatch of viewport origin for redo");
1726       }
1727       originalSource.updateHiddenColumns();
1728       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1729       // null
1730       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1731       // viewport.getColumnSelection()
1732       // .getHiddenColumns().size() > 0);
1733       originalSource.firePropertyChange("alignment", null, originalSource
1734               .getAlignment().getSequences());
1735     }
1736   }
1737
1738   AlignmentViewport getOriginatingSource(CommandI command)
1739   {
1740     AlignmentViewport originalSource = null;
1741     // For sequence removal and addition, we need to fire
1742     // the property change event FROM the viewport where the
1743     // original alignment was altered
1744     AlignmentI al = null;
1745     if (command instanceof EditCommand)
1746     {
1747       EditCommand editCommand = (EditCommand) command;
1748       al = editCommand.getAlignment();
1749       List<Component> comps = PaintRefresher.components.get(viewport
1750               .getSequenceSetId());
1751
1752       for (Component comp : comps)
1753       {
1754         if (comp instanceof AlignmentPanel)
1755         {
1756           if (al == ((AlignmentPanel) comp).av.getAlignment())
1757           {
1758             originalSource = ((AlignmentPanel) comp).av;
1759             break;
1760           }
1761         }
1762       }
1763     }
1764
1765     if (originalSource == null)
1766     {
1767       // The original view is closed, we must validate
1768       // the current view against the closed view first
1769       if (al != null)
1770       {
1771         PaintRefresher.validateSequences(al, viewport.getAlignment());
1772       }
1773
1774       originalSource = viewport;
1775     }
1776
1777     return originalSource;
1778   }
1779
1780   /**
1781    * DOCUMENT ME!
1782    *
1783    * @param up
1784    *          DOCUMENT ME!
1785    */
1786   public void moveSelectedSequences(boolean up)
1787   {
1788     SequenceGroup sg = viewport.getSelectionGroup();
1789
1790     if (sg == null)
1791     {
1792       return;
1793     }
1794     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1795             viewport.getHiddenRepSequences(), up);
1796     alignPanel.paintAlignment(true);
1797   }
1798
1799   synchronized void slideSequences(boolean right, int size)
1800   {
1801     List<SequenceI> sg = new ArrayList<>();
1802     if (viewport.cursorMode)
1803     {
1804       sg.add(viewport.getAlignment().getSequenceAt(
1805               alignPanel.getSeqPanel().seqCanvas.cursorY));
1806     }
1807     else if (viewport.getSelectionGroup() != null
1808             && viewport.getSelectionGroup().getSize() != viewport
1809                     .getAlignment().getHeight())
1810     {
1811       sg = viewport.getSelectionGroup().getSequences(
1812               viewport.getHiddenRepSequences());
1813     }
1814
1815     if (sg.size() < 1)
1816     {
1817       return;
1818     }
1819
1820     List<SequenceI> invertGroup = new ArrayList<>();
1821
1822     for (SequenceI seq : viewport.getAlignment().getSequences())
1823     {
1824       if (!sg.contains(seq))
1825       {
1826         invertGroup.add(seq);
1827       }
1828     }
1829
1830     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1831
1832     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1833     for (int i = 0; i < invertGroup.size(); i++)
1834     {
1835       seqs2[i] = invertGroup.get(i);
1836     }
1837
1838     SlideSequencesCommand ssc;
1839     if (right)
1840     {
1841       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1842               size, viewport.getGapCharacter());
1843     }
1844     else
1845     {
1846       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1847               size, viewport.getGapCharacter());
1848     }
1849
1850     int groupAdjustment = 0;
1851     if (ssc.getGapsInsertedBegin() && right)
1852     {
1853       if (viewport.cursorMode)
1854       {
1855         alignPanel.getSeqPanel().moveCursor(size, 0);
1856       }
1857       else
1858       {
1859         groupAdjustment = size;
1860       }
1861     }
1862     else if (!ssc.getGapsInsertedBegin() && !right)
1863     {
1864       if (viewport.cursorMode)
1865       {
1866         alignPanel.getSeqPanel().moveCursor(-size, 0);
1867       }
1868       else
1869       {
1870         groupAdjustment = -size;
1871       }
1872     }
1873
1874     if (groupAdjustment != 0)
1875     {
1876       viewport.getSelectionGroup().setStartRes(
1877               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1878       viewport.getSelectionGroup().setEndRes(
1879               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1880     }
1881
1882     /*
1883      * just extend the last slide command if compatible; but not if in
1884      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1885      */
1886     boolean appendHistoryItem = false;
1887     Deque<CommandI> historyList = viewport.getHistoryList();
1888     boolean inSplitFrame = getSplitViewContainer() != null;
1889     if (!inSplitFrame && historyList != null && historyList.size() > 0
1890             && historyList.peek() instanceof SlideSequencesCommand)
1891     {
1892       appendHistoryItem = ssc
1893               .appendSlideCommand((SlideSequencesCommand) historyList
1894                       .peek());
1895     }
1896
1897     if (!appendHistoryItem)
1898     {
1899       addHistoryItem(ssc);
1900     }
1901
1902     repaint();
1903   }
1904
1905   /**
1906    * DOCUMENT ME!
1907    *
1908    * @param e
1909    *          DOCUMENT ME!
1910    */
1911   @Override
1912   protected void copy_actionPerformed(ActionEvent e)
1913   {
1914     System.gc();
1915     if (viewport.getSelectionGroup() == null)
1916     {
1917       return;
1918     }
1919     // TODO: preserve the ordering of displayed alignment annotation in any
1920     // internal paste (particularly sequence associated annotation)
1921     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1922     String[] omitHidden = null;
1923
1924     if (viewport.hasHiddenColumns())
1925     {
1926       omitHidden = viewport.getViewAsString(true);
1927     }
1928
1929     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1930             seqs, omitHidden, null);
1931
1932     StringSelection ss = new StringSelection(output);
1933
1934     try
1935     {
1936       jalview.gui.Desktop.internalCopy = true;
1937       // Its really worth setting the clipboard contents
1938       // to empty before setting the large StringSelection!!
1939       Toolkit.getDefaultToolkit().getSystemClipboard()
1940               .setContents(new StringSelection(""), null);
1941
1942       Toolkit.getDefaultToolkit().getSystemClipboard()
1943               .setContents(ss, Desktop.instance);
1944     } catch (OutOfMemoryError er)
1945     {
1946       new OOMWarning("copying region", er);
1947       return;
1948     }
1949
1950     ArrayList<int[]> hiddenColumns = null;
1951     if (viewport.hasHiddenColumns())
1952     {
1953       hiddenColumns = new ArrayList<>();
1954       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1955               .getSelectionGroup().getEndRes();
1956       for (int[] region : viewport.getAlignment().getHiddenColumns()
1957               .getHiddenRegions())
1958       {
1959         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1960         {
1961           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1962               region[1] - hiddenOffset });
1963         }
1964       }
1965     }
1966
1967     Desktop.jalviewClipboard = new Object[] { seqs,
1968         viewport.getAlignment().getDataset(), hiddenColumns };
1969     statusBar.setText(MessageManager.formatMessage(
1970             "label.copied_sequences_to_clipboard", new Object[] { Integer
1971                     .valueOf(seqs.length).toString() }));
1972   }
1973
1974   /**
1975    * DOCUMENT ME!
1976    *
1977    * @param e
1978    *          DOCUMENT ME!
1979    * @throws InterruptedException
1980    * @throws IOException
1981    */
1982   @Override
1983   protected void pasteNew_actionPerformed(ActionEvent e)
1984           throws IOException, InterruptedException
1985   {
1986     paste(true);
1987   }
1988
1989   /**
1990    * DOCUMENT ME!
1991    *
1992    * @param e
1993    *          DOCUMENT ME!
1994    * @throws InterruptedException
1995    * @throws IOException
1996    */
1997   @Override
1998   protected void pasteThis_actionPerformed(ActionEvent e)
1999           throws IOException, InterruptedException
2000   {
2001     paste(false);
2002   }
2003
2004   /**
2005    * Paste contents of Jalview clipboard
2006    *
2007    * @param newAlignment
2008    *          true to paste to a new alignment, otherwise add to this.
2009    * @throws InterruptedException
2010    * @throws IOException
2011    */
2012   void paste(boolean newAlignment) throws IOException, InterruptedException
2013   {
2014     boolean externalPaste = true;
2015     try
2016     {
2017       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2018       Transferable contents = c.getContents(this);
2019
2020       if (contents == null)
2021       {
2022         return;
2023       }
2024
2025       String str;
2026       FileFormatI format;
2027       try
2028       {
2029         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2030         if (str.length() < 1)
2031         {
2032           return;
2033         }
2034
2035         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2036
2037       } catch (OutOfMemoryError er)
2038       {
2039         new OOMWarning("Out of memory pasting sequences!!", er);
2040         return;
2041       }
2042
2043       SequenceI[] sequences;
2044       boolean annotationAdded = false;
2045       AlignmentI alignment = null;
2046
2047       if (Desktop.jalviewClipboard != null)
2048       {
2049         // The clipboard was filled from within Jalview, we must use the
2050         // sequences
2051         // And dataset from the copied alignment
2052         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2053         // be doubly sure that we create *new* sequence objects.
2054         sequences = new SequenceI[newseq.length];
2055         for (int i = 0; i < newseq.length; i++)
2056         {
2057           sequences[i] = new Sequence(newseq[i]);
2058         }
2059         alignment = new Alignment(sequences);
2060         externalPaste = false;
2061       }
2062       else
2063       {
2064         // parse the clipboard as an alignment.
2065         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2066                 format);
2067         sequences = alignment.getSequencesArray();
2068       }
2069
2070       int alwidth = 0;
2071       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2072       int fgroup = -1;
2073
2074       if (newAlignment)
2075       {
2076
2077         if (Desktop.jalviewClipboard != null)
2078         {
2079           // dataset is inherited
2080           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2081         }
2082         else
2083         {
2084           // new dataset is constructed
2085           alignment.setDataset(null);
2086         }
2087         alwidth = alignment.getWidth() + 1;
2088       }
2089       else
2090       {
2091         AlignmentI pastedal = alignment; // preserve pasted alignment object
2092         // Add pasted sequences and dataset into existing alignment.
2093         alignment = viewport.getAlignment();
2094         alwidth = alignment.getWidth() + 1;
2095         // decide if we need to import sequences from an existing dataset
2096         boolean importDs = Desktop.jalviewClipboard != null
2097                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2098         // importDs==true instructs us to copy over new dataset sequences from
2099         // an existing alignment
2100         Vector newDs = (importDs) ? new Vector() : null; // used to create
2101         // minimum dataset set
2102
2103         for (int i = 0; i < sequences.length; i++)
2104         {
2105           if (importDs)
2106           {
2107             newDs.addElement(null);
2108           }
2109           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2110           // paste
2111           if (importDs && ds != null)
2112           {
2113             if (!newDs.contains(ds))
2114             {
2115               newDs.setElementAt(ds, i);
2116               ds = new Sequence(ds);
2117               // update with new dataset sequence
2118               sequences[i].setDatasetSequence(ds);
2119             }
2120             else
2121             {
2122               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2123             }
2124           }
2125           else
2126           {
2127             // copy and derive new dataset sequence
2128             sequences[i] = sequences[i].deriveSequence();
2129             alignment.getDataset().addSequence(
2130                     sequences[i].getDatasetSequence());
2131             // TODO: avoid creation of duplicate dataset sequences with a
2132             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2133           }
2134           alignment.addSequence(sequences[i]); // merges dataset
2135         }
2136         if (newDs != null)
2137         {
2138           newDs.clear(); // tidy up
2139         }
2140         if (alignment.getAlignmentAnnotation() != null)
2141         {
2142           for (AlignmentAnnotation alan : alignment
2143                   .getAlignmentAnnotation())
2144           {
2145             if (alan.graphGroup > fgroup)
2146             {
2147               fgroup = alan.graphGroup;
2148             }
2149           }
2150         }
2151         if (pastedal.getAlignmentAnnotation() != null)
2152         {
2153           // Add any annotation attached to alignment.
2154           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2155           for (int i = 0; i < alann.length; i++)
2156           {
2157             annotationAdded = true;
2158             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2159             {
2160               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2161               if (newann.graphGroup > -1)
2162               {
2163                 if (newGraphGroups.size() <= newann.graphGroup
2164                         || newGraphGroups.get(newann.graphGroup) == null)
2165                 {
2166                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2167                   {
2168                     newGraphGroups.add(q, null);
2169                   }
2170                   newGraphGroups.set(newann.graphGroup, new Integer(
2171                           ++fgroup));
2172                 }
2173                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2174                         .intValue();
2175               }
2176
2177               newann.padAnnotation(alwidth);
2178               alignment.addAnnotation(newann);
2179             }
2180           }
2181         }
2182       }
2183       if (!newAlignment)
2184       {
2185         // /////
2186         // ADD HISTORY ITEM
2187         //
2188         addHistoryItem(new EditCommand(
2189                 MessageManager.getString("label.add_sequences"),
2190                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2191       }
2192       // Add any annotations attached to sequences
2193       for (int i = 0; i < sequences.length; i++)
2194       {
2195         if (sequences[i].getAnnotation() != null)
2196         {
2197           AlignmentAnnotation newann;
2198           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2199           {
2200             annotationAdded = true;
2201             newann = sequences[i].getAnnotation()[a];
2202             newann.adjustForAlignment();
2203             newann.padAnnotation(alwidth);
2204             if (newann.graphGroup > -1)
2205             {
2206               if (newann.graphGroup > -1)
2207               {
2208                 if (newGraphGroups.size() <= newann.graphGroup
2209                         || newGraphGroups.get(newann.graphGroup) == null)
2210                 {
2211                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2212                   {
2213                     newGraphGroups.add(q, null);
2214                   }
2215                   newGraphGroups.set(newann.graphGroup, new Integer(
2216                           ++fgroup));
2217                 }
2218                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2219                         .intValue();
2220               }
2221             }
2222             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2223             // was
2224             // duplicated
2225             // earlier
2226             alignment
2227                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2228           }
2229         }
2230       }
2231       if (!newAlignment)
2232       {
2233
2234         // propagate alignment changed.
2235         vpRanges.setEndSeq(alignment.getHeight());
2236         if (annotationAdded)
2237         {
2238           // Duplicate sequence annotation in all views.
2239           AlignmentI[] alview = this.getViewAlignments();
2240           for (int i = 0; i < sequences.length; i++)
2241           {
2242             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2243             if (sann == null)
2244             {
2245               continue;
2246             }
2247             for (int avnum = 0; avnum < alview.length; avnum++)
2248             {
2249               if (alview[avnum] != alignment)
2250               {
2251                 // duplicate in a view other than the one with input focus
2252                 int avwidth = alview[avnum].getWidth() + 1;
2253                 // this relies on sann being preserved after we
2254                 // modify the sequence's annotation array for each duplication
2255                 for (int a = 0; a < sann.length; a++)
2256                 {
2257                   AlignmentAnnotation newann = new AlignmentAnnotation(
2258                           sann[a]);
2259                   sequences[i].addAlignmentAnnotation(newann);
2260                   newann.padAnnotation(avwidth);
2261                   alview[avnum].addAnnotation(newann); // annotation was
2262                   // duplicated earlier
2263                   // TODO JAL-1145 graphGroups are not updated for sequence
2264                   // annotation added to several views. This may cause
2265                   // strangeness
2266                   alview[avnum].setAnnotationIndex(newann, a);
2267                 }
2268               }
2269             }
2270           }
2271           buildSortByAnnotationScoresMenu();
2272         }
2273         viewport.firePropertyChange("alignment", null,
2274                 alignment.getSequences());
2275         if (alignPanels != null)
2276         {
2277           for (AlignmentPanel ap : alignPanels)
2278           {
2279             ap.validateAnnotationDimensions(false);
2280           }
2281         }
2282         else
2283         {
2284           alignPanel.validateAnnotationDimensions(false);
2285         }
2286
2287       }
2288       else
2289       {
2290         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2291                 DEFAULT_HEIGHT);
2292         String newtitle = new String("Copied sequences");
2293
2294         if (Desktop.jalviewClipboard != null
2295                 && Desktop.jalviewClipboard[2] != null)
2296         {
2297           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2298           for (int[] region : hc)
2299           {
2300             af.viewport.hideColumns(region[0], region[1]);
2301           }
2302         }
2303
2304         // >>>This is a fix for the moment, until a better solution is
2305         // found!!<<<
2306         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2307                 .transferSettings(
2308                         alignPanel.getSeqPanel().seqCanvas
2309                                 .getFeatureRenderer());
2310
2311         // TODO: maintain provenance of an alignment, rather than just make the
2312         // title a concatenation of operations.
2313         if (!externalPaste)
2314         {
2315           if (title.startsWith("Copied sequences"))
2316           {
2317             newtitle = title;
2318           }
2319           else
2320           {
2321             newtitle = newtitle.concat("- from " + title);
2322           }
2323         }
2324         else
2325         {
2326           newtitle = new String("Pasted sequences");
2327         }
2328
2329         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2330                 DEFAULT_HEIGHT);
2331
2332       }
2333
2334     } catch (Exception ex)
2335     {
2336       ex.printStackTrace();
2337       System.out.println("Exception whilst pasting: " + ex);
2338       // could be anything being pasted in here
2339     }
2340   }
2341
2342   @Override
2343   protected void expand_newalign(ActionEvent e)
2344   {
2345     try
2346     {
2347       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2348               .getAlignment(), -1);
2349       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2350               DEFAULT_HEIGHT);
2351       String newtitle = new String("Flanking alignment");
2352
2353       if (Desktop.jalviewClipboard != null
2354               && Desktop.jalviewClipboard[2] != null)
2355       {
2356         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2357         for (int region[] : hc)
2358         {
2359           af.viewport.hideColumns(region[0], region[1]);
2360         }
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(
2367                       alignPanel.getSeqPanel().seqCanvas
2368                               .getFeatureRenderer());
2369
2370       // TODO: maintain provenance of an alignment, rather than just make the
2371       // title a concatenation of operations.
2372       {
2373         if (title.startsWith("Copied sequences"))
2374         {
2375           newtitle = title;
2376         }
2377         else
2378         {
2379           newtitle = newtitle.concat("- from " + title);
2380         }
2381       }
2382
2383       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2384
2385     } catch (Exception ex)
2386     {
2387       ex.printStackTrace();
2388       System.out.println("Exception whilst pasting: " + ex);
2389       // could be anything being pasted in here
2390     } catch (OutOfMemoryError oom)
2391     {
2392       new OOMWarning("Viewing flanking region of alignment", oom);
2393     }
2394   }
2395
2396   /**
2397    * DOCUMENT ME!
2398    *
2399    * @param e
2400    *          DOCUMENT ME!
2401    */
2402   @Override
2403   protected void cut_actionPerformed(ActionEvent e)
2404   {
2405     copy_actionPerformed(null);
2406     delete_actionPerformed(null);
2407   }
2408
2409   /**
2410    * DOCUMENT ME!
2411    *
2412    * @param e
2413    *          DOCUMENT ME!
2414    */
2415   @Override
2416   protected void delete_actionPerformed(ActionEvent evt)
2417   {
2418
2419     SequenceGroup sg = viewport.getSelectionGroup();
2420     if (sg == null)
2421     {
2422       return;
2423     }
2424
2425     /*
2426      * If the cut affects all sequences, warn, remove highlighted columns
2427      */
2428     if (sg.getSize() == viewport.getAlignment().getHeight())
2429     {
2430       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2431               .getAlignment().getWidth()) ? true : false;
2432       if (isEntireAlignWidth)
2433       {
2434         int confirm = JvOptionPane.showConfirmDialog(this,
2435                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2436                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2437                 JvOptionPane.OK_CANCEL_OPTION);
2438
2439         if (confirm == JvOptionPane.CANCEL_OPTION
2440                 || confirm == JvOptionPane.CLOSED_OPTION)
2441         {
2442           return;
2443         }
2444       }
2445       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2446               sg.getEndRes() + 1);
2447     }
2448     SequenceI[] cut = sg.getSequences()
2449             .toArray(new SequenceI[sg.getSize()]);
2450
2451     addHistoryItem(new EditCommand(
2452             MessageManager.getString("label.cut_sequences"), Action.CUT,
2453             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2454             viewport.getAlignment()));
2455
2456     viewport.setSelectionGroup(null);
2457     viewport.sendSelection();
2458     viewport.getAlignment().deleteGroup(sg);
2459
2460     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2461             .getSequences());
2462     if (viewport.getAlignment().getHeight() < 1)
2463     {
2464       try
2465       {
2466         this.setClosed(true);
2467       } catch (Exception ex)
2468       {
2469       }
2470     }
2471   }
2472
2473   /**
2474    * DOCUMENT ME!
2475    *
2476    * @param e
2477    *          DOCUMENT ME!
2478    */
2479   @Override
2480   protected void deleteGroups_actionPerformed(ActionEvent e)
2481   {
2482     if (avc.deleteGroups())
2483     {
2484       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2485       alignPanel.updateAnnotation();
2486       alignPanel.paintAlignment(true);
2487     }
2488   }
2489
2490   /**
2491    * DOCUMENT ME!
2492    *
2493    * @param e
2494    *          DOCUMENT ME!
2495    */
2496   @Override
2497   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2498   {
2499     SequenceGroup sg = new SequenceGroup();
2500
2501     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2502     {
2503       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2504     }
2505
2506     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2507     viewport.setSelectionGroup(sg);
2508     viewport.sendSelection();
2509     // JAL-2034 - should delegate to
2510     // alignPanel to decide if overview needs
2511     // updating.
2512     alignPanel.paintAlignment(false);
2513     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2514   }
2515
2516   /**
2517    * DOCUMENT ME!
2518    *
2519    * @param e
2520    *          DOCUMENT ME!
2521    */
2522   @Override
2523   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2524   {
2525     if (viewport.cursorMode)
2526     {
2527       alignPanel.getSeqPanel().keyboardNo1 = null;
2528       alignPanel.getSeqPanel().keyboardNo2 = null;
2529     }
2530     viewport.setSelectionGroup(null);
2531     viewport.getColumnSelection().clear();
2532     viewport.setSelectionGroup(null);
2533     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2534     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2535     // JAL-2034 - should delegate to
2536     // alignPanel to decide if overview needs
2537     // updating.
2538     alignPanel.paintAlignment(false);
2539     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2540     viewport.sendSelection();
2541   }
2542
2543   /**
2544    * DOCUMENT ME!
2545    *
2546    * @param e
2547    *          DOCUMENT ME!
2548    */
2549   @Override
2550   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2551   {
2552     SequenceGroup sg = viewport.getSelectionGroup();
2553
2554     if (sg == null)
2555     {
2556       selectAllSequenceMenuItem_actionPerformed(null);
2557
2558       return;
2559     }
2560
2561     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2562     {
2563       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2564     }
2565     // JAL-2034 - should delegate to
2566     // alignPanel to decide if overview needs
2567     // updating.
2568
2569     alignPanel.paintAlignment(true);
2570     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2571     viewport.sendSelection();
2572   }
2573
2574   @Override
2575   public void invertColSel_actionPerformed(ActionEvent e)
2576   {
2577     viewport.invertColumnSelection();
2578     alignPanel.paintAlignment(true);
2579     viewport.sendSelection();
2580   }
2581
2582   /**
2583    * DOCUMENT ME!
2584    *
2585    * @param e
2586    *          DOCUMENT ME!
2587    */
2588   @Override
2589   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2590   {
2591     trimAlignment(true);
2592   }
2593
2594   /**
2595    * DOCUMENT ME!
2596    *
2597    * @param e
2598    *          DOCUMENT ME!
2599    */
2600   @Override
2601   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2602   {
2603     trimAlignment(false);
2604   }
2605
2606   void trimAlignment(boolean trimLeft)
2607   {
2608     ColumnSelection colSel = viewport.getColumnSelection();
2609     int column;
2610
2611     if (!colSel.isEmpty())
2612     {
2613       if (trimLeft)
2614       {
2615         column = colSel.getMin();
2616       }
2617       else
2618       {
2619         column = colSel.getMax();
2620       }
2621
2622       SequenceI[] seqs;
2623       if (viewport.getSelectionGroup() != null)
2624       {
2625         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2626                 viewport.getHiddenRepSequences());
2627       }
2628       else
2629       {
2630         seqs = viewport.getAlignment().getSequencesArray();
2631       }
2632
2633       TrimRegionCommand trimRegion;
2634       if (trimLeft)
2635       {
2636         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2637                 column, viewport.getAlignment());
2638         vpRanges.setStartRes(0);
2639       }
2640       else
2641       {
2642         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2643                 column, viewport.getAlignment());
2644       }
2645
2646       statusBar.setText(MessageManager.formatMessage(
2647               "label.removed_columns",
2648               new String[] { Integer.valueOf(trimRegion.getSize())
2649                       .toString() }));
2650
2651       addHistoryItem(trimRegion);
2652
2653       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2654       {
2655         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2656                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2657         {
2658           viewport.getAlignment().deleteGroup(sg);
2659         }
2660       }
2661
2662       viewport.firePropertyChange("alignment", null, viewport
2663               .getAlignment().getSequences());
2664     }
2665   }
2666
2667   /**
2668    * DOCUMENT ME!
2669    *
2670    * @param e
2671    *          DOCUMENT ME!
2672    */
2673   @Override
2674   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2675   {
2676     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2677
2678     SequenceI[] seqs;
2679     if (viewport.getSelectionGroup() != null)
2680     {
2681       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2682               viewport.getHiddenRepSequences());
2683       start = viewport.getSelectionGroup().getStartRes();
2684       end = viewport.getSelectionGroup().getEndRes();
2685     }
2686     else
2687     {
2688       seqs = viewport.getAlignment().getSequencesArray();
2689     }
2690
2691     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2692             "Remove Gapped Columns", seqs, start, end,
2693             viewport.getAlignment());
2694
2695     addHistoryItem(removeGapCols);
2696
2697     statusBar.setText(MessageManager.formatMessage(
2698             "label.removed_empty_columns",
2699             new Object[] { Integer.valueOf(removeGapCols.getSize())
2700                     .toString() }));
2701
2702     // This is to maintain viewport position on first residue
2703     // of first sequence
2704     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2705     int startRes = seq.findPosition(vpRanges.getStartRes());
2706     // ShiftList shifts;
2707     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2708     // edit.alColumnChanges=shifts.getInverse();
2709     // if (viewport.hasHiddenColumns)
2710     // viewport.getColumnSelection().compensateForEdits(shifts);
2711     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2712     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2713             .getSequences());
2714
2715   }
2716
2717   /**
2718    * DOCUMENT ME!
2719    *
2720    * @param e
2721    *          DOCUMENT ME!
2722    */
2723   @Override
2724   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2725   {
2726     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2727
2728     SequenceI[] seqs;
2729     if (viewport.getSelectionGroup() != null)
2730     {
2731       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2732               viewport.getHiddenRepSequences());
2733       start = viewport.getSelectionGroup().getStartRes();
2734       end = viewport.getSelectionGroup().getEndRes();
2735     }
2736     else
2737     {
2738       seqs = viewport.getAlignment().getSequencesArray();
2739     }
2740
2741     // This is to maintain viewport position on first residue
2742     // of first sequence
2743     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2744     int startRes = seq.findPosition(vpRanges.getStartRes());
2745
2746     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2747             viewport.getAlignment()));
2748
2749     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2750
2751     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2752             .getSequences());
2753
2754   }
2755
2756   /**
2757    * DOCUMENT ME!
2758    *
2759    * @param e
2760    *          DOCUMENT ME!
2761    */
2762   @Override
2763   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2764   {
2765     viewport.setPadGaps(padGapsMenuitem.isSelected());
2766     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2767             .getSequences());
2768   }
2769
2770   /**
2771    * DOCUMENT ME!
2772    *
2773    * @param e
2774    *          DOCUMENT ME!
2775    */
2776   @Override
2777   public void findMenuItem_actionPerformed(ActionEvent e)
2778   {
2779     new Finder();
2780   }
2781
2782   /**
2783    * Create a new view of the current alignment.
2784    */
2785   @Override
2786   public void newView_actionPerformed(ActionEvent e)
2787   {
2788     newView(null, true);
2789   }
2790
2791   /**
2792    * Creates and shows a new view of the current alignment.
2793    *
2794    * @param viewTitle
2795    *          title of newly created view; if null, one will be generated
2796    * @param copyAnnotation
2797    *          if true then duplicate all annnotation, groups and settings
2798    * @return new alignment panel, already displayed.
2799    */
2800   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2801   {
2802     /*
2803      * Create a new AlignmentPanel (with its own, new Viewport)
2804      */
2805     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2806             true);
2807     if (!copyAnnotation)
2808     {
2809       /*
2810        * remove all groups and annotation except for the automatic stuff
2811        */
2812       newap.av.getAlignment().deleteAllGroups();
2813       newap.av.getAlignment().deleteAllAnnotations(false);
2814     }
2815
2816     newap.av.setGatherViewsHere(false);
2817
2818     if (viewport.viewName == null)
2819     {
2820       viewport.viewName = MessageManager
2821               .getString("label.view_name_original");
2822     }
2823
2824     /*
2825      * Views share the same edits undo and redo stacks
2826      */
2827     newap.av.setHistoryList(viewport.getHistoryList());
2828     newap.av.setRedoList(viewport.getRedoList());
2829
2830     /*
2831      * Views share the same mappings; need to deregister any new mappings
2832      * created by copyAlignPanel, and register the new reference to the shared
2833      * mappings
2834      */
2835     newap.av.replaceMappings(viewport.getAlignment());
2836
2837     /*
2838      * start up cDNA consensus (if applicable) now mappings are in place
2839      */
2840     if (newap.av.initComplementConsensus())
2841     {
2842       newap.refresh(true); // adjust layout of annotations
2843     }
2844
2845     newap.av.viewName = getNewViewName(viewTitle);
2846
2847     addAlignmentPanel(newap, true);
2848     newap.alignmentChanged();
2849
2850     if (alignPanels.size() == 2)
2851     {
2852       viewport.setGatherViewsHere(true);
2853     }
2854     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2855     return newap;
2856   }
2857
2858   /**
2859    * Make a new name for the view, ensuring it is unique within the current
2860    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2861    * these now use viewId. Unique view names are still desirable for usability.)
2862    *
2863    * @param viewTitle
2864    * @return
2865    */
2866   protected String getNewViewName(String viewTitle)
2867   {
2868     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2869     boolean addFirstIndex = false;
2870     if (viewTitle == null || viewTitle.trim().length() == 0)
2871     {
2872       viewTitle = MessageManager.getString("action.view");
2873       addFirstIndex = true;
2874     }
2875     else
2876     {
2877       index = 1;// we count from 1 if given a specific name
2878     }
2879     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2880
2881     List<Component> comps = PaintRefresher.components.get(viewport
2882             .getSequenceSetId());
2883
2884     List<String> existingNames = getExistingViewNames(comps);
2885
2886     while (existingNames.contains(newViewName))
2887     {
2888       newViewName = viewTitle + " " + (++index);
2889     }
2890     return newViewName;
2891   }
2892
2893   /**
2894    * Returns a list of distinct view names found in the given list of
2895    * components. View names are held on the viewport of an AlignmentPanel.
2896    *
2897    * @param comps
2898    * @return
2899    */
2900   protected List<String> getExistingViewNames(List<Component> comps)
2901   {
2902     List<String> existingNames = new ArrayList<>();
2903     for (Component comp : comps)
2904     {
2905       if (comp instanceof AlignmentPanel)
2906       {
2907         AlignmentPanel ap = (AlignmentPanel) comp;
2908         if (!existingNames.contains(ap.av.viewName))
2909         {
2910           existingNames.add(ap.av.viewName);
2911         }
2912       }
2913     }
2914     return existingNames;
2915   }
2916
2917   /**
2918    * Explode tabbed views into separate windows.
2919    */
2920   @Override
2921   public void expandViews_actionPerformed(ActionEvent e)
2922   {
2923     Desktop.explodeViews(this);
2924   }
2925
2926   /**
2927    * Gather views in separate windows back into a tabbed presentation.
2928    */
2929   @Override
2930   public void gatherViews_actionPerformed(ActionEvent e)
2931   {
2932     Desktop.instance.gatherViews(this);
2933   }
2934
2935   /**
2936    * DOCUMENT ME!
2937    *
2938    * @param e
2939    *          DOCUMENT ME!
2940    */
2941   @Override
2942   public void font_actionPerformed(ActionEvent e)
2943   {
2944     new FontChooser(alignPanel);
2945   }
2946
2947   /**
2948    * DOCUMENT ME!
2949    *
2950    * @param e
2951    *          DOCUMENT ME!
2952    */
2953   @Override
2954   protected void seqLimit_actionPerformed(ActionEvent e)
2955   {
2956     viewport.setShowJVSuffix(seqLimits.isSelected());
2957
2958     alignPanel.getIdPanel().getIdCanvas()
2959             .setPreferredSize(alignPanel.calculateIdWidth());
2960     alignPanel.paintAlignment(true);
2961   }
2962
2963   @Override
2964   public void idRightAlign_actionPerformed(ActionEvent e)
2965   {
2966     viewport.setRightAlignIds(idRightAlign.isSelected());
2967     alignPanel.paintAlignment(true);
2968   }
2969
2970   @Override
2971   public void centreColumnLabels_actionPerformed(ActionEvent e)
2972   {
2973     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2974     alignPanel.paintAlignment(true);
2975   }
2976
2977   /*
2978    * (non-Javadoc)
2979    *
2980    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2981    */
2982   @Override
2983   protected void followHighlight_actionPerformed()
2984   {
2985     /*
2986      * Set the 'follow' flag on the Viewport (and scroll to position if now
2987      * true).
2988      */
2989     final boolean state = this.followHighlightMenuItem.getState();
2990     viewport.setFollowHighlight(state);
2991     if (state)
2992     {
2993       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2994     }
2995   }
2996
2997   /**
2998    * DOCUMENT ME!
2999    *
3000    * @param e
3001    *          DOCUMENT ME!
3002    */
3003   @Override
3004   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3005   {
3006     viewport.setColourText(colourTextMenuItem.isSelected());
3007     alignPanel.paintAlignment(true);
3008   }
3009
3010   /**
3011    * DOCUMENT ME!
3012    *
3013    * @param e
3014    *          DOCUMENT ME!
3015    */
3016   @Override
3017   public void wrapMenuItem_actionPerformed(ActionEvent e)
3018   {
3019     scaleAbove.setVisible(wrapMenuItem.isSelected());
3020     scaleLeft.setVisible(wrapMenuItem.isSelected());
3021     scaleRight.setVisible(wrapMenuItem.isSelected());
3022     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3023     alignPanel.updateLayout();
3024   }
3025
3026   @Override
3027   public void showAllSeqs_actionPerformed(ActionEvent e)
3028   {
3029     viewport.showAllHiddenSeqs();
3030   }
3031
3032   @Override
3033   public void showAllColumns_actionPerformed(ActionEvent e)
3034   {
3035     viewport.showAllHiddenColumns();
3036     repaint();
3037     viewport.sendSelection();
3038   }
3039
3040   @Override
3041   public void hideSelSequences_actionPerformed(ActionEvent e)
3042   {
3043     viewport.hideAllSelectedSeqs();
3044     // alignPanel.paintAlignment(true);
3045   }
3046
3047   /**
3048    * called by key handler and the hide all/show all menu items
3049    *
3050    * @param toggleSeqs
3051    * @param toggleCols
3052    */
3053   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3054   {
3055
3056     boolean hide = false;
3057     SequenceGroup sg = viewport.getSelectionGroup();
3058     if (!toggleSeqs && !toggleCols)
3059     {
3060       // Hide everything by the current selection - this is a hack - we do the
3061       // invert and then hide
3062       // first check that there will be visible columns after the invert.
3063       if (viewport.hasSelectedColumns()
3064               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3065                       .getEndRes()))
3066       {
3067         // now invert the sequence set, if required - empty selection implies
3068         // that no hiding is required.
3069         if (sg != null)
3070         {
3071           invertSequenceMenuItem_actionPerformed(null);
3072           sg = viewport.getSelectionGroup();
3073           toggleSeqs = true;
3074
3075         }
3076         viewport.expandColSelection(sg, true);
3077         // finally invert the column selection and get the new sequence
3078         // selection.
3079         invertColSel_actionPerformed(null);
3080         toggleCols = true;
3081       }
3082     }
3083
3084     if (toggleSeqs)
3085     {
3086       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3087       {
3088         hideSelSequences_actionPerformed(null);
3089         hide = true;
3090       }
3091       else if (!(toggleCols && viewport.hasSelectedColumns()))
3092       {
3093         showAllSeqs_actionPerformed(null);
3094       }
3095     }
3096
3097     if (toggleCols)
3098     {
3099       if (viewport.hasSelectedColumns())
3100       {
3101         hideSelColumns_actionPerformed(null);
3102         if (!toggleSeqs)
3103         {
3104           viewport.setSelectionGroup(sg);
3105         }
3106       }
3107       else if (!hide)
3108       {
3109         showAllColumns_actionPerformed(null);
3110       }
3111     }
3112   }
3113
3114   /*
3115    * (non-Javadoc)
3116    *
3117    * @see
3118    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3119    * event.ActionEvent)
3120    */
3121   @Override
3122   public void hideAllButSelection_actionPerformed(ActionEvent e)
3123   {
3124     toggleHiddenRegions(false, false);
3125     viewport.sendSelection();
3126   }
3127
3128   /*
3129    * (non-Javadoc)
3130    *
3131    * @see
3132    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3133    * .ActionEvent)
3134    */
3135   @Override
3136   public void hideAllSelection_actionPerformed(ActionEvent e)
3137   {
3138     SequenceGroup sg = viewport.getSelectionGroup();
3139     viewport.expandColSelection(sg, false);
3140     viewport.hideAllSelectedSeqs();
3141     viewport.hideSelectedColumns();
3142     alignPanel.paintAlignment(true);
3143     viewport.sendSelection();
3144   }
3145
3146   /*
3147    * (non-Javadoc)
3148    *
3149    * @see
3150    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3151    * ActionEvent)
3152    */
3153   @Override
3154   public void showAllhidden_actionPerformed(ActionEvent e)
3155   {
3156     viewport.showAllHiddenColumns();
3157     viewport.showAllHiddenSeqs();
3158     alignPanel.paintAlignment(true);
3159     viewport.sendSelection();
3160   }
3161
3162   @Override
3163   public void hideSelColumns_actionPerformed(ActionEvent e)
3164   {
3165     viewport.hideSelectedColumns();
3166     alignPanel.paintAlignment(true);
3167     viewport.sendSelection();
3168   }
3169
3170   @Override
3171   public void hiddenMarkers_actionPerformed(ActionEvent e)
3172   {
3173     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3174     repaint();
3175   }
3176
3177   /**
3178    * DOCUMENT ME!
3179    *
3180    * @param e
3181    *          DOCUMENT ME!
3182    */
3183   @Override
3184   protected void scaleAbove_actionPerformed(ActionEvent e)
3185   {
3186     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3187     alignPanel.paintAlignment(true);
3188   }
3189
3190   /**
3191    * DOCUMENT ME!
3192    *
3193    * @param e
3194    *          DOCUMENT ME!
3195    */
3196   @Override
3197   protected void scaleLeft_actionPerformed(ActionEvent e)
3198   {
3199     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3200     alignPanel.paintAlignment(true);
3201   }
3202
3203   /**
3204    * DOCUMENT ME!
3205    *
3206    * @param e
3207    *          DOCUMENT ME!
3208    */
3209   @Override
3210   protected void scaleRight_actionPerformed(ActionEvent e)
3211   {
3212     viewport.setScaleRightWrapped(scaleRight.isSelected());
3213     alignPanel.paintAlignment(true);
3214   }
3215
3216   /**
3217    * DOCUMENT ME!
3218    *
3219    * @param e
3220    *          DOCUMENT ME!
3221    */
3222   @Override
3223   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3224   {
3225     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3226     alignPanel.paintAlignment(true);
3227   }
3228
3229   /**
3230    * DOCUMENT ME!
3231    *
3232    * @param e
3233    *          DOCUMENT ME!
3234    */
3235   @Override
3236   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3237   {
3238     viewport.setShowText(viewTextMenuItem.isSelected());
3239     alignPanel.paintAlignment(true);
3240   }
3241
3242   /**
3243    * DOCUMENT ME!
3244    *
3245    * @param e
3246    *          DOCUMENT ME!
3247    */
3248   @Override
3249   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3250   {
3251     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3252     alignPanel.paintAlignment(true);
3253   }
3254
3255   public FeatureSettings featureSettings;
3256
3257   @Override
3258   public FeatureSettingsControllerI getFeatureSettingsUI()
3259   {
3260     return featureSettings;
3261   }
3262
3263   @Override
3264   public void featureSettings_actionPerformed(ActionEvent e)
3265   {
3266     if (featureSettings != null)
3267     {
3268       featureSettings.close();
3269       featureSettings = null;
3270     }
3271     if (!showSeqFeatures.isSelected())
3272     {
3273       // make sure features are actually displayed
3274       showSeqFeatures.setSelected(true);
3275       showSeqFeatures_actionPerformed(null);
3276     }
3277     featureSettings = new FeatureSettings(this);
3278   }
3279
3280   /**
3281    * Set or clear 'Show Sequence Features'
3282    *
3283    * @param evt
3284    *          DOCUMENT ME!
3285    */
3286   @Override
3287   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3288   {
3289     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3290     alignPanel.paintAlignment(true);
3291     if (alignPanel.getOverviewPanel() != null)
3292     {
3293       alignPanel.getOverviewPanel().updateOverviewImage();
3294     }
3295   }
3296
3297   /**
3298    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3299    * the annotations panel as a whole.
3300    *
3301    * The options to show/hide all annotations should be enabled when the panel
3302    * is shown, and disabled when the panel is hidden.
3303    *
3304    * @param e
3305    */
3306   @Override
3307   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3308   {
3309     final boolean setVisible = annotationPanelMenuItem.isSelected();
3310     viewport.setShowAnnotation(setVisible);
3311     this.showAllSeqAnnotations.setEnabled(setVisible);
3312     this.hideAllSeqAnnotations.setEnabled(setVisible);
3313     this.showAllAlAnnotations.setEnabled(setVisible);
3314     this.hideAllAlAnnotations.setEnabled(setVisible);
3315     alignPanel.updateLayout();
3316   }
3317
3318   @Override
3319   public void alignmentProperties()
3320   {
3321     JEditorPane editPane = new JEditorPane("text/html", "");
3322     editPane.setEditable(false);
3323     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3324             .formatAsHtml();
3325     editPane.setText(MessageManager.formatMessage("label.html_content",
3326             new Object[] { contents.toString() }));
3327     JInternalFrame frame = new JInternalFrame();
3328     frame.getContentPane().add(new JScrollPane(editPane));
3329
3330     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3331             "label.alignment_properties", new Object[] { getTitle() }),
3332             500, 400);
3333   }
3334
3335   /**
3336    * DOCUMENT ME!
3337    *
3338    * @param e
3339    *          DOCUMENT ME!
3340    */
3341   @Override
3342   public void overviewMenuItem_actionPerformed(ActionEvent e)
3343   {
3344     if (alignPanel.overviewPanel != null)
3345     {
3346       return;
3347     }
3348
3349     JInternalFrame frame = new JInternalFrame();
3350     OverviewPanel overview = new OverviewPanel(alignPanel);
3351     frame.setContentPane(overview);
3352     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3353             "label.overview_params", new Object[] { this.getTitle() }),
3354             true, frame.getWidth(), frame.getHeight(), true, true);
3355     frame.pack();
3356     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3357     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3358     {
3359       @Override
3360       public void internalFrameClosed(
3361               javax.swing.event.InternalFrameEvent evt)
3362       {
3363         alignPanel.setOverviewPanel(null);
3364       };
3365     });
3366
3367     alignPanel.setOverviewPanel(overview);
3368   }
3369
3370   @Override
3371   public void textColour_actionPerformed()
3372   {
3373     new TextColourChooser().chooseColour(alignPanel, null);
3374   }
3375
3376   /*
3377    * public void covariationColour_actionPerformed() {
3378    * changeColour(new
3379    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3380    * ()[0])); }
3381    */
3382   @Override
3383   public void annotationColour_actionPerformed()
3384   {
3385     new AnnotationColourChooser(viewport, alignPanel);
3386   }
3387
3388   @Override
3389   public void annotationColumn_actionPerformed(ActionEvent e)
3390   {
3391     new AnnotationColumnChooser(viewport, alignPanel);
3392   }
3393
3394   /**
3395    * Action on the user checking or unchecking the option to apply the selected
3396    * colour scheme to all groups. If unchecked, groups may have their own
3397    * independent colour schemes.
3398    *
3399    * @param selected
3400    */
3401   @Override
3402   public void applyToAllGroups_actionPerformed(boolean selected)
3403   {
3404     viewport.setColourAppliesToAllGroups(selected);
3405   }
3406
3407   /**
3408    * Action on user selecting a colour from the colour menu
3409    *
3410    * @param name
3411    *          the name (not the menu item label!) of the colour scheme
3412    */
3413   @Override
3414   public void changeColour_actionPerformed(String name)
3415   {
3416     /*
3417      * 'User Defined' opens a panel to configure or load a
3418      * user-defined colour scheme
3419      */
3420     if (ResidueColourScheme.USER_DEFINED.equals(name))
3421     {
3422       new UserDefinedColours(alignPanel);
3423       return;
3424     }
3425
3426     /*
3427      * otherwise set the chosen colour scheme (or null for 'None')
3428      */
3429     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3430             viewport.getAlignment(), viewport.getHiddenRepSequences());
3431     changeColour(cs);
3432   }
3433
3434   /**
3435    * Actions on setting or changing the alignment colour scheme
3436    *
3437    * @param cs
3438    */
3439   @Override
3440   public void changeColour(ColourSchemeI cs)
3441   {
3442     // TODO: pull up to controller method
3443     ColourMenuHelper.setColourSelected(colourMenu, cs);
3444
3445     viewport.setGlobalColourScheme(cs);
3446
3447     alignPanel.paintAlignment(true);
3448   }
3449
3450   /**
3451    * Show the PID threshold slider panel
3452    */
3453   @Override
3454   protected void modifyPID_actionPerformed()
3455   {
3456     SliderPanel.setPIDSliderSource(alignPanel,
3457             viewport.getResidueShading(), alignPanel.getViewName());
3458     SliderPanel.showPIDSlider();
3459   }
3460
3461   /**
3462    * Show the Conservation slider panel
3463    */
3464   @Override
3465   protected void modifyConservation_actionPerformed()
3466   {
3467     SliderPanel.setConservationSlider(alignPanel,
3468             viewport.getResidueShading(), alignPanel.getViewName());
3469     SliderPanel.showConservationSlider();
3470   }
3471
3472   /**
3473    * Action on selecting or deselecting (Colour) By Conservation
3474    */
3475   @Override
3476   public void conservationMenuItem_actionPerformed(boolean selected)
3477   {
3478     modifyConservation.setEnabled(selected);
3479     viewport.setConservationSelected(selected);
3480     viewport.getResidueShading().setConservationApplied(selected);
3481
3482     changeColour(viewport.getGlobalColourScheme());
3483     if (selected)
3484     {
3485       modifyConservation_actionPerformed();
3486     }
3487     else
3488     {
3489       SliderPanel.hideConservationSlider();
3490     }
3491   }
3492
3493   /**
3494    * Action on selecting or deselecting (Colour) Above PID Threshold
3495    */
3496   @Override
3497   public void abovePIDThreshold_actionPerformed(boolean selected)
3498   {
3499     modifyPID.setEnabled(selected);
3500     viewport.setAbovePIDThreshold(selected);
3501     if (!selected)
3502     {
3503       viewport.getResidueShading().setThreshold(0,
3504               viewport.isIgnoreGapsConsensus());
3505     }
3506
3507     changeColour(viewport.getGlobalColourScheme());
3508     if (selected)
3509     {
3510       modifyPID_actionPerformed();
3511     }
3512     else
3513     {
3514       SliderPanel.hidePIDSlider();
3515     }
3516   }
3517
3518   /**
3519    * DOCUMENT ME!
3520    *
3521    * @param e
3522    *          DOCUMENT ME!
3523    */
3524   @Override
3525   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3526   {
3527     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3528     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3529             .getAlignment().getSequenceAt(0));
3530     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3531             viewport.getAlignment()));
3532     alignPanel.paintAlignment(true);
3533   }
3534
3535   /**
3536    * DOCUMENT ME!
3537    *
3538    * @param e
3539    *          DOCUMENT ME!
3540    */
3541   @Override
3542   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3543   {
3544     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3545     AlignmentSorter.sortByID(viewport.getAlignment());
3546     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3547             viewport.getAlignment()));
3548     alignPanel.paintAlignment(true);
3549   }
3550
3551   /**
3552    * DOCUMENT ME!
3553    *
3554    * @param e
3555    *          DOCUMENT ME!
3556    */
3557   @Override
3558   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3559   {
3560     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3561     AlignmentSorter.sortByLength(viewport.getAlignment());
3562     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3563             viewport.getAlignment()));
3564     alignPanel.paintAlignment(true);
3565   }
3566
3567   /**
3568    * DOCUMENT ME!
3569    *
3570    * @param e
3571    *          DOCUMENT ME!
3572    */
3573   @Override
3574   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3575   {
3576     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3577     AlignmentSorter.sortByGroup(viewport.getAlignment());
3578     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3579             viewport.getAlignment()));
3580
3581     alignPanel.paintAlignment(true);
3582   }
3583
3584   /**
3585    * DOCUMENT ME!
3586    *
3587    * @param e
3588    *          DOCUMENT ME!
3589    */
3590   @Override
3591   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3592   {
3593     new RedundancyPanel(alignPanel, this);
3594   }
3595
3596   /**
3597    * DOCUMENT ME!
3598    *
3599    * @param e
3600    *          DOCUMENT ME!
3601    */
3602   @Override
3603   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3604   {
3605     if ((viewport.getSelectionGroup() == null)
3606             || (viewport.getSelectionGroup().getSize() < 2))
3607     {
3608       JvOptionPane.showInternalMessageDialog(this, MessageManager
3609               .getString("label.you_must_select_least_two_sequences"),
3610               MessageManager.getString("label.invalid_selection"),
3611               JvOptionPane.WARNING_MESSAGE);
3612     }
3613     else
3614     {
3615       JInternalFrame frame = new JInternalFrame();
3616       frame.setContentPane(new PairwiseAlignPanel(viewport));
3617       Desktop.addInternalFrame(frame,
3618               MessageManager.getString("action.pairwise_alignment"), 600,
3619               500);
3620     }
3621   }
3622
3623   @Override
3624   public void autoCalculate_actionPerformed(ActionEvent e)
3625   {
3626     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3627     if (viewport.autoCalculateConsensus)
3628     {
3629       viewport.firePropertyChange("alignment", null, viewport
3630               .getAlignment().getSequences());
3631     }
3632   }
3633
3634   @Override
3635   public void sortByTreeOption_actionPerformed(ActionEvent e)
3636   {
3637     viewport.sortByTree = sortByTree.isSelected();
3638   }
3639
3640   @Override
3641   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3642   {
3643     viewport.followSelection = listenToViewSelections.isSelected();
3644   }
3645
3646   /**
3647    * Constructs a tree panel and adds it to the desktop
3648    *
3649    * @param type
3650    *          tree type (NJ or AV)
3651    * @param modelName
3652    *          name of score model used to compute the tree
3653    * @param options
3654    *          parameters for the distance or similarity calculation
3655    */
3656   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3657   {
3658     String frameTitle = "";
3659     TreePanel tp;
3660
3661     boolean onSelection = false;
3662     if (viewport.getSelectionGroup() != null
3663             && viewport.getSelectionGroup().getSize() > 0)
3664     {
3665       SequenceGroup sg = viewport.getSelectionGroup();
3666
3667       /* Decide if the selection is a column region */
3668       for (SequenceI _s : sg.getSequences())
3669       {
3670         if (_s.getLength() < sg.getEndRes())
3671         {
3672           JvOptionPane
3673                   .showMessageDialog(
3674                           Desktop.desktop,
3675                           MessageManager
3676                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3677                           MessageManager
3678                                   .getString("label.sequences_selection_not_aligned"),
3679                           JvOptionPane.WARNING_MESSAGE);
3680
3681           return;
3682         }
3683       }
3684       onSelection = true;
3685     }
3686     else
3687     {
3688       if (viewport.getAlignment().getHeight() < 2)
3689       {
3690         return;
3691       }
3692     }
3693
3694     tp = new TreePanel(alignPanel, type, modelName, options);
3695     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3696
3697     frameTitle += " from ";
3698
3699     if (viewport.viewName != null)
3700     {
3701       frameTitle += viewport.viewName + " of ";
3702     }
3703
3704     frameTitle += this.title;
3705
3706     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3707   }
3708
3709   /**
3710    * DOCUMENT ME!
3711    *
3712    * @param title
3713    *          DOCUMENT ME!
3714    * @param order
3715    *          DOCUMENT ME!
3716    */
3717   public void addSortByOrderMenuItem(String title,
3718           final AlignmentOrder order)
3719   {
3720     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3721             "action.by_title_param", new Object[] { title }));
3722     sort.add(item);
3723     item.addActionListener(new java.awt.event.ActionListener()
3724     {
3725       @Override
3726       public void actionPerformed(ActionEvent e)
3727       {
3728         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3729
3730         // TODO: JBPNote - have to map order entries to curent SequenceI
3731         // pointers
3732         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3733
3734         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3735                 .getAlignment()));
3736
3737         alignPanel.paintAlignment(true);
3738       }
3739     });
3740   }
3741
3742   /**
3743    * Add a new sort by annotation score menu item
3744    *
3745    * @param sort
3746    *          the menu to add the option to
3747    * @param scoreLabel
3748    *          the label used to retrieve scores for each sequence on the
3749    *          alignment
3750    */
3751   public void addSortByAnnotScoreMenuItem(JMenu sort,
3752           final String scoreLabel)
3753   {
3754     final JMenuItem item = new JMenuItem(scoreLabel);
3755     sort.add(item);
3756     item.addActionListener(new java.awt.event.ActionListener()
3757     {
3758       @Override
3759       public void actionPerformed(ActionEvent e)
3760       {
3761         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3762         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3763                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3764         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3765                 viewport.getAlignment()));
3766         alignPanel.paintAlignment(true);
3767       }
3768     });
3769   }
3770
3771   /**
3772    * last hash for alignment's annotation array - used to minimise cost of
3773    * rebuild.
3774    */
3775   protected int _annotationScoreVectorHash;
3776
3777   /**
3778    * search the alignment and rebuild the sort by annotation score submenu the
3779    * last alignment annotation vector hash is stored to minimize cost of
3780    * rebuilding in subsequence calls.
3781    *
3782    */
3783   @Override
3784   public void buildSortByAnnotationScoresMenu()
3785   {
3786     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3787     {
3788       return;
3789     }
3790
3791     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3792     {
3793       sortByAnnotScore.removeAll();
3794       // almost certainly a quicker way to do this - but we keep it simple
3795       Hashtable scoreSorts = new Hashtable();
3796       AlignmentAnnotation aann[];
3797       for (SequenceI sqa : viewport.getAlignment().getSequences())
3798       {
3799         aann = sqa.getAnnotation();
3800         for (int i = 0; aann != null && i < aann.length; i++)
3801         {
3802           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3803           {
3804             scoreSorts.put(aann[i].label, aann[i].label);
3805           }
3806         }
3807       }
3808       Enumeration labels = scoreSorts.keys();
3809       while (labels.hasMoreElements())
3810       {
3811         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3812                 (String) labels.nextElement());
3813       }
3814       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3815       scoreSorts.clear();
3816
3817       _annotationScoreVectorHash = viewport.getAlignment()
3818               .getAlignmentAnnotation().hashCode();
3819     }
3820   }
3821
3822   /**
3823    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3824    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3825    * call. Listeners are added to remove the menu item when the treePanel is
3826    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3827    * modified.
3828    */
3829   @Override
3830   public void buildTreeSortMenu()
3831   {
3832     sortByTreeMenu.removeAll();
3833
3834     List<Component> comps = PaintRefresher.components.get(viewport
3835             .getSequenceSetId());
3836     List<TreePanel> treePanels = new ArrayList<>();
3837     for (Component comp : comps)
3838     {
3839       if (comp instanceof TreePanel)
3840       {
3841         treePanels.add((TreePanel) comp);
3842       }
3843     }
3844
3845     if (treePanels.size() < 1)
3846     {
3847       sortByTreeMenu.setVisible(false);
3848       return;
3849     }
3850
3851     sortByTreeMenu.setVisible(true);
3852
3853     for (final TreePanel tp : treePanels)
3854     {
3855       final JMenuItem item = new JMenuItem(tp.getTitle());
3856       item.addActionListener(new java.awt.event.ActionListener()
3857       {
3858         @Override
3859         public void actionPerformed(ActionEvent e)
3860         {
3861           tp.sortByTree_actionPerformed();
3862           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3863
3864         }
3865       });
3866
3867       sortByTreeMenu.add(item);
3868     }
3869   }
3870
3871   public boolean sortBy(AlignmentOrder alorder, String undoname)
3872   {
3873     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3874     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3875     if (undoname != null)
3876     {
3877       addHistoryItem(new OrderCommand(undoname, oldOrder,
3878               viewport.getAlignment()));
3879     }
3880     alignPanel.paintAlignment(true);
3881     return true;
3882   }
3883
3884   /**
3885    * Work out whether the whole set of sequences or just the selected set will
3886    * be submitted for multiple alignment.
3887    *
3888    */
3889   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3890   {
3891     // Now, check we have enough sequences
3892     AlignmentView msa = null;
3893
3894     if ((viewport.getSelectionGroup() != null)
3895             && (viewport.getSelectionGroup().getSize() > 1))
3896     {
3897       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3898       // some common interface!
3899       /*
3900        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3901        * SequenceI[sz = seqs.getSize(false)];
3902        *
3903        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3904        * seqs.getSequenceAt(i); }
3905        */
3906       msa = viewport.getAlignmentView(true);
3907     }
3908     else if (viewport.getSelectionGroup() != null
3909             && viewport.getSelectionGroup().getSize() == 1)
3910     {
3911       int option = JvOptionPane.showConfirmDialog(this,
3912               MessageManager.getString("warn.oneseq_msainput_selection"),
3913               MessageManager.getString("label.invalid_selection"),
3914               JvOptionPane.OK_CANCEL_OPTION);
3915       if (option == JvOptionPane.OK_OPTION)
3916       {
3917         msa = viewport.getAlignmentView(false);
3918       }
3919     }
3920     else
3921     {
3922       msa = viewport.getAlignmentView(false);
3923     }
3924     return msa;
3925   }
3926
3927   /**
3928    * Decides what is submitted to a secondary structure prediction service: the
3929    * first sequence in the alignment, or in the current selection, or, if the
3930    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3931    * region or the whole alignment. (where the first sequence in the set is the
3932    * one that the prediction will be for).
3933    */
3934   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3935   {
3936     AlignmentView seqs = null;
3937
3938     if ((viewport.getSelectionGroup() != null)
3939             && (viewport.getSelectionGroup().getSize() > 0))
3940     {
3941       seqs = viewport.getAlignmentView(true);
3942     }
3943     else
3944     {
3945       seqs = viewport.getAlignmentView(false);
3946     }
3947     // limit sequences - JBPNote in future - could spawn multiple prediction
3948     // jobs
3949     // TODO: viewport.getAlignment().isAligned is a global state - the local
3950     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3951     if (!viewport.getAlignment().isAligned(false))
3952     {
3953       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3954       // TODO: if seqs.getSequences().length>1 then should really have warned
3955       // user!
3956
3957     }
3958     return seqs;
3959   }
3960
3961   /**
3962    * DOCUMENT ME!
3963    *
3964    * @param e
3965    *          DOCUMENT ME!
3966    */
3967   @Override
3968   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3969   {
3970     // Pick the tree file
3971     JalviewFileChooser chooser = new JalviewFileChooser(
3972             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3973     chooser.setFileView(new JalviewFileView());
3974     chooser.setDialogTitle(MessageManager
3975             .getString("label.select_newick_like_tree_file"));
3976     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3977
3978     int value = chooser.showOpenDialog(null);
3979
3980     if (value == JalviewFileChooser.APPROVE_OPTION)
3981     {
3982       String filePath = chooser.getSelectedFile().getPath();
3983       Cache.setProperty("LAST_DIRECTORY", filePath);
3984       NewickFile fin = null;
3985       try
3986       {
3987         fin = new NewickFile(filePath, DataSourceType.FILE);
3988         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3989       } catch (Exception ex)
3990       {
3991         JvOptionPane
3992                 .showMessageDialog(
3993                         Desktop.desktop,
3994                         ex.getMessage(),
3995                         MessageManager
3996                                 .getString("label.problem_reading_tree_file"),
3997                         JvOptionPane.WARNING_MESSAGE);
3998         ex.printStackTrace();
3999       }
4000       if (fin != null && fin.hasWarningMessage())
4001       {
4002         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4003                 .getWarningMessage(), MessageManager
4004                 .getString("label.possible_problem_with_tree_file"),
4005                 JvOptionPane.WARNING_MESSAGE);
4006       }
4007     }
4008   }
4009
4010   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4011   {
4012     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4013   }
4014
4015   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4016           int h, int x, int y)
4017   {
4018     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4019   }
4020
4021   /**
4022    * Add a treeviewer for the tree extracted from a Newick file object to the
4023    * current alignment view
4024    *
4025    * @param nf
4026    *          the tree
4027    * @param title
4028    *          tree viewer title
4029    * @param input
4030    *          Associated alignment input data (or null)
4031    * @param w
4032    *          width
4033    * @param h
4034    *          height
4035    * @param x
4036    *          position
4037    * @param y
4038    *          position
4039    * @return TreePanel handle
4040    */
4041   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4042           AlignmentView input, int w, int h, int x, int y)
4043   {
4044     TreePanel tp = null;
4045
4046     try
4047     {
4048       nf.parse();
4049
4050       if (nf.getTree() != null)
4051       {
4052         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4053
4054         tp.setSize(w, h);
4055
4056         if (x > 0 && y > 0)
4057         {
4058           tp.setLocation(x, y);
4059         }
4060
4061         Desktop.addInternalFrame(tp, treeTitle, w, h);
4062       }
4063     } catch (Exception ex)
4064     {
4065       ex.printStackTrace();
4066     }
4067
4068     return tp;
4069   }
4070
4071   private boolean buildingMenu = false;
4072
4073   /**
4074    * Generates menu items and listener event actions for web service clients
4075    *
4076    */
4077   public void BuildWebServiceMenu()
4078   {
4079     while (buildingMenu)
4080     {
4081       try
4082       {
4083         System.err.println("Waiting for building menu to finish.");
4084         Thread.sleep(10);
4085       } catch (Exception e)
4086       {
4087       }
4088     }
4089     final AlignFrame me = this;
4090     buildingMenu = true;
4091     new Thread(new Runnable()
4092     {
4093       @Override
4094       public void run()
4095       {
4096         final List<JMenuItem> legacyItems = new ArrayList<>();
4097         try
4098         {
4099           // System.err.println("Building ws menu again "
4100           // + Thread.currentThread());
4101           // TODO: add support for context dependent disabling of services based
4102           // on
4103           // alignment and current selection
4104           // TODO: add additional serviceHandle parameter to specify abstract
4105           // handler
4106           // class independently of AbstractName
4107           // TODO: add in rediscovery GUI function to restart discoverer
4108           // TODO: group services by location as well as function and/or
4109           // introduce
4110           // object broker mechanism.
4111           final Vector<JMenu> wsmenu = new Vector<>();
4112           final IProgressIndicator af = me;
4113
4114           /*
4115            * do not i18n these strings - they are hard-coded in class
4116            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4117            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4118            */
4119           final JMenu msawsmenu = new JMenu("Alignment");
4120           final JMenu secstrmenu = new JMenu(
4121                   "Secondary Structure Prediction");
4122           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4123           final JMenu analymenu = new JMenu("Analysis");
4124           final JMenu dismenu = new JMenu("Protein Disorder");
4125           // JAL-940 - only show secondary structure prediction services from
4126           // the legacy server
4127           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4128               // &&
4129           Discoverer.services != null && (Discoverer.services.size() > 0))
4130           {
4131             // TODO: refactor to allow list of AbstractName/Handler bindings to
4132             // be
4133             // stored or retrieved from elsewhere
4134             // No MSAWS used any more:
4135             // Vector msaws = null; // (Vector)
4136             // Discoverer.services.get("MsaWS");
4137             Vector secstrpr = (Vector) Discoverer.services
4138                     .get("SecStrPred");
4139             if (secstrpr != null)
4140             {
4141               // Add any secondary structure prediction services
4142               for (int i = 0, j = secstrpr.size(); i < j; i++)
4143               {
4144                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4145                         .get(i);
4146                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4147                         .getServiceClient(sh);
4148                 int p = secstrmenu.getItemCount();
4149                 impl.attachWSMenuEntry(secstrmenu, me);
4150                 int q = secstrmenu.getItemCount();
4151                 for (int litm = p; litm < q; litm++)
4152                 {
4153                   legacyItems.add(secstrmenu.getItem(litm));
4154                 }
4155               }
4156             }
4157           }
4158
4159           // Add all submenus in the order they should appear on the web
4160           // services menu
4161           wsmenu.add(msawsmenu);
4162           wsmenu.add(secstrmenu);
4163           wsmenu.add(dismenu);
4164           wsmenu.add(analymenu);
4165           // No search services yet
4166           // wsmenu.add(seqsrchmenu);
4167
4168           javax.swing.SwingUtilities.invokeLater(new Runnable()
4169           {
4170             @Override
4171             public void run()
4172             {
4173               try
4174               {
4175                 webService.removeAll();
4176                 // first, add discovered services onto the webservices menu
4177                 if (wsmenu.size() > 0)
4178                 {
4179                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4180                   {
4181                     webService.add(wsmenu.get(i));
4182                   }
4183                 }
4184                 else
4185                 {
4186                   webService.add(me.webServiceNoServices);
4187                 }
4188                 // TODO: move into separate menu builder class.
4189                 boolean new_sspred = false;
4190                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4191                 {
4192                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4193                   if (jws2servs != null)
4194                   {
4195                     if (jws2servs.hasServices())
4196                     {
4197                       jws2servs.attachWSMenuEntry(webService, me);
4198                       for (Jws2Instance sv : jws2servs.getServices())
4199                       {
4200                         if (sv.description.toLowerCase().contains("jpred"))
4201                         {
4202                           for (JMenuItem jmi : legacyItems)
4203                           {
4204                             jmi.setVisible(false);
4205                           }
4206                         }
4207                       }
4208
4209                     }
4210                     if (jws2servs.isRunning())
4211                     {
4212                       JMenuItem tm = new JMenuItem(
4213                               "Still discovering JABA Services");
4214                       tm.setEnabled(false);
4215                       webService.add(tm);
4216                     }
4217                   }
4218                 }
4219                 build_urlServiceMenu(me.webService);
4220                 build_fetchdbmenu(webService);
4221                 for (JMenu item : wsmenu)
4222                 {
4223                   if (item.getItemCount() == 0)
4224                   {
4225                     item.setEnabled(false);
4226                   }
4227                   else
4228                   {
4229                     item.setEnabled(true);
4230                   }
4231                 }
4232               } catch (Exception e)
4233               {
4234                 Cache.log
4235                         .debug("Exception during web service menu building process.",
4236                                 e);
4237               }
4238             }
4239           });
4240         } catch (Exception e)
4241         {
4242         }
4243         buildingMenu = false;
4244       }
4245     }).start();
4246
4247   }
4248
4249   /**
4250    * construct any groupURL type service menu entries.
4251    *
4252    * @param webService
4253    */
4254   private void build_urlServiceMenu(JMenu webService)
4255   {
4256     // TODO: remove this code when 2.7 is released
4257     // DEBUG - alignmentView
4258     /*
4259      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4260      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4261      *
4262      * @Override public void actionPerformed(ActionEvent e) {
4263      * jalview.datamodel.AlignmentView
4264      * .testSelectionViews(af.viewport.getAlignment(),
4265      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4266      *
4267      * }); webService.add(testAlView);
4268      */
4269     // TODO: refactor to RestClient discoverer and merge menu entries for
4270     // rest-style services with other types of analysis/calculation service
4271     // SHmmr test client - still being implemented.
4272     // DEBUG - alignmentView
4273
4274     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4275             .getRestClients())
4276     {
4277       client.attachWSMenuEntry(
4278               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4279               this);
4280     }
4281   }
4282
4283   /**
4284    * Searches the alignment sequences for xRefs and builds the Show
4285    * Cross-References menu (formerly called Show Products), with database
4286    * sources for which cross-references are found (protein sources for a
4287    * nucleotide alignment and vice versa)
4288    *
4289    * @return true if Show Cross-references menu should be enabled
4290    */
4291   public boolean canShowProducts()
4292   {
4293     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4294     AlignmentI dataset = viewport.getAlignment().getDataset();
4295
4296     showProducts.removeAll();
4297     final boolean dna = viewport.getAlignment().isNucleotide();
4298
4299     if (seqs == null || seqs.length == 0)
4300     {
4301       // nothing to see here.
4302       return false;
4303     }
4304
4305     boolean showp = false;
4306     try
4307     {
4308       List<String> ptypes = new CrossRef(seqs, dataset)
4309               .findXrefSourcesForSequences(dna);
4310
4311       for (final String source : ptypes)
4312       {
4313         showp = true;
4314         final AlignFrame af = this;
4315         JMenuItem xtype = new JMenuItem(source);
4316         xtype.addActionListener(new ActionListener()
4317         {
4318           @Override
4319           public void actionPerformed(ActionEvent e)
4320           {
4321             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4322           }
4323         });
4324         showProducts.add(xtype);
4325       }
4326       showProducts.setVisible(showp);
4327       showProducts.setEnabled(showp);
4328     } catch (Exception e)
4329     {
4330       Cache.log
4331               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4332                       e);
4333       return false;
4334     }
4335     return showp;
4336   }
4337
4338   /**
4339    * Finds and displays cross-references for the selected sequences (protein
4340    * products for nucleotide sequences, dna coding sequences for peptides).
4341    *
4342    * @param sel
4343    *          the sequences to show cross-references for
4344    * @param dna
4345    *          true if from a nucleotide alignment (so showing proteins)
4346    * @param source
4347    *          the database to show cross-references for
4348    */
4349   protected void showProductsFor(final SequenceI[] sel,
4350           final boolean _odna, final String source)
4351   {
4352     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4353             .start();
4354   }
4355
4356   /**
4357    * Construct and display a new frame containing the translation of this
4358    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4359    */
4360   @Override
4361   public void showTranslation_actionPerformed(ActionEvent e)
4362   {
4363     AlignmentI al = null;
4364     try
4365     {
4366       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4367
4368       al = dna.translateCdna();
4369     } catch (Exception ex)
4370     {
4371       jalview.bin.Cache.log.error(
4372               "Exception during translation. Please report this !", ex);
4373       final String msg = MessageManager
4374               .getString("label.error_when_translating_sequences_submit_bug_report");
4375       final String errorTitle = MessageManager
4376               .getString("label.implementation_error")
4377               + MessageManager.getString("label.translation_failed");
4378       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4379               JvOptionPane.ERROR_MESSAGE);
4380       return;
4381     }
4382     if (al == null || al.getHeight() == 0)
4383     {
4384       final String msg = MessageManager
4385               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4386       final String errorTitle = MessageManager
4387               .getString("label.translation_failed");
4388       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4389               JvOptionPane.WARNING_MESSAGE);
4390     }
4391     else
4392     {
4393       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4394       af.setFileFormat(this.currentFileFormat);
4395       final String newTitle = MessageManager.formatMessage(
4396               "label.translation_of_params",
4397               new Object[] { this.getTitle() });
4398       af.setTitle(newTitle);
4399       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4400       {
4401         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4402         viewport.openSplitFrame(af, new Alignment(seqs));
4403       }
4404       else
4405       {
4406         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4407                 DEFAULT_HEIGHT);
4408       }
4409     }
4410   }
4411
4412   /**
4413    * Set the file format
4414    *
4415    * @param format
4416    */
4417   public void setFileFormat(FileFormatI format)
4418   {
4419     this.currentFileFormat = format;
4420   }
4421
4422   /**
4423    * Try to load a features file onto the alignment.
4424    *
4425    * @param file
4426    *          contents or path to retrieve file
4427    * @param sourceType
4428    *          access mode of file (see jalview.io.AlignFile)
4429    * @return true if features file was parsed correctly.
4430    */
4431   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4432   {
4433     return avc.parseFeaturesFile(file, sourceType,
4434             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4435
4436   }
4437
4438   @Override
4439   public void refreshFeatureUI(boolean enableIfNecessary)
4440   {
4441     // note - currently this is only still here rather than in the controller
4442     // because of the featureSettings hard reference that is yet to be
4443     // abstracted
4444     if (enableIfNecessary)
4445     {
4446       viewport.setShowSequenceFeatures(true);
4447       showSeqFeatures.setSelected(true);
4448     }
4449
4450   }
4451
4452   @Override
4453   public void dragEnter(DropTargetDragEvent evt)
4454   {
4455   }
4456
4457   @Override
4458   public void dragExit(DropTargetEvent evt)
4459   {
4460   }
4461
4462   @Override
4463   public void dragOver(DropTargetDragEvent evt)
4464   {
4465   }
4466
4467   @Override
4468   public void dropActionChanged(DropTargetDragEvent evt)
4469   {
4470   }
4471
4472   @Override
4473   public void drop(DropTargetDropEvent evt)
4474   {
4475     // JAL-1552 - acceptDrop required before getTransferable call for
4476     // Java's Transferable for native dnd
4477     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4478     Transferable t = evt.getTransferable();
4479     List<String> files = new ArrayList<>();
4480     List<DataSourceType> protocols = new ArrayList<>();
4481
4482     try
4483     {
4484       Desktop.transferFromDropTarget(files, protocols, evt, t);
4485     } catch (Exception e)
4486     {
4487       e.printStackTrace();
4488     }
4489     if (files != null)
4490     {
4491       try
4492       {
4493         // check to see if any of these files have names matching sequences in
4494         // the alignment
4495         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4496                 .getAlignment().getSequencesArray());
4497         /**
4498          * Object[] { String,SequenceI}
4499          */
4500         ArrayList<Object[]> filesmatched = new ArrayList<>();
4501         ArrayList<String> filesnotmatched = new ArrayList<>();
4502         for (int i = 0; i < files.size(); i++)
4503         {
4504           String file = files.get(i).toString();
4505           String pdbfn = "";
4506           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4507           if (protocol == DataSourceType.FILE)
4508           {
4509             File fl = new File(file);
4510             pdbfn = fl.getName();
4511           }
4512           else if (protocol == DataSourceType.URL)
4513           {
4514             URL url = new URL(file);
4515             pdbfn = url.getFile();
4516           }
4517           if (pdbfn.length() > 0)
4518           {
4519             // attempt to find a match in the alignment
4520             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4521             int l = 0, c = pdbfn.indexOf(".");
4522             while (mtch == null && c != -1)
4523             {
4524               do
4525               {
4526                 l = c;
4527               } while ((c = pdbfn.indexOf(".", l)) > l);
4528               if (l > -1)
4529               {
4530                 pdbfn = pdbfn.substring(0, l);
4531               }
4532               mtch = idm.findAllIdMatches(pdbfn);
4533             }
4534             if (mtch != null)
4535             {
4536               FileFormatI type = null;
4537               try
4538               {
4539                 type = new IdentifyFile().identify(file, protocol);
4540               } catch (Exception ex)
4541               {
4542                 type = null;
4543               }
4544               if (type != null && type.isStructureFile())
4545               {
4546                 filesmatched.add(new Object[] { file, protocol, mtch });
4547                 continue;
4548               }
4549             }
4550             // File wasn't named like one of the sequences or wasn't a PDB file.
4551             filesnotmatched.add(file);
4552           }
4553         }
4554         int assocfiles = 0;
4555         if (filesmatched.size() > 0)
4556         {
4557           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4558                   || JvOptionPane
4559                           .showConfirmDialog(
4560                                   this,
4561                                   MessageManager
4562                                           .formatMessage(
4563                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4564                                                   new Object[] { Integer
4565                                                           .valueOf(
4566                                                                   filesmatched
4567                                                                           .size())
4568                                                           .toString() }),
4569                                   MessageManager
4570                                           .getString("label.automatically_associate_structure_files_by_name"),
4571                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4572
4573           {
4574             for (Object[] fm : filesmatched)
4575             {
4576               // try and associate
4577               // TODO: may want to set a standard ID naming formalism for
4578               // associating PDB files which have no IDs.
4579               for (SequenceI toassoc : (SequenceI[]) fm[2])
4580               {
4581                 PDBEntry pe = new AssociatePdbFileWithSeq()
4582                         .associatePdbWithSeq((String) fm[0],
4583                                 (DataSourceType) fm[1], toassoc, false,
4584                                 Desktop.instance);
4585                 if (pe != null)
4586                 {
4587                   System.err.println("Associated file : "
4588                           + ((String) fm[0]) + " with "
4589                           + toassoc.getDisplayId(true));
4590                   assocfiles++;
4591                 }
4592               }
4593               alignPanel.paintAlignment(true);
4594             }
4595           }
4596         }
4597         if (filesnotmatched.size() > 0)
4598         {
4599           if (assocfiles > 0
4600                   && (Cache.getDefault(
4601                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4602                           .showConfirmDialog(
4603                                   this,
4604                                   "<html>"
4605                                           + MessageManager
4606                                                   .formatMessage(
4607                                                           "label.ignore_unmatched_dropped_files_info",
4608                                                           new Object[] { Integer
4609                                                                   .valueOf(
4610                                                                           filesnotmatched
4611                                                                                   .size())
4612                                                                   .toString() })
4613                                           + "</html>",
4614                                   MessageManager
4615                                           .getString("label.ignore_unmatched_dropped_files"),
4616                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4617           {
4618             return;
4619           }
4620           for (String fn : filesnotmatched)
4621           {
4622             loadJalviewDataFile(fn, null, null, null);
4623           }
4624
4625         }
4626       } catch (Exception ex)
4627       {
4628         ex.printStackTrace();
4629       }
4630     }
4631   }
4632
4633   /**
4634    * Attempt to load a "dropped" file or URL string, by testing in turn for
4635    * <ul>
4636    * <li>an Annotation file</li>
4637    * <li>a JNet file</li>
4638    * <li>a features file</li>
4639    * <li>else try to interpret as an alignment file</li>
4640    * </ul>
4641    *
4642    * @param file
4643    *          either a filename or a URL string.
4644    * @throws InterruptedException
4645    * @throws IOException
4646    */
4647   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4648           FileFormatI format, SequenceI assocSeq)
4649           throws IOException, InterruptedException
4650   {
4651     try
4652     {
4653       if (sourceType == null)
4654       {
4655         sourceType = FormatAdapter.checkProtocol(file);
4656       }
4657       // if the file isn't identified, or not positively identified as some
4658       // other filetype (PFAM is default unidentified alignment file type) then
4659       // try to parse as annotation.
4660       boolean isAnnotation = (format == null || FileFormat.Pfam
4661               .equals(format)) ? new AnnotationFile()
4662               .annotateAlignmentView(viewport, file, sourceType) : false;
4663
4664       if (!isAnnotation)
4665       {
4666         // first see if its a T-COFFEE score file
4667         TCoffeeScoreFile tcf = null;
4668         try
4669         {
4670           tcf = new TCoffeeScoreFile(file, sourceType);
4671           if (tcf.isValid())
4672           {
4673             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4674             {
4675               buildColourMenu();
4676               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4677               isAnnotation = true;
4678               statusBar
4679                       .setText(MessageManager
4680                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4681             }
4682             else
4683             {
4684               // some problem - if no warning its probable that the ID matching
4685               // process didn't work
4686               JvOptionPane
4687                       .showMessageDialog(
4688                               Desktop.desktop,
4689                               tcf.getWarningMessage() == null ? MessageManager
4690                                       .getString("label.check_file_matches_sequence_ids_alignment")
4691                                       : tcf.getWarningMessage(),
4692                               MessageManager
4693                                       .getString("label.problem_reading_tcoffee_score_file"),
4694                               JvOptionPane.WARNING_MESSAGE);
4695             }
4696           }
4697           else
4698           {
4699             tcf = null;
4700           }
4701         } catch (Exception x)
4702         {
4703           Cache.log
4704                   .debug("Exception when processing data source as T-COFFEE score file",
4705                           x);
4706           tcf = null;
4707         }
4708         if (tcf == null)
4709         {
4710           // try to see if its a JNet 'concise' style annotation file *before*
4711           // we
4712           // try to parse it as a features file
4713           if (format == null)
4714           {
4715             format = new IdentifyFile().identify(file, sourceType);
4716           }
4717           if (FileFormat.ScoreMatrix == format)
4718           {
4719             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4720                     sourceType));
4721             sm.parse();
4722             // todo: i18n this message
4723             statusBar
4724                     .setText(MessageManager.formatMessage(
4725                             "label.successfully_loaded_matrix",
4726                             sm.getMatrixName()));
4727           }
4728           else if (FileFormat.HMMER3.equals(format))
4729           {
4730             HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); // TODO
4731                                                                             // need
4732                                                                             // to
4733                                                                             // follow
4734                                                                             // standard
4735                                                                             // pipeline
4736             hmmFile.parse();
4737             HiddenMarkovModel hmm = hmmFile.getHMM();
4738             SequenceI hmmSeq = hmm.initHMMSequence(this, 0);
4739             getViewport().initInformation(hmmSeq);
4740             new Thread(new InformationThread(getViewport(),
4741                     getViewport().getAlignPanel())
4742             {
4743             }).start();
4744
4745             isAnnotation = true;
4746
4747           }
4748           else if (FileFormat.Jnet.equals(format))
4749           {
4750             JPredFile predictions = new JPredFile(file, sourceType);
4751             new JnetAnnotationMaker();
4752             JnetAnnotationMaker.add_annotation(predictions,
4753                     viewport.getAlignment(), 0, false);
4754             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4755             viewport.getAlignment().setSeqrep(repseq);
4756             HiddenColumns cs = new HiddenColumns();
4757             cs.hideInsertionsFor(repseq);
4758             viewport.getAlignment().setHiddenColumns(cs);
4759             isAnnotation = true;
4760           }
4761           // else if (IdentifyFile.FeaturesFile.equals(format))
4762           else if (FileFormat.Features.equals(format))
4763           {
4764             if (parseFeaturesFile(file, sourceType))
4765             {
4766               alignPanel.paintAlignment(true);
4767             }
4768           }
4769           else
4770           {
4771             new FileLoader().LoadFile(viewport, file, sourceType, format);
4772           }
4773         }
4774       }
4775       if (isAnnotation)
4776       {
4777         alignPanel.adjustAnnotationHeight();
4778         viewport.updateSequenceIdColours();
4779         buildSortByAnnotationScoresMenu();
4780         alignPanel.paintAlignment(true);
4781       }
4782     } catch (Exception ex)
4783     {
4784       ex.printStackTrace();
4785     } catch (OutOfMemoryError oom)
4786     {
4787       try
4788       {
4789         System.gc();
4790       } catch (Exception x)
4791       {
4792       }
4793       new OOMWarning(
4794               "loading data "
4795                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4796                               : "using " + sourceType + " from " + file)
4797                               : ".")
4798                       + (format != null ? "(parsing as '" + format
4799                               + "' file)" : ""), oom, Desktop.desktop);
4800     }
4801     if (autoAlignNewSequences && !recurring)
4802     {
4803       recurring = true;
4804       HiddenMarkovModel hmm = getViewport().getAlignment()
4805               .getHMMConsensusSequences(false).get(0).getHMM();
4806       HMMERCommands.hmmAlign(this, false, hmm);
4807     }
4808     recurring = false;
4809   }
4810
4811   /**
4812    * Method invoked by the ChangeListener on the tabbed pane, in other words
4813    * when a different tabbed pane is selected by the user or programmatically.
4814    */
4815   @Override
4816   public void tabSelectionChanged(int index)
4817   {
4818     if (index > -1)
4819     {
4820       alignPanel = alignPanels.get(index);
4821       viewport = alignPanel.av;
4822       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4823       setMenusFromViewport(viewport);
4824     }
4825
4826     /*
4827      * 'focus' any colour slider that is open to the selected viewport
4828      */
4829     if (viewport.getConservationSelected())
4830     {
4831       SliderPanel.setConservationSlider(alignPanel,
4832               viewport.getResidueShading(), alignPanel.getViewName());
4833     }
4834     else
4835     {
4836       SliderPanel.hideConservationSlider();
4837     }
4838     if (viewport.getAbovePIDThreshold())
4839     {
4840       SliderPanel.setPIDSliderSource(alignPanel,
4841               viewport.getResidueShading(), alignPanel.getViewName());
4842     }
4843     else
4844     {
4845       SliderPanel.hidePIDSlider();
4846     }
4847
4848     /*
4849      * If there is a frame linked to this one in a SplitPane, switch it to the
4850      * same view tab index. No infinite recursion of calls should happen, since
4851      * tabSelectionChanged() should not get invoked on setting the selected
4852      * index to an unchanged value. Guard against setting an invalid index
4853      * before the new view peer tab has been created.
4854      */
4855     final AlignViewportI peer = viewport.getCodingComplement();
4856     if (peer != null)
4857     {
4858       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4859       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4860       {
4861         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4862       }
4863     }
4864   }
4865
4866   /**
4867    * On right mouse click on view tab, prompt for and set new view name.
4868    */
4869   @Override
4870   public void tabbedPane_mousePressed(MouseEvent e)
4871   {
4872     if (e.isPopupTrigger())
4873     {
4874       String msg = MessageManager.getString("label.enter_view_name");
4875       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4876               JvOptionPane.QUESTION_MESSAGE);
4877
4878       if (reply != null)
4879       {
4880         viewport.viewName = reply;
4881         // TODO warn if reply is in getExistingViewNames()?
4882         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4883       }
4884     }
4885   }
4886
4887   public AlignViewport getCurrentView()
4888   {
4889     return viewport;
4890   }
4891
4892   /**
4893    * Open the dialog for regex description parsing.
4894    */
4895   @Override
4896   protected void extractScores_actionPerformed(ActionEvent e)
4897   {
4898     ParseProperties pp = new jalview.analysis.ParseProperties(
4899             viewport.getAlignment());
4900     // TODO: verify regex and introduce GUI dialog for version 2.5
4901     // if (pp.getScoresFromDescription("col", "score column ",
4902     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4903     // true)>0)
4904     if (pp.getScoresFromDescription("description column",
4905             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4906     {
4907       buildSortByAnnotationScoresMenu();
4908     }
4909   }
4910
4911   /*
4912    * (non-Javadoc)
4913    *
4914    * @see
4915    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4916    * )
4917    */
4918   @Override
4919   protected void showDbRefs_actionPerformed(ActionEvent e)
4920   {
4921     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4922   }
4923
4924   /*
4925    * (non-Javadoc)
4926    *
4927    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4928    * ActionEvent)
4929    */
4930   @Override
4931   protected void showNpFeats_actionPerformed(ActionEvent e)
4932   {
4933     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4934   }
4935
4936   /**
4937    * find the viewport amongst the tabs in this alignment frame and close that
4938    * tab
4939    *
4940    * @param av
4941    */
4942   public boolean closeView(AlignViewportI av)
4943   {
4944     if (viewport == av)
4945     {
4946       this.closeMenuItem_actionPerformed(false);
4947       return true;
4948     }
4949     Component[] comp = tabbedPane.getComponents();
4950     for (int i = 0; comp != null && i < comp.length; i++)
4951     {
4952       if (comp[i] instanceof AlignmentPanel)
4953       {
4954         if (((AlignmentPanel) comp[i]).av == av)
4955         {
4956           // close the view.
4957           closeView((AlignmentPanel) comp[i]);
4958           return true;
4959         }
4960       }
4961     }
4962     return false;
4963   }
4964
4965   protected void build_fetchdbmenu(JMenu webService)
4966   {
4967     // Temporary hack - DBRef Fetcher always top level ws entry.
4968     // TODO We probably want to store a sequence database checklist in
4969     // preferences and have checkboxes.. rather than individual sources selected
4970     // here
4971     final JMenu rfetch = new JMenu(
4972             MessageManager.getString("action.fetch_db_references"));
4973     rfetch.setToolTipText(MessageManager
4974             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4975     webService.add(rfetch);
4976
4977     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4978             MessageManager.getString("option.trim_retrieved_seqs"));
4979     trimrs.setToolTipText(MessageManager
4980             .getString("label.trim_retrieved_sequences"));
4981     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4982     trimrs.addActionListener(new ActionListener()
4983     {
4984       @Override
4985       public void actionPerformed(ActionEvent e)
4986       {
4987         trimrs.setSelected(trimrs.isSelected());
4988         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4989                 Boolean.valueOf(trimrs.isSelected()).toString());
4990       };
4991     });
4992     rfetch.add(trimrs);
4993     JMenuItem fetchr = new JMenuItem(
4994             MessageManager.getString("label.standard_databases"));
4995     fetchr.setToolTipText(MessageManager
4996             .getString("label.fetch_embl_uniprot"));
4997     fetchr.addActionListener(new ActionListener()
4998     {
4999
5000       @Override
5001       public void actionPerformed(ActionEvent e)
5002       {
5003         new Thread(new Runnable()
5004         {
5005           @Override
5006           public void run()
5007           {
5008             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5009                     .getAlignment().isNucleotide();
5010             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5011                     .getSequenceSelection(), alignPanel.alignFrame, null,
5012                     alignPanel.alignFrame.featureSettings, isNucleotide);
5013             dbRefFetcher.addListener(new FetchFinishedListenerI()
5014             {
5015               @Override
5016               public void finished()
5017               {
5018                 AlignFrame.this.setMenusForViewport();
5019               }
5020             });
5021             dbRefFetcher.fetchDBRefs(false);
5022           }
5023         }).start();
5024
5025       }
5026
5027     });
5028     rfetch.add(fetchr);
5029     final AlignFrame me = this;
5030     new Thread(new Runnable()
5031     {
5032       @Override
5033       public void run()
5034       {
5035         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5036                 .getSequenceFetcherSingleton(me);
5037         javax.swing.SwingUtilities.invokeLater(new Runnable()
5038         {
5039           @Override
5040           public void run()
5041           {
5042             String[] dbclasses = sf.getOrderedSupportedSources();
5043             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5044             // jalview.util.QuickSort.sort(otherdb, otherdb);
5045             List<DbSourceProxy> otherdb;
5046             JMenu dfetch = new JMenu();
5047             JMenu ifetch = new JMenu();
5048             JMenuItem fetchr = null;
5049             int comp = 0, icomp = 0, mcomp = 15;
5050             String mname = null;
5051             int dbi = 0;
5052             for (String dbclass : dbclasses)
5053             {
5054               otherdb = sf.getSourceProxy(dbclass);
5055               // add a single entry for this class, or submenu allowing 'fetch
5056               // all' or pick one
5057               if (otherdb == null || otherdb.size() < 1)
5058               {
5059                 continue;
5060               }
5061               // List<DbSourceProxy> dbs=otherdb;
5062               // otherdb=new ArrayList<DbSourceProxy>();
5063               // for (DbSourceProxy db:dbs)
5064               // {
5065               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5066               // }
5067               if (mname == null)
5068               {
5069                 mname = "From " + dbclass;
5070               }
5071               if (otherdb.size() == 1)
5072               {
5073                 final DbSourceProxy[] dassource = otherdb
5074                         .toArray(new DbSourceProxy[0]);
5075                 DbSourceProxy src = otherdb.get(0);
5076                 fetchr = new JMenuItem(src.getDbSource());
5077                 fetchr.addActionListener(new ActionListener()
5078                 {
5079
5080                   @Override
5081                   public void actionPerformed(ActionEvent e)
5082                   {
5083                     new Thread(new Runnable()
5084                     {
5085
5086                       @Override
5087                       public void run()
5088                       {
5089                         boolean isNucleotide = alignPanel.alignFrame
5090                                 .getViewport().getAlignment()
5091                                 .isNucleotide();
5092                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5093                                 alignPanel.av.getSequenceSelection(),
5094                                 alignPanel.alignFrame, dassource,
5095                                 alignPanel.alignFrame.featureSettings,
5096                                 isNucleotide);
5097                         dbRefFetcher
5098                                 .addListener(new FetchFinishedListenerI()
5099                                 {
5100                                   @Override
5101                                   public void finished()
5102                                   {
5103                                     AlignFrame.this.setMenusForViewport();
5104                                   }
5105                                 });
5106                         dbRefFetcher.fetchDBRefs(false);
5107                       }
5108                     }).start();
5109                   }
5110
5111                 });
5112                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5113                         MessageManager.formatMessage(
5114                                 "label.fetch_retrieve_from",
5115                                 new Object[] { src.getDbName() })));
5116                 dfetch.add(fetchr);
5117                 comp++;
5118               }
5119               else
5120               {
5121                 final DbSourceProxy[] dassource = otherdb
5122                         .toArray(new DbSourceProxy[0]);
5123                 // fetch all entry
5124                 DbSourceProxy src = otherdb.get(0);
5125                 fetchr = new JMenuItem(MessageManager.formatMessage(
5126                         "label.fetch_all_param",
5127                         new Object[] { src.getDbSource() }));
5128                 fetchr.addActionListener(new ActionListener()
5129                 {
5130                   @Override
5131                   public void actionPerformed(ActionEvent e)
5132                   {
5133                     new Thread(new Runnable()
5134                     {
5135
5136                       @Override
5137                       public void run()
5138                       {
5139                         boolean isNucleotide = alignPanel.alignFrame
5140                                 .getViewport().getAlignment()
5141                                 .isNucleotide();
5142                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5143                                 alignPanel.av.getSequenceSelection(),
5144                                 alignPanel.alignFrame, dassource,
5145                                 alignPanel.alignFrame.featureSettings,
5146                                 isNucleotide);
5147                         dbRefFetcher
5148                                 .addListener(new FetchFinishedListenerI()
5149                                 {
5150                                   @Override
5151                                   public void finished()
5152                                   {
5153                                     AlignFrame.this.setMenusForViewport();
5154                                   }
5155                                 });
5156                         dbRefFetcher.fetchDBRefs(false);
5157                       }
5158                     }).start();
5159                   }
5160                 });
5161
5162                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5163                         MessageManager.formatMessage(
5164                                 "label.fetch_retrieve_from_all_sources",
5165                                 new Object[] {
5166                                     Integer.valueOf(otherdb.size())
5167                                             .toString(), src.getDbSource(),
5168                                     src.getDbName() })));
5169                 dfetch.add(fetchr);
5170                 comp++;
5171                 // and then build the rest of the individual menus
5172                 ifetch = new JMenu(MessageManager.formatMessage(
5173                         "label.source_from_db_source",
5174                         new Object[] { src.getDbSource() }));
5175                 icomp = 0;
5176                 String imname = null;
5177                 int i = 0;
5178                 for (DbSourceProxy sproxy : otherdb)
5179                 {
5180                   String dbname = sproxy.getDbName();
5181                   String sname = dbname.length() > 5 ? dbname.substring(0,
5182                           5) + "..." : dbname;
5183                   String msname = dbname.length() > 10 ? dbname.substring(
5184                           0, 10) + "..." : dbname;
5185                   if (imname == null)
5186                   {
5187                     imname = MessageManager.formatMessage(
5188                             "label.from_msname", new Object[] { sname });
5189                   }
5190                   fetchr = new JMenuItem(msname);
5191                   final DbSourceProxy[] dassrc = { sproxy };
5192                   fetchr.addActionListener(new ActionListener()
5193                   {
5194
5195                     @Override
5196                     public void actionPerformed(ActionEvent e)
5197                     {
5198                       new Thread(new Runnable()
5199                       {
5200
5201                         @Override
5202                         public void run()
5203                         {
5204                           boolean isNucleotide = alignPanel.alignFrame
5205                                   .getViewport().getAlignment()
5206                                   .isNucleotide();
5207                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5208                                   alignPanel.av.getSequenceSelection(),
5209                                   alignPanel.alignFrame, dassrc,
5210                                   alignPanel.alignFrame.featureSettings,
5211                                   isNucleotide);
5212                           dbRefFetcher
5213                                   .addListener(new FetchFinishedListenerI()
5214                                   {
5215                                     @Override
5216                                     public void finished()
5217                                     {
5218                                       AlignFrame.this.setMenusForViewport();
5219                                     }
5220                                   });
5221                           dbRefFetcher.fetchDBRefs(false);
5222                         }
5223                       }).start();
5224                     }
5225
5226                   });
5227                   fetchr.setToolTipText("<html>"
5228                           + MessageManager.formatMessage(
5229                                   "label.fetch_retrieve_from", new Object[]
5230                                   { dbname }));
5231                   ifetch.add(fetchr);
5232                   ++i;
5233                   if (++icomp >= mcomp || i == (otherdb.size()))
5234                   {
5235                     ifetch.setText(MessageManager.formatMessage(
5236                             "label.source_to_target", imname, sname));
5237                     dfetch.add(ifetch);
5238                     ifetch = new JMenu();
5239                     imname = null;
5240                     icomp = 0;
5241                     comp++;
5242                   }
5243                 }
5244               }
5245               ++dbi;
5246               if (comp >= mcomp || dbi >= (dbclasses.length))
5247               {
5248                 dfetch.setText(MessageManager.formatMessage(
5249                         "label.source_to_target", mname, dbclass));
5250                 rfetch.add(dfetch);
5251                 dfetch = new JMenu();
5252                 mname = null;
5253                 comp = 0;
5254               }
5255             }
5256           }
5257         });
5258       }
5259     }).start();
5260
5261   }
5262
5263   /**
5264    * Left justify the whole alignment.
5265    */
5266   @Override
5267   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5268   {
5269     AlignmentI al = viewport.getAlignment();
5270     al.justify(false);
5271     viewport.firePropertyChange("alignment", null, al);
5272   }
5273
5274   /**
5275    * Right justify the whole alignment.
5276    */
5277   @Override
5278   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5279   {
5280     AlignmentI al = viewport.getAlignment();
5281     al.justify(true);
5282     viewport.firePropertyChange("alignment", null, al);
5283   }
5284
5285   @Override
5286   public void setShowSeqFeatures(boolean b)
5287   {
5288     showSeqFeatures.setSelected(b);
5289     viewport.setShowSequenceFeatures(b);
5290   }
5291
5292   /*
5293    * (non-Javadoc)
5294    *
5295    * @see
5296    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5297    * awt.event.ActionEvent)
5298    */
5299   @Override
5300   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5301   {
5302     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5303     alignPanel.paintAlignment(true);
5304   }
5305
5306   /*
5307    * (non-Javadoc)
5308    *
5309    * @see
5310    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5311    * .ActionEvent)
5312    */
5313   @Override
5314   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5315   {
5316     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5317     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5318
5319   }
5320
5321   /*
5322    * (non-Javadoc)
5323    *
5324    * @see
5325    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5326    * .event.ActionEvent)
5327    */
5328   @Override
5329   protected void showGroupConservation_actionPerformed(ActionEvent e)
5330   {
5331     viewport.setShowGroupConservation(showGroupConservation.getState());
5332     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5333   }
5334
5335   /*
5336    * (non-Javadoc)
5337    *
5338    * @see
5339    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5340    * .event.ActionEvent)
5341    */
5342   @Override
5343   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5344   {
5345     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5346     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5347   }
5348
5349   /*
5350    * (non-Javadoc)
5351    *
5352    * @see
5353    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5354    * .event.ActionEvent)
5355    */
5356   @Override
5357   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5358   {
5359     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5360     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5361   }
5362
5363   @Override
5364   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5365   {
5366     showSequenceLogo.setState(true);
5367     viewport.setShowSequenceLogo(true);
5368     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5369     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5370   }
5371
5372   @Override
5373   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5374   {
5375     viewport.setShowInformationHistogram(
5376             showInformationHistogram.getState());
5377     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5378   }
5379
5380   @Override
5381   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5382   {
5383     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5384     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5385   }
5386
5387   @Override
5388   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5389   {
5390     showHMMSequenceLogo.setState(true);
5391     viewport.setShowHMMSequenceLogo(true);
5392     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5393     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5394   }
5395
5396   @Override
5397   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5398   {
5399     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5400   }
5401
5402   /*
5403    * (non-Javadoc)
5404    *
5405    * @see
5406    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5407    * .event.ActionEvent)
5408    */
5409   @Override
5410   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5411   {
5412     if (avc.makeGroupsFromSelection())
5413     {
5414       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5415       alignPanel.updateAnnotation();
5416       alignPanel.paintAlignment(true);
5417     }
5418   }
5419
5420   public void clearAlignmentSeqRep()
5421   {
5422     // TODO refactor alignmentseqrep to controller
5423     if (viewport.getAlignment().hasSeqrep())
5424     {
5425       viewport.getAlignment().setSeqrep(null);
5426       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5427       alignPanel.updateAnnotation();
5428       alignPanel.paintAlignment(true);
5429     }
5430   }
5431
5432   @Override
5433   protected void createGroup_actionPerformed(ActionEvent e)
5434   {
5435     if (avc.createGroup())
5436     {
5437       alignPanel.alignmentChanged();
5438     }
5439   }
5440
5441   @Override
5442   protected void unGroup_actionPerformed(ActionEvent e)
5443   {
5444     if (avc.unGroup())
5445     {
5446       alignPanel.alignmentChanged();
5447     }
5448   }
5449
5450   /**
5451    * make the given alignmentPanel the currently selected tab
5452    *
5453    * @param alignmentPanel
5454    */
5455   public void setDisplayedView(AlignmentPanel alignmentPanel)
5456   {
5457     if (!viewport.getSequenceSetId().equals(
5458             alignmentPanel.av.getSequenceSetId()))
5459     {
5460       throw new Error(
5461               MessageManager
5462                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5463     }
5464     if (tabbedPane != null
5465             && tabbedPane.getTabCount() > 0
5466             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5467                     .getSelectedIndex())
5468     {
5469       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5470     }
5471   }
5472
5473   /**
5474    * Action on selection of menu options to Show or Hide annotations.
5475    *
5476    * @param visible
5477    * @param forSequences
5478    *          update sequence-related annotations
5479    * @param forAlignment
5480    *          update non-sequence-related annotations
5481    */
5482   @Override
5483   protected void setAnnotationsVisibility(boolean visible,
5484           boolean forSequences, boolean forAlignment)
5485   {
5486     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5487             .getAlignmentAnnotation();
5488     if (anns == null)
5489     {
5490       return;
5491     }
5492     for (AlignmentAnnotation aa : anns)
5493     {
5494       /*
5495        * don't display non-positional annotations on an alignment
5496        */
5497       if (aa.annotations == null)
5498       {
5499         continue;
5500       }
5501       boolean apply = (aa.sequenceRef == null && forAlignment)
5502               || (aa.sequenceRef != null && forSequences);
5503       if (apply)
5504       {
5505         aa.visible = visible;
5506       }
5507     }
5508     alignPanel.validateAnnotationDimensions(true);
5509     alignPanel.alignmentChanged();
5510   }
5511
5512   /**
5513    * Store selected annotation sort order for the view and repaint.
5514    */
5515   @Override
5516   protected void sortAnnotations_actionPerformed()
5517   {
5518     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5519     this.alignPanel.av
5520             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5521     alignPanel.paintAlignment(true);
5522   }
5523
5524   /**
5525    *
5526    * @return alignment panels in this alignment frame
5527    */
5528   public List<? extends AlignmentViewPanel> getAlignPanels()
5529   {
5530     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5531   }
5532
5533   /**
5534    * Open a new alignment window, with the cDNA associated with this (protein)
5535    * alignment, aligned as is the protein.
5536    */
5537   protected void viewAsCdna_actionPerformed()
5538   {
5539     // TODO no longer a menu action - refactor as required
5540     final AlignmentI alignment = getViewport().getAlignment();
5541     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5542     if (mappings == null)
5543     {
5544       return;
5545     }
5546     List<SequenceI> cdnaSeqs = new ArrayList<>();
5547     for (SequenceI aaSeq : alignment.getSequences())
5548     {
5549       for (AlignedCodonFrame acf : mappings)
5550       {
5551         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5552         if (dnaSeq != null)
5553         {
5554           /*
5555            * There is a cDNA mapping for this protein sequence - add to new
5556            * alignment. It will share the same dataset sequence as other mapped
5557            * cDNA (no new mappings need to be created).
5558            */
5559           final Sequence newSeq = new Sequence(dnaSeq);
5560           newSeq.setDatasetSequence(dnaSeq);
5561           cdnaSeqs.add(newSeq);
5562         }
5563       }
5564     }
5565     if (cdnaSeqs.size() == 0)
5566     {
5567       // show a warning dialog no mapped cDNA
5568       return;
5569     }
5570     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5571             .size()]));
5572     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5573             AlignFrame.DEFAULT_HEIGHT);
5574     cdna.alignAs(alignment);
5575     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5576             + this.title;
5577     Desktop.addInternalFrame(alignFrame, newtitle,
5578             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5579   }
5580
5581   /**
5582    * Set visibility of dna/protein complement view (available when shown in a
5583    * split frame).
5584    *
5585    * @param show
5586    */
5587   @Override
5588   protected void showComplement_actionPerformed(boolean show)
5589   {
5590     SplitContainerI sf = getSplitViewContainer();
5591     if (sf != null)
5592     {
5593       sf.setComplementVisible(this, show);
5594     }
5595   }
5596
5597   /**
5598    * Generate the reverse (optionally complemented) of the selected sequences,
5599    * and add them to the alignment
5600    */
5601   @Override
5602   protected void showReverse_actionPerformed(boolean complement)
5603   {
5604     AlignmentI al = null;
5605     try
5606     {
5607       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5608       al = dna.reverseCdna(complement);
5609       viewport.addAlignment(al, "");
5610       addHistoryItem(new EditCommand(
5611               MessageManager.getString("label.add_sequences"),
5612               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5613               viewport.getAlignment()));
5614     } catch (Exception ex)
5615     {
5616       System.err.println(ex.getMessage());
5617       return;
5618     }
5619   }
5620
5621   /**
5622    * Try to run a script in the Groovy console, having first ensured that this
5623    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5624    * be targeted at this alignment.
5625    */
5626   @Override
5627   protected void runGroovy_actionPerformed()
5628   {
5629     Jalview.setCurrentAlignFrame(this);
5630     groovy.ui.Console console = Desktop.getGroovyConsole();
5631     if (console != null)
5632     {
5633       try
5634       {
5635         console.runScript();
5636       } catch (Exception ex)
5637       {
5638         System.err.println((ex.toString()));
5639         JvOptionPane
5640                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5641                         .getString("label.couldnt_run_groovy_script"),
5642                         MessageManager
5643                                 .getString("label.groovy_support_failed"),
5644                         JvOptionPane.ERROR_MESSAGE);
5645       }
5646     }
5647     else
5648     {
5649       System.err.println("Can't run Groovy script as console not found");
5650     }
5651   }
5652
5653   /**
5654    * Hides columns containing (or not containing) a specified feature, provided
5655    * that would not leave all columns hidden
5656    *
5657    * @param featureType
5658    * @param columnsContaining
5659    * @return
5660    */
5661   public boolean hideFeatureColumns(String featureType,
5662           boolean columnsContaining)
5663   {
5664     boolean notForHiding = avc.markColumnsContainingFeatures(
5665             columnsContaining, false, false, featureType);
5666     if (notForHiding)
5667     {
5668       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5669               false, featureType))
5670       {
5671         getViewport().hideSelectedColumns();
5672         return true;
5673       }
5674     }
5675     return false;
5676   }
5677
5678   @Override
5679   protected void selectHighlightedColumns_actionPerformed(
5680           ActionEvent actionEvent)
5681   {
5682     // include key modifier check in case user selects from menu
5683     avc.markHighlightedColumns(
5684             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5685             true,
5686             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5687   }
5688
5689   /**
5690    * Rebuilds the Colour menu, including any user-defined colours which have
5691    * been loaded either on startup or during the session
5692    */
5693   public void buildColourMenu()
5694   {
5695     colourMenu.removeAll();
5696
5697     colourMenu.add(applyToAllGroups);
5698     colourMenu.add(textColour);
5699     colourMenu.addSeparator();
5700
5701     ColourMenuHelper.addMenuItems(colourMenu, this,
5702             viewport.getAlignment(), false);
5703
5704     colourMenu.addSeparator();
5705     colourMenu.add(conservationMenuItem);
5706     colourMenu.add(modifyConservation);
5707     colourMenu.add(abovePIDThreshold);
5708     colourMenu.add(modifyPID);
5709     colourMenu.add(annotationColour);
5710
5711     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5712     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5713   }
5714
5715   /**
5716    * Open a dialog (if not already open) that allows the user to select and
5717    * calculate PCA or Tree analysis
5718    */
5719   protected void openTreePcaDialog()
5720   {
5721     if (alignPanel.getCalculationDialog() == null)
5722     {
5723       new CalculationChooser(AlignFrame.this);
5724     }
5725   }
5726 }
5727
5728 class PrintThread extends Thread
5729 {
5730   AlignmentPanel ap;
5731
5732   public PrintThread(AlignmentPanel ap)
5733   {
5734     this.ap = ap;
5735   }
5736
5737   static PageFormat pf;
5738
5739   @Override
5740   public void run()
5741   {
5742     PrinterJob printJob = PrinterJob.getPrinterJob();
5743
5744     if (pf != null)
5745     {
5746       printJob.setPrintable(ap, pf);
5747     }
5748     else
5749     {
5750       printJob.setPrintable(ap);
5751     }
5752
5753     if (printJob.printDialog())
5754     {
5755       try
5756       {
5757         printJob.print();
5758       } catch (Exception PrintException)
5759       {
5760         PrintException.printStackTrace();
5761       }
5762     }
5763   }
5764 }