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.AlignExportSettingsI;
  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.AlignExportSettingsAdapter;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.HiddenColumns;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.io.vcf.VCFLoader;
  85 import jalview.jbgui.GAlignFrame;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemes;
  88 import jalview.schemes.ResidueColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.util.ImageMaker.TYPE;
  91 import jalview.util.MessageManager;
  92 import jalview.util.Platform;
  93 import jalview.viewmodel.AlignmentViewport;
  94 import jalview.viewmodel.ViewportRanges;
  95 import jalview.ws.DBRefFetcher;
  96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Color;
 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.PrintWriter;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.JCheckBoxMenuItem;
 141 import javax.swing.JComponent;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLabel;
 145 import javax.swing.JLayeredPane;
 146 import javax.swing.JMenu;
 147 import javax.swing.JMenuItem;
 148 import javax.swing.JPanel;
 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   public static final int DEFAULT_WIDTH = 700;
 163
 164   public static final int DEFAULT_HEIGHT = 500;
 165
 166   /*
 167    * The currently displayed panel (selected tabbed view if more than one)
 168    */
 169   public AlignmentPanel alignPanel;
 170
 171   AlignViewport viewport;
 172
 173   public AlignViewControllerI avc;
 174
 175   List<AlignmentPanel> alignPanels = new ArrayList<>();
 176
 177   /**
 178    * Last format used to load or save alignments in this window
 179    */
 180   FileFormatI currentFileFormat = null;
 181
 182   /**
 183    * Current filename for this alignment
 184    */
 185   String fileName = null;
 186
 187   File fileObject;
 188
 189   /**
 190    * Creates a new AlignFrame object with specific width and height.
 191    *
 192    * @param al
 193    * @param width
 194    * @param height
 195    */
 196   public AlignFrame(AlignmentI al, int width, int height)
 197   {
 198     this(al, null, width, height);
 199   }
 200
 201   /**
 202    * Creates a new AlignFrame object with specific width, height and
 203    * sequenceSetId
 204    *
 205    * @param al
 206    * @param width
 207    * @param height
 208    * @param sequenceSetId
 209    */
 210   public AlignFrame(AlignmentI al, int width, int height,
 211           String sequenceSetId)
 212   {
 213     this(al, null, width, height, sequenceSetId);
 214   }
 215
 216   /**
 217    * Creates a new AlignFrame object with specific width, height and
 218    * sequenceSetId
 219    *
 220    * @param al
 221    * @param width
 222    * @param height
 223    * @param sequenceSetId
 224    * @param viewId
 225    */
 226   public AlignFrame(AlignmentI al, int width, int height,
 227           String sequenceSetId, String viewId)
 228   {
 229     this(al, null, width, height, sequenceSetId, viewId);
 230   }
 231
 232   /**
 233    * new alignment window with hidden columns
 234    *
 235    * @param al
 236    *          AlignmentI
 237    * @param hiddenColumns
 238    *          ColumnSelection or null
 239    * @param width
 240    *          Width of alignment frame
 241    * @param height
 242    *          height of frame.
 243    */
 244   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 245           int height)
 246   {
 247     this(al, hiddenColumns, width, height, null);
 248   }
 249
 250   /**
 251    * Create alignment frame for al with hiddenColumns, a specific width and
 252    * height, and specific sequenceId
 253    *
 254    * @param al
 255    * @param hiddenColumns
 256    * @param width
 257    * @param height
 258    * @param sequenceSetId
 259    *          (may be null)
 260    */
 261   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 262           int height, String sequenceSetId)
 263   {
 264     this(al, hiddenColumns, width, height, sequenceSetId, null);
 265   }
 266
 267   /**
 268    * Create alignment frame for al with hiddenColumns, a specific width and
 269    * height, and specific sequenceId
 270    *
 271    * @param al
 272    * @param hiddenColumns
 273    * @param width
 274    * @param height
 275    * @param sequenceSetId
 276    *          (may be null)
 277    * @param viewId
 278    *          (may be null)
 279    */
 280   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 281           int height, String sequenceSetId, String viewId)
 282   {
 283     setSize(width, height);
 284
 285     if (al.getDataset() == null)
 286     {
 287       al.setDataset(null);
 288     }
 289
 290     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 291
 292     alignPanel = new AlignmentPanel(this, viewport);
 293
 294     addAlignmentPanel(alignPanel, true);
 295     init();
 296   }
 297
 298   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 299           HiddenColumns hiddenColumns, int width, int height)
 300   {
 301     setSize(width, height);
 302
 303     if (al.getDataset() == null)
 304     {
 305       al.setDataset(null);
 306     }
 307
 308     viewport = new AlignViewport(al, hiddenColumns);
 309
 310     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 311     {
 312       viewport.hideSequence(hiddenSeqs);
 313     }
 314     alignPanel = new AlignmentPanel(this, viewport);
 315     addAlignmentPanel(alignPanel, true);
 316     init();
 317   }
 318
 319   /**
 320    * Make a new AlignFrame from existing alignmentPanels
 321    *
 322    * @param ap
 323    *          AlignmentPanel
 324    * @param av
 325    *          AlignViewport
 326    */
 327   public AlignFrame(AlignmentPanel ap)
 328   {
 329     viewport = ap.av;
 330     alignPanel = ap;
 331     addAlignmentPanel(ap, false);
 332     init();
 333   }
 334
 335   /**
 336    * initalise the alignframe from the underlying viewport data and the
 337    * configurations
 338    */
 339   void init()
 340   {
 341 //        setBackground(Color.white); // BH 2019
 342
 343     if (!Jalview.isHeadlessMode())
 344     {
 345       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 346     }
 347
 348     avc = new jalview.controller.AlignViewController(this, viewport,
 349             alignPanel);
 350     if (viewport.getAlignmentConservationAnnotation() == null)
 351     {
 352       // BLOSUM62Colour.setEnabled(false);
 353       conservationMenuItem.setEnabled(false);
 354       modifyConservation.setEnabled(false);
 355       // PIDColour.setEnabled(false);
 356       // abovePIDThreshold.setEnabled(false);
 357       // modifyPID.setEnabled(false);
 358     }
 359
 360     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 361             "No sort");
 362
 363     if (sortby.equals("Id"))
 364     {
 365       sortIDMenuItem_actionPerformed(null);
 366     }
 367     else if (sortby.equals("Pairwise Identity"))
 368     {
 369       sortPairwiseMenuItem_actionPerformed(null);
 370     }
 371
 372     this.alignPanel.av
 373             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 374
 375     setMenusFromViewport(viewport);
 376     buildSortByAnnotationScoresMenu();
 377     calculateTree.addActionListener(new ActionListener()
 378     {
 379
 380       @Override
 381       public void actionPerformed(ActionEvent e)
 382       {
 383         openTreePcaDialog();
 384       }
 385     });
 386     buildColourMenu();
 387
 388     if (Desktop.desktop != null)
 389     {
 390       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 391       /**
 392        * BH 2018 ignore service listeners
 393        *
 394        * @j2sNative
 395        *
 396        */
 397       {
 398         addServiceListeners();
 399       }
 400       setGUINucleotide();
 401     }
 402
 403     if (viewport.getWrapAlignment())
 404     {
 405       wrapMenuItem_actionPerformed(null);
 406     }
 407
 408     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 409     {
 410       this.overviewMenuItem_actionPerformed(null);
 411     }
 412
 413     addKeyListener();
 414
 415     final List<AlignmentPanel> selviews = new ArrayList<>();
 416     final List<AlignmentPanel> origview = new ArrayList<>();
 417     final String menuLabel = MessageManager
 418             .getString("label.copy_format_from");
 419     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 420             new ViewSetProvider()
 421             {
 422
 423               @Override
 424               public AlignmentPanel[] getAllAlignmentPanels()
 425               {
 426                 origview.clear();
 427                 origview.add(alignPanel);
 428                 // make an array of all alignment panels except for this one
 429                 List<AlignmentPanel> aps = new ArrayList<>(
 430                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 431                 aps.remove(AlignFrame.this.alignPanel);
 432                 return aps.toArray(new AlignmentPanel[aps.size()]);
 433               }
 434             }, selviews, new ItemListener()
 435             {
 436
 437               @Override
 438               public void itemStateChanged(ItemEvent e)
 439               {
 440                 if (origview.size() > 0)
 441                 {
 442                   final AlignmentPanel ap = origview.get(0);
 443
 444                   /*
 445                    * Copy the ViewStyle of the selected panel to 'this one'.
 446                    * Don't change value of 'scaleProteinAsCdna' unless copying
 447                    * from a SplitFrame.
 448                    */
 449                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 450                           .getViewStyle();
 451                   boolean fromSplitFrame = selviews.get(0)
 452                           .getAlignViewport().getCodingComplement() != null;
 453                   if (!fromSplitFrame)
 454                   {
 455                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 456                             .getViewStyle().isScaleProteinAsCdna());
 457                   }
 458                   ap.getAlignViewport().setViewStyle(vs);
 459
 460                   /*
 461                    * Also rescale ViewStyle of SplitFrame complement if there is
 462                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 463                    * the whole ViewStyle (allow cDNA protein to have different
 464                    * fonts)
 465                    */
 466                   AlignViewportI complement = ap.getAlignViewport()
 467                           .getCodingComplement();
 468                   if (complement != null && vs.isScaleProteinAsCdna())
 469                   {
 470                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 471                     ((SplitFrame) af.getSplitViewContainer())
 472                             .adjustLayout();
 473                     af.setMenusForViewport();
 474                   }
 475
 476                   ap.updateLayout();
 477                   ap.setSelected(true);
 478                   ap.alignFrame.setMenusForViewport();
 479
 480                 }
 481               }
 482             });
 483     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 484             .indexOf("devel") > -1
 485             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 486                     .indexOf("test") > -1)
 487     {
 488       formatMenu.add(vsel);
 489     }
 490     addFocusListener(new FocusAdapter()
 491     {
 492       @Override
 493       public void focusGained(FocusEvent e)
 494       {
 495         Jalview.setCurrentAlignFrame(AlignFrame.this);
 496       }
 497     });
 498
 499   }
 500
 501   /**
 502    * Change the filename and format for the alignment, and enable the 'reload'
 503    * button functionality.
 504    *
 505    * @param file
 506    *          valid filename
 507    * @param format
 508    *          format of file
 509    */
 510   public void setFileName(String file, FileFormatI format)
 511   {
 512     fileName = file;
 513     setFileFormat(format);
 514     reload.setEnabled(true);
 515   }
 516
 517   /**
 518    * JavaScript will have this, maybe others. More dependable than a file name
 519    * and maintains a reference to the actual bytes loaded.
 520    *
 521    * @param file
 522    */
 523   public void setFileObject(File file)
 524   {
 525     this.fileObject = file;
 526   }
 527
 528   /**
 529    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 530    * events
 531    */
 532   void addKeyListener()
 533   {
 534     addKeyListener(new KeyAdapter()
 535     {
 536       @Override
 537       public void keyPressed(KeyEvent evt)
 538       {
 539         if (viewport.cursorMode
 540                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 541                         && evt.getKeyCode() <= KeyEvent.VK_9)
 542                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 543                                 && evt.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,
 584                     alignPanel.getSeqPanel().getKeyboardNo1());
 585           }
 586           else
 587           {
 588             alignPanel.getSeqPanel().moveCursor(-1, 0);
 589           }
 590
 591           break;
 592
 593         case KeyEvent.VK_RIGHT:
 594           if (evt.isAltDown() || !viewport.cursorMode)
 595           {
 596             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 597           }
 598           else
 599           {
 600             alignPanel.getSeqPanel().moveCursor(1, 0);
 601           }
 602           break;
 603
 604         case KeyEvent.VK_SPACE:
 605           if (viewport.cursorMode)
 606           {
 607             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 608                     || evt.isShiftDown() || 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();
 628           }
 629           else
 630           {
 631             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 632                     || evt.isShiftDown() || evt.isAltDown());
 633           }
 634
 635           break;
 636
 637         case KeyEvent.VK_S:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setCursorRow();
 641           }
 642           break;
 643         case KeyEvent.VK_C:
 644           if (viewport.cursorMode && !evt.isControlDown())
 645           {
 646             alignPanel.getSeqPanel().setCursorColumn();
 647           }
 648           break;
 649         case KeyEvent.VK_P:
 650           if (viewport.cursorMode)
 651           {
 652             alignPanel.getSeqPanel().setCursorPosition();
 653           }
 654           break;
 655
 656         case KeyEvent.VK_ENTER:
 657         case KeyEvent.VK_COMMA:
 658           if (viewport.cursorMode)
 659           {
 660             alignPanel.getSeqPanel().setCursorRowAndColumn();
 661           }
 662           break;
 663
 664         case KeyEvent.VK_Q:
 665           if (viewport.cursorMode)
 666           {
 667             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 668           }
 669           break;
 670         case KeyEvent.VK_M:
 671           if (viewport.cursorMode)
 672           {
 673             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 674           }
 675           break;
 676
 677         case KeyEvent.VK_F2:
 678           viewport.cursorMode = !viewport.cursorMode;
 679           setStatus(MessageManager
 680                   .formatMessage("label.keyboard_editing_mode", new String[]
 681                   { (viewport.cursorMode ? "on" : "off") }));
 682           if (viewport.cursorMode)
 683           {
 684             ViewportRanges ranges = viewport.getRanges();
 685             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 686                     .getStartRes();
 687             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 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           viewport.getRanges().pageUp();
 721           break;
 722         case KeyEvent.VK_PAGE_DOWN:
 723           viewport.getRanges().pageDown();
 724           break;
 725         }
 726       }
 727
 728       @Override
 729       public void keyReleased(KeyEvent evt)
 730       {
 731         switch (evt.getKeyCode())
 732         {
 733         case KeyEvent.VK_LEFT:
 734           if (evt.isAltDown() || !viewport.cursorMode)
 735           {
 736             viewport.firePropertyChange("alignment", null,
 737                     viewport.getAlignment().getSequences());
 738           }
 739           break;
 740
 741         case KeyEvent.VK_RIGHT:
 742           if (evt.isAltDown() || !viewport.cursorMode)
 743           {
 744             viewport.firePropertyChange("alignment", null,
 745                     viewport.getAlignment().getSequences());
 746           }
 747           break;
 748         }
 749       }
 750     });
 751   }
 752
 753   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 754   {
 755     ap.alignFrame = this;
 756     avc = new jalview.controller.AlignViewController(this, viewport,
 757             alignPanel);
 758
 759     alignPanels.add(ap);
 760
 761     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 762
 763     int aSize = alignPanels.size();
 764
 765     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 766
 767     if (aSize == 1 && ap.av.getViewName() == null)
 768     {
 769       this.getContentPane().add(ap, BorderLayout.CENTER);
 770     }
 771     else
 772     {
 773       if (aSize == 2)
 774       {
 775         setInitialTabVisible();
 776       }
 777
 778       expandViews.setEnabled(true);
 779       gatherViews.setEnabled(true);
 780       tabbedPane.addTab(ap.av.getViewName(), ap);
 781
 782       ap.setVisible(false);
 783     }
 784
 785     if (newPanel)
 786     {
 787       if (ap.av.isPadGaps())
 788       {
 789         ap.av.getAlignment().padGaps();
 790       }
 791       ap.av.updateConservation(ap);
 792       ap.av.updateConsensus(ap);
 793       ap.av.updateStrucConsensus(ap);
 794     }
 795   }
 796
 797   public void setInitialTabVisible()
 798   {
 799     expandViews.setEnabled(true);
 800     gatherViews.setEnabled(true);
 801     tabbedPane.setVisible(true);
 802     AlignmentPanel first = alignPanels.get(0);
 803     tabbedPane.addTab(first.av.getViewName(), first);
 804     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 805   }
 806
 807   public AlignViewport getViewport()
 808   {
 809     return viewport;
 810   }
 811
 812   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 813   private void addServiceListeners()
 814   {
 815     final java.beans.PropertyChangeListener thisListener;
 816     Desktop.instance.addJalviewPropertyChangeListener("services",
 817             thisListener = new java.beans.PropertyChangeListener()
 818             {
 819               @Override
 820               public void propertyChange(PropertyChangeEvent evt)
 821               {
 822                 // // System.out.println("Discoverer property change.");
 823                 // if (evt.getPropertyName().equals("services"))
 824                 {
 825                   SwingUtilities.invokeLater(new Runnable()
 826                   {
 827
 828                     @Override
 829                     public void run()
 830                     {
 831                       System.err.println(
 832                               "Rebuild WS Menu for service change");
 833                       BuildWebServiceMenu();
 834                     }
 835
 836                   });
 837                 }
 838               }
 839             });
 840     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 841     {
 842       @Override
 843       public void internalFrameClosed(
 844               javax.swing.event.InternalFrameEvent evt)
 845       {
 846         // System.out.println("deregistering discoverer listener");
 847         Desktop.instance.removeJalviewPropertyChangeListener("services",
 848                 thisListener);
 849         closeMenuItem_actionPerformed(true);
 850       };
 851     });
 852     // Finally, build the menu once to get current service state
 853     new Thread(new Runnable()
 854     {
 855       @Override
 856       public void run()
 857       {
 858         BuildWebServiceMenu();
 859       }
 860     }).start();
 861   }
 862
 863   /**
 864    * Configure menu items that vary according to whether the alignment is
 865    * nucleotide or protein
 866    */
 867   public void setGUINucleotide()
 868   {
 869     AlignmentI al = getViewport().getAlignment();
 870     boolean nucleotide = al.isNucleotide();
 871
 872     loadVcf.setVisible(nucleotide);
 873     showTranslation.setVisible(nucleotide);
 874     showReverse.setVisible(nucleotide);
 875     showReverseComplement.setVisible(nucleotide);
 876     conservationMenuItem.setEnabled(!nucleotide);
 877     modifyConservation
 878             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 879     showGroupConservation.setEnabled(!nucleotide);
 880
 881     showComplementMenuItem
 882             .setText(nucleotide ? MessageManager.getString("label.protein")
 883                     : MessageManager.getString("label.nucleotide"));
 884   }
 885
 886   /**
 887    * set up menus for the current viewport. This may be called after any
 888    * operation that affects the data in the current view (selection changed,
 889    * etc) to update the menus to reflect the new state.
 890    */
 891   @Override
 892   public void setMenusForViewport()
 893   {
 894     setMenusFromViewport(viewport);
 895   }
 896
 897   /**
 898    * Need to call this method when tabs are selected for multiple views, or when
 899    * loading from Jalview2XML.java
 900    *
 901    * @param av
 902    *          AlignViewport
 903    */
 904   public void setMenusFromViewport(AlignViewport av)
 905   {
 906     padGapsMenuitem.setSelected(av.isPadGaps());
 907     colourTextMenuItem.setSelected(av.isShowColourText());
 908     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 909     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 910     conservationMenuItem.setSelected(av.getConservationSelected());
 911     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 912     seqLimits.setSelected(av.getShowJVSuffix());
 913     idRightAlign.setSelected(av.isRightAlignIds());
 914     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 915     renderGapsMenuItem.setSelected(av.isRenderGaps());
 916     wrapMenuItem.setSelected(av.getWrapAlignment());
 917     scaleAbove.setVisible(av.getWrapAlignment());
 918     scaleLeft.setVisible(av.getWrapAlignment());
 919     scaleRight.setVisible(av.getWrapAlignment());
 920     annotationPanelMenuItem.setState(av.isShowAnnotation());
 921     /*
 922      * Show/hide annotations only enabled if annotation panel is shown
 923      */
 924     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 925     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 926     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 927     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 928     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 929     viewTextMenuItem.setSelected(av.getShowText());
 930     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 931     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 932     showGroupConservation.setSelected(av.isShowGroupConservation());
 933     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 934     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 935     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 936
 937     ColourMenuHelper.setColourSelected(colourMenu,
 938             av.getGlobalColourScheme());
 939
 940     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 941     hiddenMarkers.setState(av.getShowHiddenMarkers());
 942     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 943     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 944     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 945     autoCalculate.setSelected(av.autoCalculateConsensus);
 946     sortByTree.setSelected(av.sortByTree);
 947     listenToViewSelections.setSelected(av.followSelection);
 948
 949     showProducts.setEnabled(canShowProducts());
 950     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 951
 952     updateEditMenuBar();
 953   }
 954
 955   /**
 956    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 957    *
 958    * @param b
 959    */
 960   public void setGroovyEnabled(boolean b)
 961   {
 962     runGroovy.setEnabled(b);
 963   }
 964
 965   private IProgressIndicator progressBar;
 966
 967   /*
 968    * (non-Javadoc)
 969    *
 970    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 971    */
 972   @Override
 973   public void setProgressBar(String message, long id)
 974   {
 975     progressBar.setProgressBar(message, id);
 976   }
 977
 978   @Override
 979   public void registerHandler(final long id,
 980           final IProgressIndicatorHandler handler)
 981   {
 982     progressBar.registerHandler(id, handler);
 983   }
 984
 985   /**
 986    *
 987    * @return true if any progress bars are still active
 988    */
 989   @Override
 990   public boolean operationInProgress()
 991   {
 992     return progressBar.operationInProgress();
 993   }
 994
 995   @Override
 996   public void setStatus(String text)
 997   {
 998           // BH note: If text width and height are 0, then the layout manager
 999           // will dispense of it and change the frame height.
1000           // In JavaScript, we use \u00A0  -- unicode "non-breaking space"
1001           // which is the unicode encoding of &nbsp;
1002
1003     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1004   }
1005
1006   /*
1007    * Added so Castor Mapping file can obtain Jalview Version
1008    */
1009   public String getVersion()
1010   {
1011     return jalview.bin.Cache.getProperty("VERSION");
1012   }
1013
1014   public FeatureRenderer getFeatureRenderer()
1015   {
1016     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1017   }
1018
1019   @Override
1020   public void fetchSequence_actionPerformed()
1021   {
1022     new SequenceFetcher(this);
1023   }
1024
1025   @Override
1026   public void addFromFile_actionPerformed(ActionEvent e)
1027   {
1028     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1029   }
1030
1031   @Override
1032   public void reload_actionPerformed(ActionEvent e)
1033   {
1034     if (fileName != null)
1035     {
1036       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1037       // originating file's format
1038       // TODO: work out how to recover feature settings for correct view(s) when
1039       // file is reloaded.
1040       if (FileFormat.Jalview.equals(currentFileFormat))
1041       {
1042         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1043         for (int i = 0; i < frames.length; i++)
1044         {
1045           if (frames[i] instanceof AlignFrame && frames[i] != this
1046                   && ((AlignFrame) frames[i]).fileName != null
1047                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1048           {
1049             try
1050             {
1051               frames[i].setSelected(true);
1052               Desktop.instance.closeAssociatedWindows();
1053             } catch (java.beans.PropertyVetoException ex)
1054             {
1055             }
1056           }
1057
1058         }
1059         Desktop.instance.closeAssociatedWindows();
1060
1061         FileLoader loader = new FileLoader();
1062         DataSourceType protocol = fileName.startsWith("http:")
1063                 ? DataSourceType.URL
1064                 : DataSourceType.FILE;
1065         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1066       }
1067       else
1068       {
1069         Rectangle bounds = this.getBounds();
1070
1071         FileLoader loader = new FileLoader();
1072
1073         AlignFrame newframe = null;
1074
1075         if (fileObject == null)
1076         {
1077
1078           DataSourceType protocol = (fileName.startsWith("http:")
1079                   ? DataSourceType.URL
1080                   : DataSourceType.FILE);
1081           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1082                   currentFileFormat);
1083         }
1084         else
1085         {
1086           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1087                   DataSourceType.FILE, currentFileFormat);
1088         }
1089
1090         newframe.setBounds(bounds);
1091         if (featureSettings != null && featureSettings.isShowing())
1092         {
1093           final Rectangle fspos = featureSettings.frame.getBounds();
1094           // TODO: need a 'show feature settings' function that takes bounds -
1095           // need to refactor Desktop.addFrame
1096           newframe.featureSettings_actionPerformed(null);
1097           final FeatureSettings nfs = newframe.featureSettings;
1098           SwingUtilities.invokeLater(new Runnable()
1099           {
1100             @Override
1101             public void run()
1102             {
1103               nfs.frame.setBounds(fspos);
1104             }
1105           });
1106           this.featureSettings.close();
1107           this.featureSettings = null;
1108         }
1109         this.closeMenuItem_actionPerformed(true);
1110       }
1111     }
1112   }
1113
1114   @Override
1115   public void addFromText_actionPerformed(ActionEvent e)
1116   {
1117     Desktop.instance
1118             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1119   }
1120
1121   @Override
1122   public void addFromURL_actionPerformed(ActionEvent e)
1123   {
1124     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1125   }
1126
1127   @Override
1128   public void save_actionPerformed(ActionEvent e)
1129   {
1130     if (fileName == null || (currentFileFormat == null)
1131             || fileName.startsWith("http"))
1132     {
1133       saveAs_actionPerformed();
1134     }
1135     else
1136     {
1137       saveAlignment(fileName, currentFileFormat);
1138     }
1139   }
1140
1141   /**
1142    * Saves the alignment to a file with a name chosen by the user, if necessary
1143    * warning if a file would be overwritten
1144    */
1145   @Override
1146   public void saveAs_actionPerformed()
1147   {
1148     String format = currentFileFormat == null ? null
1149             : currentFileFormat.getName();
1150     JalviewFileChooser chooser = JalviewFileChooser
1151             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1152
1153     chooser.setFileView(new JalviewFileView());
1154     chooser.setDialogTitle(
1155             MessageManager.getString("label.save_alignment_to_file"));
1156     chooser.setToolTipText(MessageManager.getString("action.save"));
1157
1158     int value = chooser.showSaveDialog(this);
1159
1160     if (value != JalviewFileChooser.APPROVE_OPTION)
1161     {
1162       return;
1163     }
1164     currentFileFormat = chooser.getSelectedFormat();
1165     // todo is this (2005) test now obsolete - value is never null?
1166     while (currentFileFormat == null)
1167     {
1168       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1169               MessageManager
1170                       .getString("label.select_file_format_before_saving"),
1171               MessageManager.getString("label.file_format_not_specified"),
1172               JvOptionPane.WARNING_MESSAGE);
1173       currentFileFormat = chooser.getSelectedFormat();
1174       value = chooser.showSaveDialog(this);
1175       if (value != JalviewFileChooser.APPROVE_OPTION)
1176       {
1177         return;
1178       }
1179     }
1180
1181     fileName = chooser.getSelectedFile().getPath();
1182
1183     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1184     Cache.setProperty("LAST_DIRECTORY", fileName);
1185     saveAlignment(fileName, currentFileFormat);
1186   }
1187
1188   boolean lastSaveSuccessful = false;
1189
1190   FileFormatI lastFormatSaved;
1191
1192   String lastFilenameSaved;
1193
1194   /**
1195    * Raise a dialog or status message for the last call to saveAlignment.
1196    *
1197    * @return true if last call to saveAlignment(file, format) was successful.
1198    */
1199   public boolean isSaveAlignmentSuccessful()
1200   {
1201
1202     if (!lastSaveSuccessful)
1203     {
1204       JvOptionPane.showInternalMessageDialog(this, MessageManager
1205               .formatMessage("label.couldnt_save_file", new Object[]
1206               { lastFilenameSaved }),
1207               MessageManager.getString("label.error_saving_file"),
1208               JvOptionPane.WARNING_MESSAGE);
1209     }
1210     else
1211     {
1212
1213       setStatus(MessageManager.formatMessage(
1214               "label.successfully_saved_to_file_in_format", new Object[]
1215               { lastFilenameSaved, lastFormatSaved }));
1216
1217     }
1218     return lastSaveSuccessful;
1219   }
1220
1221   /**
1222    * Saves the alignment to the specified file path, in the specified format,
1223    * which may be an alignment format, or Jalview project format. If the
1224    * alignment has hidden regions, or the format is one capable of including
1225    * non-sequence data (features, annotations, groups), then the user may be
1226    * prompted to specify what to include in the output.
1227    *
1228    * @param file
1229    * @param format
1230    */
1231   public void saveAlignment(String file, FileFormatI format)
1232   {
1233     lastSaveSuccessful = false;
1234     lastFilenameSaved = file;
1235     lastFormatSaved = format;
1236
1237     if (FileFormat.Jalview.equals(format))
1238     {
1239       String shortName = title;
1240       if (shortName.indexOf(File.separatorChar) > -1)
1241       {
1242         shortName = shortName.substring(
1243                 shortName.lastIndexOf(File.separatorChar) + 1);
1244       }
1245       lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
1246               shortName);
1247
1248       statusBar.setText(MessageManager.formatMessage(
1249               "label.successfully_saved_to_file_in_format", new Object[]
1250               { fileName, format }));
1251
1252       return;
1253     }
1254
1255     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1256     Runnable cancelAction = new Runnable()
1257     {
1258       @Override
1259       public void run()
1260       {
1261         lastSaveSuccessful = false;
1262       }
1263     };
1264     Runnable outputAction = new Runnable()
1265     {
1266       @Override
1267       public void run()
1268       {
1269         // todo defer this to inside formatSequences (or later)
1270         AlignmentExportData exportData = viewport
1271                 .getAlignExportData(options);
1272         String output = new FormatAdapter(alignPanel, options)
1273                 .formatSequences(format, exportData.getAlignment(),
1274                         exportData.getOmitHidden(),
1275                         exportData.getStartEndPostions(),
1276                         viewport.getAlignment().getHiddenColumns());
1277         if (output == null)
1278         {
1279           lastSaveSuccessful = false;
1280         }
1281         else
1282         {
1283           try
1284           {
1285             PrintWriter out = new PrintWriter(new FileWriter(file));
1286             out.print(output);
1287             out.close();
1288             AlignFrame.this.setTitle(file);
1289             setStatus(MessageManager.formatMessage(
1290                     "label.successfully_saved_to_file_in_format",
1291                     new Object[]
1292                     { fileName, format.getName() }));
1293           } catch (Exception ex)
1294           {
1295             lastSaveSuccessful = false;
1296             ex.printStackTrace();
1297           }
1298         }
1299       }
1300     };
1301
1302     /*
1303      * show dialog with export options if applicable; else just do it
1304      */
1305     if (AlignExportOptions.isNeeded(viewport, format))
1306     {
1307       AlignExportOptions choices = new AlignExportOptions(
1308               alignPanel.getAlignViewport(), format, options);
1309       choices.setResponseAction(0, outputAction);
1310       choices.setResponseAction(1, cancelAction);
1311       choices.showDialog();
1312     }
1313     else
1314     {
1315       outputAction.run();
1316     }
1317   }
1318
1319   /**
1320    * Outputs the alignment to textbox in the requested format, if necessary
1321    * first prompting the user for whether to include hidden regions or
1322    * non-sequence data
1323    *
1324    * @param fileFormatName
1325    */
1326   @Override
1327   protected void outputText_actionPerformed(String fileFormatName)
1328   {
1329     FileFormatI fileFormat = FileFormats.getInstance()
1330             .forName(fileFormatName);
1331     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1332     Runnable outputAction = new Runnable()
1333     {
1334       @Override
1335       public void run()
1336       {
1337         // todo defer this to inside formatSequences (or later)
1338         AlignmentExportData exportData = viewport
1339                 .getAlignExportData(options);
1340         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1341         cap.setForInput(null);
1342         try
1343         {
1344           FileFormatI format = fileFormat;
1345           cap.setText(new FormatAdapter(alignPanel, options)
1346                   .formatSequences(format, exportData.getAlignment(),
1347                           exportData.getOmitHidden(),
1348                           exportData.getStartEndPostions(),
1349                           viewport.getAlignment().getHiddenColumns()));
1350           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1351                   "label.alignment_output_command", new Object[]
1352                   { fileFormat.getName() }), 600, 500);
1353         } catch (OutOfMemoryError oom)
1354         {
1355           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1356                   oom);
1357           cap.dispose();
1358         }
1359       }
1360     };
1361
1362     /*
1363      * show dialog with export options if applicable; else just do it
1364      */
1365     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1366     {
1367       AlignExportOptions choices = new AlignExportOptions(
1368               alignPanel.getAlignViewport(), fileFormat, options);
1369       choices.setResponseAction(0, outputAction);
1370       choices.showDialog();
1371     }
1372     else
1373     {
1374       outputAction.run();
1375     }
1376   }
1377
1378   /**
1379    * DOCUMENT ME!
1380    *
1381    * @param e
1382    *          DOCUMENT ME!
1383    */
1384   @Override
1385   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1386   {
1387     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1388     htmlSVG.exportHTML(null);
1389   }
1390
1391   @Override
1392   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1393   {
1394     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1395     bjs.exportHTML(null);
1396   }
1397
1398   public void createImageMap(File file, String image)
1399   {
1400     alignPanel.makePNGImageMap(file, image);
1401   }
1402
1403   /**
1404    * Creates a PNG image of the alignment and writes it to the given file. If
1405    * the file is null, the user is prompted to choose a file.
1406    *
1407    * @param f
1408    */
1409   @Override
1410   public void createPNG(File f)
1411   {
1412     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1413   }
1414
1415   /**
1416    * Creates an EPS image of the alignment and writes it to the given file. If
1417    * the file is null, the user is prompted to choose a file.
1418    *
1419    * @param f
1420    */
1421   @Override
1422   public void createEPS(File f)
1423   {
1424     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1425   }
1426
1427   /**
1428    * Creates an SVG image of the alignment and writes it to the given file. If
1429    * the file is null, the user is prompted to choose a file.
1430    *
1431    * @param f
1432    */
1433   @Override
1434   public void createSVG(File f)
1435   {
1436     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1437   }
1438
1439   @Override
1440   public void pageSetup_actionPerformed(ActionEvent e)
1441   {
1442     PrinterJob printJob = PrinterJob.getPrinterJob();
1443     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1444   }
1445
1446   /**
1447    * DOCUMENT ME!
1448    *
1449    * @param e
1450    *          DOCUMENT ME!
1451    */
1452   @Override
1453   public void printMenuItem_actionPerformed(ActionEvent e)
1454   {
1455     // Putting in a thread avoids Swing painting problems
1456     PrintThread thread = new PrintThread(alignPanel);
1457     thread.start();
1458   }
1459
1460   @Override
1461   public void exportFeatures_actionPerformed(ActionEvent e)
1462   {
1463     new AnnotationExporter(alignPanel).exportFeatures();
1464   }
1465
1466   @Override
1467   public void exportAnnotations_actionPerformed(ActionEvent e)
1468   {
1469     new AnnotationExporter(alignPanel).exportAnnotations();
1470   }
1471
1472   @Override
1473   public void associatedData_actionPerformed(ActionEvent e)
1474   {
1475     final JalviewFileChooser chooser = new JalviewFileChooser(
1476             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1477     chooser.setFileView(new JalviewFileView());
1478     chooser.setDialogTitle(
1479             MessageManager.getString("label.load_jalview_annotations"));
1480     chooser.setToolTipText(
1481             MessageManager.getString("label.load_jalview_annotations"));
1482     chooser.setResponseHandler(0, new Runnable()
1483     {
1484       @Override
1485       public void run()
1486       {
1487         String choice = chooser.getSelectedFile().getPath();
1488         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1489         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1490       }
1491     });
1492
1493     chooser.showOpenDialog(this);
1494   }
1495
1496   /**
1497    * Close the current view or all views in the alignment frame. If the frame
1498    * only contains one view then the alignment will be removed from memory.
1499    *
1500    * @param closeAllTabs
1501    */
1502   @Override
1503   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1504   {
1505     if (alignPanels != null && alignPanels.size() < 2)
1506     {
1507       closeAllTabs = true;
1508     }
1509
1510     try
1511     {
1512       if (alignPanels != null)
1513       {
1514         if (closeAllTabs)
1515         {
1516           if (this.isClosed())
1517           {
1518             // really close all the windows - otherwise wait till
1519             // setClosed(true) is called
1520             for (int i = 0; i < alignPanels.size(); i++)
1521             {
1522               AlignmentPanel ap = alignPanels.get(i);
1523               ap.closePanel();
1524             }
1525           }
1526         }
1527         else
1528         {
1529           closeView(alignPanel);
1530         }
1531       }
1532
1533       if (closeAllTabs)
1534       {
1535         /*
1536          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1537          * be called recursively, with the frame now in 'closed' state
1538          */
1539         this.setClosed(true);
1540       }
1541     } catch (Exception ex)
1542     {
1543       ex.printStackTrace();
1544     }
1545   }
1546
1547   /**
1548    * Close the specified panel and close up tabs appropriately.
1549    *
1550    * @param panelToClose
1551    */
1552   public void closeView(AlignmentPanel panelToClose)
1553   {
1554     int index = tabbedPane.getSelectedIndex();
1555     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1556     alignPanels.remove(panelToClose);
1557     panelToClose.closePanel();
1558     panelToClose = null;
1559
1560     tabbedPane.removeTabAt(closedindex);
1561     tabbedPane.validate();
1562
1563     if (index > closedindex || index == tabbedPane.getTabCount())
1564     {
1565       // modify currently selected tab index if necessary.
1566       index--;
1567     }
1568
1569     this.tabSelectionChanged(index);
1570   }
1571
1572   /**
1573    * DOCUMENT ME!
1574    */
1575   void updateEditMenuBar()
1576   {
1577
1578     if (viewport.getHistoryList().size() > 0)
1579     {
1580       undoMenuItem.setEnabled(true);
1581       CommandI command = viewport.getHistoryList().peek();
1582       undoMenuItem.setText(MessageManager
1583               .formatMessage("label.undo_command", new Object[]
1584               { command.getDescription() }));
1585     }
1586     else
1587     {
1588       undoMenuItem.setEnabled(false);
1589       undoMenuItem.setText(MessageManager.getString("action.undo"));
1590     }
1591
1592     if (viewport.getRedoList().size() > 0)
1593     {
1594       redoMenuItem.setEnabled(true);
1595
1596       CommandI command = viewport.getRedoList().peek();
1597       redoMenuItem.setText(MessageManager
1598               .formatMessage("label.redo_command", new Object[]
1599               { command.getDescription() }));
1600     }
1601     else
1602     {
1603       redoMenuItem.setEnabled(false);
1604       redoMenuItem.setText(MessageManager.getString("action.redo"));
1605     }
1606   }
1607
1608   @Override
1609   public void addHistoryItem(CommandI command)
1610   {
1611     if (command.getSize() > 0)
1612     {
1613       viewport.addToHistoryList(command);
1614       viewport.clearRedoList();
1615       updateEditMenuBar();
1616       viewport.updateHiddenColumns();
1617       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1618       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1619       // viewport.getColumnSelection()
1620       // .getHiddenColumns().size() > 0);
1621     }
1622   }
1623
1624   /**
1625    *
1626    * @return alignment objects for all views
1627    */
1628   AlignmentI[] getViewAlignments()
1629   {
1630     if (alignPanels != null)
1631     {
1632       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1633       int i = 0;
1634       for (AlignmentPanel ap : alignPanels)
1635       {
1636         als[i++] = ap.av.getAlignment();
1637       }
1638       return als;
1639     }
1640     if (viewport != null)
1641     {
1642       return new AlignmentI[] { viewport.getAlignment() };
1643     }
1644     return null;
1645   }
1646
1647   /**
1648    * DOCUMENT ME!
1649    *
1650    * @param e
1651    *          DOCUMENT ME!
1652    */
1653   @Override
1654   protected void undoMenuItem_actionPerformed(ActionEvent e)
1655   {
1656     if (viewport.getHistoryList().isEmpty())
1657     {
1658       return;
1659     }
1660     CommandI command = viewport.getHistoryList().pop();
1661     viewport.addToRedoList(command);
1662     command.undoCommand(getViewAlignments());
1663
1664     AlignmentViewport originalSource = getOriginatingSource(command);
1665     updateEditMenuBar();
1666
1667     if (originalSource != null)
1668     {
1669       if (originalSource != viewport)
1670       {
1671         Cache.log.warn(
1672                 "Implementation worry: mismatch of viewport origin for undo");
1673       }
1674       originalSource.updateHiddenColumns();
1675       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1676       // null
1677       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1678       // viewport.getColumnSelection()
1679       // .getHiddenColumns().size() > 0);
1680       originalSource.firePropertyChange("alignment", null,
1681               originalSource.getAlignment().getSequences());
1682     }
1683   }
1684
1685   /**
1686    * DOCUMENT ME!
1687    *
1688    * @param e
1689    *          DOCUMENT ME!
1690    */
1691   @Override
1692   protected void redoMenuItem_actionPerformed(ActionEvent e)
1693   {
1694     if (viewport.getRedoList().size() < 1)
1695     {
1696       return;
1697     }
1698
1699     CommandI command = viewport.getRedoList().pop();
1700     viewport.addToHistoryList(command);
1701     command.doCommand(getViewAlignments());
1702
1703     AlignmentViewport originalSource = getOriginatingSource(command);
1704     updateEditMenuBar();
1705
1706     if (originalSource != null)
1707     {
1708
1709       if (originalSource != viewport)
1710       {
1711         Cache.log.warn(
1712                 "Implementation worry: mismatch of viewport origin for redo");
1713       }
1714       originalSource.updateHiddenColumns();
1715       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1716       // null
1717       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1718       // viewport.getColumnSelection()
1719       // .getHiddenColumns().size() > 0);
1720       originalSource.firePropertyChange("alignment", null,
1721               originalSource.getAlignment().getSequences());
1722     }
1723   }
1724
1725   AlignmentViewport getOriginatingSource(CommandI command)
1726   {
1727     AlignmentViewport originalSource = null;
1728     // For sequence removal and addition, we need to fire
1729     // the property change event FROM the viewport where the
1730     // original alignment was altered
1731     AlignmentI al = null;
1732     if (command instanceof EditCommand)
1733     {
1734       EditCommand editCommand = (EditCommand) command;
1735       al = editCommand.getAlignment();
1736       List<Component> comps = PaintRefresher.components
1737               .get(viewport.getSequenceSetId());
1738
1739       for (Component comp : comps)
1740       {
1741         if (comp instanceof AlignmentPanel)
1742         {
1743           if (al == ((AlignmentPanel) comp).av.getAlignment())
1744           {
1745             originalSource = ((AlignmentPanel) comp).av;
1746             break;
1747           }
1748         }
1749       }
1750     }
1751
1752     if (originalSource == null)
1753     {
1754       // The original view is closed, we must validate
1755       // the current view against the closed view first
1756       if (al != null)
1757       {
1758         PaintRefresher.validateSequences(al, viewport.getAlignment());
1759       }
1760
1761       originalSource = viewport;
1762     }
1763
1764     return originalSource;
1765   }
1766
1767   /**
1768    * DOCUMENT ME!
1769    *
1770    * @param up
1771    *          DOCUMENT ME!
1772    */
1773   public void moveSelectedSequences(boolean up)
1774   {
1775     SequenceGroup sg = viewport.getSelectionGroup();
1776
1777     if (sg == null)
1778     {
1779       return;
1780     }
1781     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1782             viewport.getHiddenRepSequences(), up);
1783     alignPanel.paintAlignment(true, false);
1784   }
1785
1786   synchronized void slideSequences(boolean right, int size)
1787   {
1788     List<SequenceI> sg = new ArrayList<>();
1789     if (viewport.cursorMode)
1790     {
1791       sg.add(viewport.getAlignment()
1792               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1793     }
1794     else if (viewport.getSelectionGroup() != null
1795             && viewport.getSelectionGroup().getSize() != viewport
1796                     .getAlignment().getHeight())
1797     {
1798       sg = viewport.getSelectionGroup()
1799               .getSequences(viewport.getHiddenRepSequences());
1800     }
1801
1802     if (sg.size() < 1)
1803     {
1804       return;
1805     }
1806
1807     List<SequenceI> invertGroup = new ArrayList<>();
1808
1809     for (SequenceI seq : viewport.getAlignment().getSequences())
1810     {
1811       if (!sg.contains(seq))
1812       {
1813         invertGroup.add(seq);
1814       }
1815     }
1816
1817     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1818
1819     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1820     for (int i = 0; i < invertGroup.size(); i++)
1821     {
1822       seqs2[i] = invertGroup.get(i);
1823     }
1824
1825     SlideSequencesCommand ssc;
1826     if (right)
1827     {
1828       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1829               viewport.getGapCharacter());
1830     }
1831     else
1832     {
1833       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1834               viewport.getGapCharacter());
1835     }
1836
1837     int groupAdjustment = 0;
1838     if (ssc.getGapsInsertedBegin() && right)
1839     {
1840       if (viewport.cursorMode)
1841       {
1842         alignPanel.getSeqPanel().moveCursor(size, 0);
1843       }
1844       else
1845       {
1846         groupAdjustment = size;
1847       }
1848     }
1849     else if (!ssc.getGapsInsertedBegin() && !right)
1850     {
1851       if (viewport.cursorMode)
1852       {
1853         alignPanel.getSeqPanel().moveCursor(-size, 0);
1854       }
1855       else
1856       {
1857         groupAdjustment = -size;
1858       }
1859     }
1860
1861     if (groupAdjustment != 0)
1862     {
1863       viewport.getSelectionGroup().setStartRes(
1864               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1865       viewport.getSelectionGroup().setEndRes(
1866               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1867     }
1868
1869     /*
1870      * just extend the last slide command if compatible; but not if in
1871      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1872      */
1873     boolean appendHistoryItem = false;
1874     Deque<CommandI> historyList = viewport.getHistoryList();
1875     boolean inSplitFrame = getSplitViewContainer() != null;
1876     if (!inSplitFrame && historyList != null && historyList.size() > 0
1877             && historyList.peek() instanceof SlideSequencesCommand)
1878     {
1879       appendHistoryItem = ssc.appendSlideCommand(
1880               (SlideSequencesCommand) historyList.peek());
1881     }
1882
1883     if (!appendHistoryItem)
1884     {
1885       addHistoryItem(ssc);
1886     }
1887
1888     repaint();
1889   }
1890
1891   /**
1892    * DOCUMENT ME!
1893    *
1894    * @param e
1895    *          DOCUMENT ME!
1896    */
1897   @Override
1898   protected void copy_actionPerformed()
1899   {
1900     if (viewport.getSelectionGroup() == null)
1901     {
1902       return;
1903     }
1904     // TODO: preserve the ordering of displayed alignment annotation in any
1905     // internal paste (particularly sequence associated annotation)
1906     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1907     String[] omitHidden = null;
1908
1909     if (viewport.hasHiddenColumns())
1910     {
1911       omitHidden = viewport.getViewAsString(true);
1912     }
1913
1914     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1915             seqs, omitHidden, null);
1916
1917     StringSelection ss = new StringSelection(output);
1918
1919     try
1920     {
1921       jalview.gui.Desktop.internalCopy = true;
1922       // Its really worth setting the clipboard contents
1923       // to empty before setting the large StringSelection!!
1924       Toolkit.getDefaultToolkit().getSystemClipboard()
1925               .setContents(new StringSelection(""), null);
1926
1927       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1928               Desktop.instance);
1929     } catch (OutOfMemoryError er)
1930     {
1931       new OOMWarning("copying region", er);
1932       return;
1933     }
1934
1935     HiddenColumns hiddenColumns = null;
1936     if (viewport.hasHiddenColumns())
1937     {
1938       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1939       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1940
1941       // create new HiddenColumns object with copy of hidden regions
1942       // between startRes and endRes, offset by startRes
1943       hiddenColumns = new HiddenColumns(
1944               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1945               hiddenCutoff, hiddenOffset);
1946     }
1947
1948     Desktop.jalviewClipboard = new Object[] { seqs,
1949         viewport.getAlignment().getDataset(), hiddenColumns };
1950     setStatus(MessageManager.formatMessage(
1951             "label.copied_sequences_to_clipboard", new Object[]
1952             { Integer.valueOf(seqs.length).toString() }));
1953   }
1954
1955   /**
1956    * DOCUMENT ME!
1957    *
1958    * @param e
1959    *          DOCUMENT ME!
1960    */
1961   @Override
1962   protected void pasteNew_actionPerformed(ActionEvent e)
1963   {
1964     paste(true);
1965   }
1966
1967   /**
1968    * DOCUMENT ME!
1969    *
1970    * @param e
1971    *          DOCUMENT ME!
1972    */
1973   @Override
1974   protected void pasteThis_actionPerformed(ActionEvent e)
1975   {
1976     paste(false);
1977   }
1978
1979   /**
1980    * Paste contents of Jalview clipboard
1981    *
1982    * @param newAlignment
1983    *          true to paste to a new alignment, otherwise add to this.
1984    */
1985   void paste(boolean newAlignment)
1986   {
1987     boolean externalPaste = true;
1988     try
1989     {
1990       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1991       Transferable contents = c.getContents(this);
1992
1993       if (contents == null)
1994       {
1995         return;
1996       }
1997
1998       String str;
1999       FileFormatI format;
2000       try
2001       {
2002         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2003         if (str.length() < 1)
2004         {
2005           return;
2006         }
2007
2008         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2009
2010       } catch (OutOfMemoryError er)
2011       {
2012         new OOMWarning("Out of memory pasting sequences!!", er);
2013         return;
2014       }
2015
2016       SequenceI[] sequences;
2017       boolean annotationAdded = false;
2018       AlignmentI alignment = null;
2019
2020       if (Desktop.jalviewClipboard != null)
2021       {
2022         // The clipboard was filled from within Jalview, we must use the
2023         // sequences
2024         // And dataset from the copied alignment
2025         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2026         // be doubly sure that we create *new* sequence objects.
2027         sequences = new SequenceI[newseq.length];
2028         for (int i = 0; i < newseq.length; i++)
2029         {
2030           sequences[i] = new Sequence(newseq[i]);
2031         }
2032         alignment = new Alignment(sequences);
2033         externalPaste = false;
2034       }
2035       else
2036       {
2037         // parse the clipboard as an alignment.
2038         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2039                 format);
2040         sequences = alignment.getSequencesArray();
2041       }
2042
2043       int alwidth = 0;
2044       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2045       int fgroup = -1;
2046
2047       if (newAlignment)
2048       {
2049
2050         if (Desktop.jalviewClipboard != null)
2051         {
2052           // dataset is inherited
2053           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2054         }
2055         else
2056         {
2057           // new dataset is constructed
2058           alignment.setDataset(null);
2059         }
2060         alwidth = alignment.getWidth() + 1;
2061       }
2062       else
2063       {
2064         AlignmentI pastedal = alignment; // preserve pasted alignment object
2065         // Add pasted sequences and dataset into existing alignment.
2066         alignment = viewport.getAlignment();
2067         alwidth = alignment.getWidth() + 1;
2068         // decide if we need to import sequences from an existing dataset
2069         boolean importDs = Desktop.jalviewClipboard != null
2070                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2071         // importDs==true instructs us to copy over new dataset sequences from
2072         // an existing alignment
2073         Vector newDs = (importDs) ? new Vector() : null; // used to create
2074         // minimum dataset set
2075
2076         for (int i = 0; i < sequences.length; i++)
2077         {
2078           if (importDs)
2079           {
2080             newDs.addElement(null);
2081           }
2082           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2083           // paste
2084           if (importDs && ds != null)
2085           {
2086             if (!newDs.contains(ds))
2087             {
2088               newDs.setElementAt(ds, i);
2089               ds = new Sequence(ds);
2090               // update with new dataset sequence
2091               sequences[i].setDatasetSequence(ds);
2092             }
2093             else
2094             {
2095               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2096             }
2097           }
2098           else
2099           {
2100             // copy and derive new dataset sequence
2101             sequences[i] = sequences[i].deriveSequence();
2102             alignment.getDataset()
2103                     .addSequence(sequences[i].getDatasetSequence());
2104             // TODO: avoid creation of duplicate dataset sequences with a
2105             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2106           }
2107           alignment.addSequence(sequences[i]); // merges dataset
2108         }
2109         if (newDs != null)
2110         {
2111           newDs.clear(); // tidy up
2112         }
2113         if (alignment.getAlignmentAnnotation() != null)
2114         {
2115           for (AlignmentAnnotation alan : alignment
2116                   .getAlignmentAnnotation())
2117           {
2118             if (alan.graphGroup > fgroup)
2119             {
2120               fgroup = alan.graphGroup;
2121             }
2122           }
2123         }
2124         if (pastedal.getAlignmentAnnotation() != null)
2125         {
2126           // Add any annotation attached to alignment.
2127           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2128           for (int i = 0; i < alann.length; i++)
2129           {
2130             annotationAdded = true;
2131             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2132             {
2133               AlignmentAnnotation newann = new AlignmentAnnotation(
2134                       alann[i]);
2135               if (newann.graphGroup > -1)
2136               {
2137                 if (newGraphGroups.size() <= newann.graphGroup
2138                         || newGraphGroups.get(newann.graphGroup) == null)
2139                 {
2140                   for (int q = newGraphGroups
2141                           .size(); q <= newann.graphGroup; q++)
2142                   {
2143                     newGraphGroups.add(q, null);
2144                   }
2145                   newGraphGroups.set(newann.graphGroup,
2146                           new Integer(++fgroup));
2147                 }
2148                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2149                         .intValue();
2150               }
2151
2152               newann.padAnnotation(alwidth);
2153               alignment.addAnnotation(newann);
2154             }
2155           }
2156         }
2157       }
2158       if (!newAlignment)
2159       {
2160         // /////
2161         // ADD HISTORY ITEM
2162         //
2163         addHistoryItem(new EditCommand(
2164                 MessageManager.getString("label.add_sequences"),
2165                 Action.PASTE, sequences, 0, alignment.getWidth(),
2166                 alignment));
2167       }
2168       // Add any annotations attached to sequences
2169       for (int i = 0; i < sequences.length; i++)
2170       {
2171         if (sequences[i].getAnnotation() != null)
2172         {
2173           AlignmentAnnotation newann;
2174           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2175           {
2176             annotationAdded = true;
2177             newann = sequences[i].getAnnotation()[a];
2178             newann.adjustForAlignment();
2179             newann.padAnnotation(alwidth);
2180             if (newann.graphGroup > -1)
2181             {
2182               if (newann.graphGroup > -1)
2183               {
2184                 if (newGraphGroups.size() <= newann.graphGroup
2185                         || newGraphGroups.get(newann.graphGroup) == null)
2186                 {
2187                   for (int q = newGraphGroups
2188                           .size(); q <= newann.graphGroup; q++)
2189                   {
2190                     newGraphGroups.add(q, null);
2191                   }
2192                   newGraphGroups.set(newann.graphGroup,
2193                           new Integer(++fgroup));
2194                 }
2195                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2196                         .intValue();
2197               }
2198             }
2199             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2200             // was
2201             // duplicated
2202             // earlier
2203             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2204                     a);
2205           }
2206         }
2207       }
2208       if (!newAlignment)
2209       {
2210
2211         // propagate alignment changed.
2212         viewport.getRanges().setEndSeq(alignment.getHeight());
2213         if (annotationAdded)
2214         {
2215           // Duplicate sequence annotation in all views.
2216           AlignmentI[] alview = this.getViewAlignments();
2217           for (int i = 0; i < sequences.length; i++)
2218           {
2219             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2220             if (sann == null)
2221             {
2222               continue;
2223             }
2224             for (int avnum = 0; avnum < alview.length; avnum++)
2225             {
2226               if (alview[avnum] != alignment)
2227               {
2228                 // duplicate in a view other than the one with input focus
2229                 int avwidth = alview[avnum].getWidth() + 1;
2230                 // this relies on sann being preserved after we
2231                 // modify the sequence's annotation array for each duplication
2232                 for (int a = 0; a < sann.length; a++)
2233                 {
2234                   AlignmentAnnotation newann = new AlignmentAnnotation(
2235                           sann[a]);
2236                   sequences[i].addAlignmentAnnotation(newann);
2237                   newann.padAnnotation(avwidth);
2238                   alview[avnum].addAnnotation(newann); // annotation was
2239                   // duplicated earlier
2240                   // TODO JAL-1145 graphGroups are not updated for sequence
2241                   // annotation added to several views. This may cause
2242                   // strangeness
2243                   alview[avnum].setAnnotationIndex(newann, a);
2244                 }
2245               }
2246             }
2247           }
2248           buildSortByAnnotationScoresMenu();
2249         }
2250         viewport.firePropertyChange("alignment", null,
2251                 alignment.getSequences());
2252         if (alignPanels != null)
2253         {
2254           for (AlignmentPanel ap : alignPanels)
2255           {
2256             ap.validateAnnotationDimensions(false);
2257           }
2258         }
2259         else
2260         {
2261           alignPanel.validateAnnotationDimensions(false);
2262         }
2263
2264       }
2265       else
2266       {
2267         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2268                 DEFAULT_HEIGHT);
2269         String newtitle = new String("Copied sequences");
2270
2271         if (Desktop.jalviewClipboard != null
2272                 && Desktop.jalviewClipboard[2] != null)
2273         {
2274           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2275           af.viewport.setHiddenColumns(hc);
2276         }
2277
2278         // >>>This is a fix for the moment, until a better solution is
2279         // found!!<<<
2280         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2281                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2282                         .getFeatureRenderer());
2283
2284         // TODO: maintain provenance of an alignment, rather than just make the
2285         // title a concatenation of operations.
2286         if (!externalPaste)
2287         {
2288           if (title.startsWith("Copied sequences"))
2289           {
2290             newtitle = title;
2291           }
2292           else
2293           {
2294             newtitle = newtitle.concat("- from " + title);
2295           }
2296         }
2297         else
2298         {
2299           newtitle = new String("Pasted sequences");
2300         }
2301
2302         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2303                 DEFAULT_HEIGHT);
2304
2305       }
2306
2307     } catch (Exception ex)
2308     {
2309       ex.printStackTrace();
2310       System.out.println("Exception whilst pasting: " + ex);
2311       // could be anything being pasted in here
2312     }
2313
2314   }
2315
2316   @Override
2317   protected void expand_newalign(ActionEvent e)
2318   {
2319     try
2320     {
2321       AlignmentI alignment = AlignmentUtils
2322               .expandContext(getViewport().getAlignment(), -1);
2323       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2324               DEFAULT_HEIGHT);
2325       String newtitle = new String("Flanking alignment");
2326
2327       if (Desktop.jalviewClipboard != null
2328               && Desktop.jalviewClipboard[2] != null)
2329       {
2330         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2331         af.viewport.setHiddenColumns(hc);
2332       }
2333
2334       // >>>This is a fix for the moment, until a better solution is
2335       // found!!<<<
2336       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2337               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2338                       .getFeatureRenderer());
2339
2340       // TODO: maintain provenance of an alignment, rather than just make the
2341       // title a concatenation of operations.
2342       {
2343         if (title.startsWith("Copied sequences"))
2344         {
2345           newtitle = title;
2346         }
2347         else
2348         {
2349           newtitle = newtitle.concat("- from " + title);
2350         }
2351       }
2352
2353       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2354
2355     } catch (Exception ex)
2356     {
2357       ex.printStackTrace();
2358       System.out.println("Exception whilst pasting: " + ex);
2359       // could be anything being pasted in here
2360     } catch (OutOfMemoryError oom)
2361     {
2362       new OOMWarning("Viewing flanking region of alignment", oom);
2363     }
2364   }
2365
2366   /**
2367    * Action Cut (delete and copy) the selected region
2368    */
2369   @Override
2370   protected void cut_actionPerformed()
2371   {
2372     copy_actionPerformed();
2373     delete_actionPerformed();
2374   }
2375
2376   /**
2377    * Performs menu option to Delete the currently selected region
2378    */
2379   @Override
2380   protected void delete_actionPerformed()
2381   {
2382
2383     SequenceGroup sg = viewport.getSelectionGroup();
2384     if (sg == null)
2385     {
2386       return;
2387     }
2388
2389     Runnable okAction = new Runnable()
2390     {
2391                 @Override
2392                 public void run()
2393                 {
2394                     SequenceI[] cut = sg.getSequences()
2395                             .toArray(new SequenceI[sg.getSize()]);
2396
2397                     addHistoryItem(new EditCommand(
2398                             MessageManager.getString("label.cut_sequences"), Action.CUT,
2399                             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2400                             viewport.getAlignment()));
2401
2402                     viewport.setSelectionGroup(null);
2403                     viewport.sendSelection();
2404                     viewport.getAlignment().deleteGroup(sg);
2405
2406                     viewport.firePropertyChange("alignment", null,
2407                             viewport.getAlignment().getSequences());
2408                     if (viewport.getAlignment().getHeight() < 1)
2409                     {
2410                       try
2411                       {
2412                         AlignFrame.this.setClosed(true);
2413                       } catch (Exception ex)
2414                       {
2415                       }
2416                     }
2417                 }};
2418
2419     /*
2420      * If the cut affects all sequences, prompt for confirmation
2421      */
2422     boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2423     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2424             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2425         if (wholeHeight && wholeWidth)
2426         {
2427             JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2428                 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2429             Object[] options = new Object[] { MessageManager.getString("action.ok"),
2430                     MessageManager.getString("action.cancel") };
2431                 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2432                     MessageManager.getString("label.delete_all"),
2433                     JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2434                     options, options[0]);
2435         } else
2436         {
2437                 okAction.run();
2438         }
2439   }
2440
2441   /**
2442    * DOCUMENT ME!
2443    *
2444    * @param e
2445    *          DOCUMENT ME!
2446    */
2447   @Override
2448   protected void deleteGroups_actionPerformed(ActionEvent e)
2449   {
2450     if (avc.deleteGroups())
2451     {
2452       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2453       alignPanel.updateAnnotation();
2454       alignPanel.paintAlignment(true, true);
2455     }
2456   }
2457
2458   /**
2459    * DOCUMENT ME!
2460    *
2461    * @param e
2462    *          DOCUMENT ME!
2463    */
2464   @Override
2465   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2466   {
2467     SequenceGroup sg = new SequenceGroup();
2468
2469     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2470     {
2471       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2472     }
2473
2474     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2475     viewport.setSelectionGroup(sg);
2476     viewport.sendSelection();
2477     // JAL-2034 - should delegate to
2478     // alignPanel to decide if overview needs
2479     // updating.
2480     alignPanel.paintAlignment(false, false);
2481     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482   }
2483
2484   /**
2485    * DOCUMENT ME!
2486    *
2487    * @param e
2488    *          DOCUMENT ME!
2489    */
2490   @Override
2491   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2492   {
2493     if (viewport.cursorMode)
2494     {
2495       alignPanel.getSeqPanel().keyboardNo1 = null;
2496       alignPanel.getSeqPanel().keyboardNo2 = null;
2497     }
2498     viewport.setSelectionGroup(null);
2499     viewport.getColumnSelection().clear();
2500     viewport.setSelectionGroup(null);
2501     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2502     // JAL-2034 - should delegate to
2503     // alignPanel to decide if overview needs
2504     // updating.
2505     alignPanel.paintAlignment(false, false);
2506     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2507     viewport.sendSelection();
2508   }
2509
2510   /**
2511    * DOCUMENT ME!
2512    *
2513    * @param e
2514    *          DOCUMENT ME!
2515    */
2516   @Override
2517   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2518   {
2519     SequenceGroup sg = viewport.getSelectionGroup();
2520
2521     if (sg == null)
2522     {
2523       selectAllSequenceMenuItem_actionPerformed(null);
2524
2525       return;
2526     }
2527
2528     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2529     {
2530       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2531     }
2532     // JAL-2034 - should delegate to
2533     // alignPanel to decide if overview needs
2534     // updating.
2535
2536     alignPanel.paintAlignment(true, false);
2537     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2538     viewport.sendSelection();
2539   }
2540
2541   @Override
2542   public void invertColSel_actionPerformed(ActionEvent e)
2543   {
2544     viewport.invertColumnSelection();
2545     alignPanel.paintAlignment(true, false);
2546     viewport.sendSelection();
2547   }
2548
2549   /**
2550    * DOCUMENT ME!
2551    *
2552    * @param e
2553    *          DOCUMENT ME!
2554    */
2555   @Override
2556   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2557   {
2558     trimAlignment(true);
2559   }
2560
2561   /**
2562    * DOCUMENT ME!
2563    *
2564    * @param e
2565    *          DOCUMENT ME!
2566    */
2567   @Override
2568   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2569   {
2570     trimAlignment(false);
2571   }
2572
2573   void trimAlignment(boolean trimLeft)
2574   {
2575     ColumnSelection colSel = viewport.getColumnSelection();
2576     int column;
2577
2578     if (!colSel.isEmpty())
2579     {
2580       if (trimLeft)
2581       {
2582         column = colSel.getMin();
2583       }
2584       else
2585       {
2586         column = colSel.getMax();
2587       }
2588
2589       SequenceI[] seqs;
2590       if (viewport.getSelectionGroup() != null)
2591       {
2592         seqs = viewport.getSelectionGroup()
2593                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2594       }
2595       else
2596       {
2597         seqs = viewport.getAlignment().getSequencesArray();
2598       }
2599
2600       TrimRegionCommand trimRegion;
2601       if (trimLeft)
2602       {
2603         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2604                 column, viewport.getAlignment());
2605         viewport.getRanges().setStartRes(0);
2606       }
2607       else
2608       {
2609         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2610                 column, viewport.getAlignment());
2611       }
2612
2613       setStatus(MessageManager
2614               .formatMessage("label.removed_columns", new String[]
2615               { Integer.valueOf(trimRegion.getSize()).toString() }));
2616
2617       addHistoryItem(trimRegion);
2618
2619       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2620       {
2621         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2622                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2623         {
2624           viewport.getAlignment().deleteGroup(sg);
2625         }
2626       }
2627
2628       viewport.firePropertyChange("alignment", null,
2629               viewport.getAlignment().getSequences());
2630     }
2631   }
2632
2633   /**
2634    * DOCUMENT ME!
2635    *
2636    * @param e
2637    *          DOCUMENT ME!
2638    */
2639   @Override
2640   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2641   {
2642     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2643
2644     SequenceI[] seqs;
2645     if (viewport.getSelectionGroup() != null)
2646     {
2647       seqs = viewport.getSelectionGroup()
2648               .getSequencesAsArray(viewport.getHiddenRepSequences());
2649       start = viewport.getSelectionGroup().getStartRes();
2650       end = viewport.getSelectionGroup().getEndRes();
2651     }
2652     else
2653     {
2654       seqs = viewport.getAlignment().getSequencesArray();
2655     }
2656
2657     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2658             "Remove Gapped Columns", seqs, start, end,
2659             viewport.getAlignment());
2660
2661     addHistoryItem(removeGapCols);
2662
2663     setStatus(MessageManager
2664             .formatMessage("label.removed_empty_columns", new Object[]
2665             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2666
2667     // This is to maintain viewport position on first residue
2668     // of first sequence
2669     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2670     ViewportRanges ranges = viewport.getRanges();
2671     int startRes = seq.findPosition(ranges.getStartRes());
2672     // ShiftList shifts;
2673     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2674     // edit.alColumnChanges=shifts.getInverse();
2675     // if (viewport.hasHiddenColumns)
2676     // viewport.getColumnSelection().compensateForEdits(shifts);
2677     ranges.setStartRes(seq.findIndex(startRes) - 1);
2678     viewport.firePropertyChange("alignment", null,
2679             viewport.getAlignment().getSequences());
2680
2681   }
2682
2683   /**
2684    * DOCUMENT ME!
2685    *
2686    * @param e
2687    *          DOCUMENT ME!
2688    */
2689   @Override
2690   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2691   {
2692     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2693
2694     SequenceI[] seqs;
2695     if (viewport.getSelectionGroup() != null)
2696     {
2697       seqs = viewport.getSelectionGroup()
2698               .getSequencesAsArray(viewport.getHiddenRepSequences());
2699       start = viewport.getSelectionGroup().getStartRes();
2700       end = viewport.getSelectionGroup().getEndRes();
2701     }
2702     else
2703     {
2704       seqs = viewport.getAlignment().getSequencesArray();
2705     }
2706
2707     // This is to maintain viewport position on first residue
2708     // of first sequence
2709     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2710     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2711
2712     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2713             viewport.getAlignment()));
2714
2715     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2716
2717     viewport.firePropertyChange("alignment", null,
2718             viewport.getAlignment().getSequences());
2719
2720   }
2721
2722   /**
2723    * DOCUMENT ME!
2724    *
2725    * @param e
2726    *          DOCUMENT ME!
2727    */
2728   @Override
2729   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2730   {
2731     viewport.setPadGaps(padGapsMenuitem.isSelected());
2732     viewport.firePropertyChange("alignment", null,
2733             viewport.getAlignment().getSequences());
2734   }
2735
2736   /**
2737    * DOCUMENT ME!
2738    *
2739    * @param e
2740    *          DOCUMENT ME!
2741    */
2742   @Override
2743   public void findMenuItem_actionPerformed(ActionEvent e)
2744   {
2745     new Finder();
2746   }
2747
2748   /**
2749    * Create a new view of the current alignment.
2750    */
2751   @Override
2752   public void newView_actionPerformed(ActionEvent e)
2753   {
2754     newView(null, true);
2755   }
2756
2757   /**
2758    * Creates and shows a new view of the current alignment.
2759    *
2760    * @param viewTitle
2761    *          title of newly created view; if null, one will be generated
2762    * @param copyAnnotation
2763    *          if true then duplicate all annnotation, groups and settings
2764    * @return new alignment panel, already displayed.
2765    */
2766   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2767   {
2768     /*
2769      * Create a new AlignmentPanel (with its own, new Viewport)
2770      */
2771     AlignmentPanel newap = new jalview.project.Jalview2XML()
2772             .copyAlignPanel(alignPanel);
2773     if (!copyAnnotation)
2774     {
2775       /*
2776        * remove all groups and annotation except for the automatic stuff
2777        */
2778       newap.av.getAlignment().deleteAllGroups();
2779       newap.av.getAlignment().deleteAllAnnotations(false);
2780     }
2781
2782     newap.av.setGatherViewsHere(false);
2783
2784     if (viewport.getViewName() == null)
2785     {
2786       viewport.setViewName(MessageManager
2787               .getString("label.view_name_original"));
2788     }
2789
2790     /*
2791      * Views share the same edits undo and redo stacks
2792      */
2793     newap.av.setHistoryList(viewport.getHistoryList());
2794     newap.av.setRedoList(viewport.getRedoList());
2795
2796     /*
2797      * Views share the same mappings; need to deregister any new mappings
2798      * created by copyAlignPanel, and register the new reference to the shared
2799      * mappings
2800      */
2801     newap.av.replaceMappings(viewport.getAlignment());
2802
2803     /*
2804      * start up cDNA consensus (if applicable) now mappings are in place
2805      */
2806     if (newap.av.initComplementConsensus())
2807     {
2808       newap.refresh(true); // adjust layout of annotations
2809     }
2810
2811     newap.av.setViewName(getNewViewName(viewTitle));
2812
2813     addAlignmentPanel(newap, true);
2814     newap.alignmentChanged();
2815
2816     if (alignPanels.size() == 2)
2817     {
2818       viewport.setGatherViewsHere(true);
2819     }
2820     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2821     return newap;
2822   }
2823
2824   /**
2825    * Make a new name for the view, ensuring it is unique within the current
2826    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2827    * these now use viewId. Unique view names are still desirable for usability.)
2828    *
2829    * @param viewTitle
2830    * @return
2831    */
2832   protected String getNewViewName(String viewTitle)
2833   {
2834     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2835     boolean addFirstIndex = false;
2836     if (viewTitle == null || viewTitle.trim().length() == 0)
2837     {
2838       viewTitle = MessageManager.getString("action.view");
2839       addFirstIndex = true;
2840     }
2841     else
2842     {
2843       index = 1;// we count from 1 if given a specific name
2844     }
2845     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2846
2847     List<Component> comps = PaintRefresher.components
2848             .get(viewport.getSequenceSetId());
2849
2850     List<String> existingNames = getExistingViewNames(comps);
2851
2852     while (existingNames.contains(newViewName))
2853     {
2854       newViewName = viewTitle + " " + (++index);
2855     }
2856     return newViewName;
2857   }
2858
2859   /**
2860    * Returns a list of distinct view names found in the given list of
2861    * components. View names are held on the viewport of an AlignmentPanel.
2862    *
2863    * @param comps
2864    * @return
2865    */
2866   protected List<String> getExistingViewNames(List<Component> comps)
2867   {
2868     List<String> existingNames = new ArrayList<>();
2869     for (Component comp : comps)
2870     {
2871       if (comp instanceof AlignmentPanel)
2872       {
2873         AlignmentPanel ap = (AlignmentPanel) comp;
2874         if (!existingNames.contains(ap.av.getViewName()))
2875         {
2876           existingNames.add(ap.av.getViewName());
2877         }
2878       }
2879     }
2880     return existingNames;
2881   }
2882
2883   /**
2884    * Explode tabbed views into separate windows.
2885    */
2886   @Override
2887   public void expandViews_actionPerformed(ActionEvent e)
2888   {
2889     Desktop.explodeViews(this);
2890   }
2891
2892   /**
2893    * Gather views in separate windows back into a tabbed presentation.
2894    */
2895   @Override
2896   public void gatherViews_actionPerformed(ActionEvent e)
2897   {
2898     Desktop.instance.gatherViews(this);
2899   }
2900
2901   /**
2902    * DOCUMENT ME!
2903    *
2904    * @param e
2905    *          DOCUMENT ME!
2906    */
2907   @Override
2908   public void font_actionPerformed(ActionEvent e)
2909   {
2910     new FontChooser(alignPanel);
2911   }
2912
2913   /**
2914    * DOCUMENT ME!
2915    *
2916    * @param e
2917    *          DOCUMENT ME!
2918    */
2919   @Override
2920   protected void seqLimit_actionPerformed(ActionEvent e)
2921   {
2922     viewport.setShowJVSuffix(seqLimits.isSelected());
2923
2924     alignPanel.getIdPanel().getIdCanvas()
2925             .setPreferredSize(alignPanel.calculateIdWidth());
2926     alignPanel.paintAlignment(true, false);
2927   }
2928
2929   @Override
2930   public void idRightAlign_actionPerformed(ActionEvent e)
2931   {
2932     viewport.setRightAlignIds(idRightAlign.isSelected());
2933     alignPanel.paintAlignment(false, false);
2934   }
2935
2936   @Override
2937   public void centreColumnLabels_actionPerformed(ActionEvent e)
2938   {
2939     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2940     alignPanel.paintAlignment(false, false);
2941   }
2942
2943   /*
2944    * (non-Javadoc)
2945    *
2946    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2947    */
2948   @Override
2949   protected void followHighlight_actionPerformed()
2950   {
2951     /*
2952      * Set the 'follow' flag on the Viewport (and scroll to position if now
2953      * true).
2954      */
2955     final boolean state = this.followHighlightMenuItem.getState();
2956     viewport.setFollowHighlight(state);
2957     if (state)
2958     {
2959       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2960     }
2961   }
2962
2963   /**
2964    * DOCUMENT ME!
2965    *
2966    * @param e
2967    *          DOCUMENT ME!
2968    */
2969   @Override
2970   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2971   {
2972     viewport.setColourText(colourTextMenuItem.isSelected());
2973     alignPanel.paintAlignment(false, false);
2974   }
2975
2976   /**
2977    * DOCUMENT ME!
2978    *
2979    * @param e
2980    *          DOCUMENT ME!
2981    */
2982   @Override
2983   public void wrapMenuItem_actionPerformed(ActionEvent e)
2984   {
2985     scaleAbove.setVisible(wrapMenuItem.isSelected());
2986     scaleLeft.setVisible(wrapMenuItem.isSelected());
2987     scaleRight.setVisible(wrapMenuItem.isSelected());
2988     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2989     alignPanel.updateLayout();
2990   }
2991
2992   @Override
2993   public void showAllSeqs_actionPerformed(ActionEvent e)
2994   {
2995     viewport.showAllHiddenSeqs();
2996   }
2997
2998   @Override
2999   public void showAllColumns_actionPerformed(ActionEvent e)
3000   {
3001     viewport.showAllHiddenColumns();
3002     alignPanel.paintAlignment(true, true);
3003     viewport.sendSelection();
3004   }
3005
3006   @Override
3007   public void hideSelSequences_actionPerformed(ActionEvent e)
3008   {
3009     viewport.hideAllSelectedSeqs();
3010   }
3011
3012   /**
3013    * called by key handler and the hide all/show all menu items
3014    *
3015    * @param toggleSeqs
3016    * @param toggleCols
3017    */
3018   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3019   {
3020
3021     boolean hide = false;
3022     SequenceGroup sg = viewport.getSelectionGroup();
3023     if (!toggleSeqs && !toggleCols)
3024     {
3025       // Hide everything by the current selection - this is a hack - we do the
3026       // invert and then hide
3027       // first check that there will be visible columns after the invert.
3028       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3029               && sg.getStartRes() <= sg.getEndRes()))
3030       {
3031         // now invert the sequence set, if required - empty selection implies
3032         // that no hiding is required.
3033         if (sg != null)
3034         {
3035           invertSequenceMenuItem_actionPerformed(null);
3036           sg = viewport.getSelectionGroup();
3037           toggleSeqs = true;
3038
3039         }
3040         viewport.expandColSelection(sg, true);
3041         // finally invert the column selection and get the new sequence
3042         // selection.
3043         invertColSel_actionPerformed(null);
3044         toggleCols = true;
3045       }
3046     }
3047
3048     if (toggleSeqs)
3049     {
3050       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3051       {
3052         hideSelSequences_actionPerformed(null);
3053         hide = true;
3054       }
3055       else if (!(toggleCols && viewport.hasSelectedColumns()))
3056       {
3057         showAllSeqs_actionPerformed(null);
3058       }
3059     }
3060
3061     if (toggleCols)
3062     {
3063       if (viewport.hasSelectedColumns())
3064       {
3065         hideSelColumns_actionPerformed(null);
3066         if (!toggleSeqs)
3067         {
3068           viewport.setSelectionGroup(sg);
3069         }
3070       }
3071       else if (!hide)
3072       {
3073         showAllColumns_actionPerformed(null);
3074       }
3075     }
3076   }
3077
3078   /*
3079    * (non-Javadoc)
3080    *
3081    * @see
3082    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3083    * event.ActionEvent)
3084    */
3085   @Override
3086   public void hideAllButSelection_actionPerformed(ActionEvent e)
3087   {
3088     toggleHiddenRegions(false, false);
3089     viewport.sendSelection();
3090   }
3091
3092   /*
3093    * (non-Javadoc)
3094    *
3095    * @see
3096    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3097    * .ActionEvent)
3098    */
3099   @Override
3100   public void hideAllSelection_actionPerformed(ActionEvent e)
3101   {
3102     SequenceGroup sg = viewport.getSelectionGroup();
3103     viewport.expandColSelection(sg, false);
3104     viewport.hideAllSelectedSeqs();
3105     viewport.hideSelectedColumns();
3106     alignPanel.paintAlignment(true, true);
3107     viewport.sendSelection();
3108   }
3109
3110   /*
3111    * (non-Javadoc)
3112    *
3113    * @see
3114    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3115    * ActionEvent)
3116    */
3117   @Override
3118   public void showAllhidden_actionPerformed(ActionEvent e)
3119   {
3120     viewport.showAllHiddenColumns();
3121     viewport.showAllHiddenSeqs();
3122     alignPanel.paintAlignment(true, true);
3123     viewport.sendSelection();
3124   }
3125
3126   @Override
3127   public void hideSelColumns_actionPerformed(ActionEvent e)
3128   {
3129     viewport.hideSelectedColumns();
3130     alignPanel.paintAlignment(true, true);
3131     viewport.sendSelection();
3132   }
3133
3134   @Override
3135   public void hiddenMarkers_actionPerformed(ActionEvent e)
3136   {
3137     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3138     repaint();
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   protected void scaleAbove_actionPerformed(ActionEvent e)
3149   {
3150     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3151     // TODO: do we actually need to update overview for scale above change ?
3152     alignPanel.paintAlignment(true, false);
3153   }
3154
3155   /**
3156    * DOCUMENT ME!
3157    *
3158    * @param e
3159    *          DOCUMENT ME!
3160    */
3161   @Override
3162   protected void scaleLeft_actionPerformed(ActionEvent e)
3163   {
3164     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3165     alignPanel.paintAlignment(true, false);
3166   }
3167
3168   /**
3169    * DOCUMENT ME!
3170    *
3171    * @param e
3172    *          DOCUMENT ME!
3173    */
3174   @Override
3175   protected void scaleRight_actionPerformed(ActionEvent e)
3176   {
3177     viewport.setScaleRightWrapped(scaleRight.isSelected());
3178     alignPanel.paintAlignment(true, false);
3179   }
3180
3181   /**
3182    * DOCUMENT ME!
3183    *
3184    * @param e
3185    *          DOCUMENT ME!
3186    */
3187   @Override
3188   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3189   {
3190     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3191     alignPanel.paintAlignment(false, false);
3192   }
3193
3194   /**
3195    * DOCUMENT ME!
3196    *
3197    * @param e
3198    *          DOCUMENT ME!
3199    */
3200   @Override
3201   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3202   {
3203     viewport.setShowText(viewTextMenuItem.isSelected());
3204     alignPanel.paintAlignment(false, false);
3205   }
3206
3207   /**
3208    * DOCUMENT ME!
3209    *
3210    * @param e
3211    *          DOCUMENT ME!
3212    */
3213   @Override
3214   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3215   {
3216     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3217     alignPanel.paintAlignment(false, false);
3218   }
3219
3220   public FeatureSettings featureSettings;
3221
3222   @Override
3223   public FeatureSettingsControllerI getFeatureSettingsUI()
3224   {
3225     return featureSettings;
3226   }
3227
3228   @Override
3229   public void featureSettings_actionPerformed(ActionEvent e)
3230   {
3231     if (featureSettings != null)
3232     {
3233       featureSettings.close();
3234       featureSettings = null;
3235     }
3236     if (!showSeqFeatures.isSelected())
3237     {
3238       // make sure features are actually displayed
3239       showSeqFeatures.setSelected(true);
3240       showSeqFeatures_actionPerformed(null);
3241     }
3242     featureSettings = new FeatureSettings(this);
3243   }
3244
3245   /**
3246    * Set or clear 'Show Sequence Features'
3247    *
3248    * @param evt
3249    *          DOCUMENT ME!
3250    */
3251   @Override
3252   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3253   {
3254     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3255     alignPanel.paintAlignment(true, true);
3256   }
3257
3258   /**
3259    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3260    * the annotations panel as a whole.
3261    *
3262    * The options to show/hide all annotations should be enabled when the panel
3263    * is shown, and disabled when the panel is hidden.
3264    *
3265    * @param e
3266    */
3267   @Override
3268   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3269   {
3270     final boolean setVisible = annotationPanelMenuItem.isSelected();
3271     viewport.setShowAnnotation(setVisible);
3272     this.showAllSeqAnnotations.setEnabled(setVisible);
3273     this.hideAllSeqAnnotations.setEnabled(setVisible);
3274     this.showAllAlAnnotations.setEnabled(setVisible);
3275     this.hideAllAlAnnotations.setEnabled(setVisible);
3276     alignPanel.updateLayout();
3277   }
3278
3279   @Override
3280   public void alignmentProperties()
3281   {
3282     JComponent pane;
3283     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3284
3285             .formatAsHtml();
3286     String content = MessageManager.formatMessage("label.html_content",
3287             new Object[]
3288             { contents.toString() });
3289     contents = null;
3290
3291     if (Platform.isJS())
3292     {
3293       JLabel textLabel = new JLabel();
3294       textLabel.setText(content);
3295       textLabel.setBackground(Color.WHITE);
3296
3297       pane = new JPanel(new BorderLayout());
3298       ((JPanel) pane).setOpaque(true);
3299       pane.setBackground(Color.WHITE);
3300       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3301     }
3302     else
3303     {
3304       JEditorPane editPane = new JEditorPane("text/html", "");
3305       editPane.setEditable(false);
3306       editPane.setText(content);
3307       pane = editPane;
3308     }
3309
3310     JInternalFrame frame = new JInternalFrame();
3311
3312     frame.getContentPane().add(new JScrollPane(pane));
3313
3314     Desktop.addInternalFrame(frame, MessageManager
3315             .formatMessage("label.alignment_properties", new Object[]
3316             { getTitle() }), 500, 400);
3317   }
3318
3319   /**
3320    * DOCUMENT ME!
3321    *
3322    * @param e
3323    *          DOCUMENT ME!
3324    */
3325   @Override
3326   public void overviewMenuItem_actionPerformed(ActionEvent e)
3327   {
3328     if (alignPanel.overviewPanel != null)
3329     {
3330       return;
3331     }
3332
3333     JInternalFrame frame = new JInternalFrame();
3334     final OverviewPanel overview = new OverviewPanel(alignPanel);
3335     frame.setContentPane(overview);
3336     Desktop.addInternalFrame(frame, MessageManager
3337             .formatMessage("label.overview_params", new Object[]
3338             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3339             true, true);
3340     frame.pack();
3341     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3342     frame.addInternalFrameListener(
3343             new javax.swing.event.InternalFrameAdapter()
3344             {
3345               @Override
3346               public void internalFrameClosed(
3347                       javax.swing.event.InternalFrameEvent evt)
3348               {
3349                 overview.dispose();
3350                 alignPanel.setOverviewPanel(null);
3351               };
3352             });
3353     if (getKeyListeners().length > 0)
3354     {
3355       frame.addKeyListener(getKeyListeners()[0]);
3356     }
3357
3358     alignPanel.setOverviewPanel(overview);
3359   }
3360
3361   @Override
3362   public void textColour_actionPerformed()
3363   {
3364     new TextColourChooser().chooseColour(alignPanel, null);
3365   }
3366
3367   /*
3368    * public void covariationColour_actionPerformed() {
3369    * changeColour(new
3370    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3371    * ()[0])); }
3372    */
3373   @Override
3374   public void annotationColour_actionPerformed()
3375   {
3376     new AnnotationColourChooser(viewport, alignPanel);
3377   }
3378
3379   @Override
3380   public void annotationColumn_actionPerformed(ActionEvent e)
3381   {
3382     new AnnotationColumnChooser(viewport, alignPanel);
3383   }
3384
3385   /**
3386    * Action on the user checking or unchecking the option to apply the selected
3387    * colour scheme to all groups. If unchecked, groups may have their own
3388    * independent colour schemes.
3389    *
3390    * @param selected
3391    */
3392   @Override
3393   public void applyToAllGroups_actionPerformed(boolean selected)
3394   {
3395     viewport.setColourAppliesToAllGroups(selected);
3396   }
3397
3398   /**
3399    * Action on user selecting a colour from the colour menu
3400    *
3401    * @param name
3402    *          the name (not the menu item label!) of the colour scheme
3403    */
3404   @Override
3405   public void changeColour_actionPerformed(String name)
3406   {
3407     /*
3408      * 'User Defined' opens a panel to configure or load a
3409      * user-defined colour scheme
3410      */
3411     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3412     {
3413       new UserDefinedColours(alignPanel);
3414       return;
3415     }
3416
3417     /*
3418      * otherwise set the chosen colour scheme (or null for 'None')
3419      */
3420     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3421             viewport.getAlignment(), viewport.getHiddenRepSequences());
3422     changeColour(cs);
3423   }
3424
3425   /**
3426    * Actions on setting or changing the alignment colour scheme
3427    *
3428    * @param cs
3429    */
3430   @Override
3431   public void changeColour(ColourSchemeI cs)
3432   {
3433     // TODO: pull up to controller method
3434     ColourMenuHelper.setColourSelected(colourMenu, cs);
3435
3436     viewport.setGlobalColourScheme(cs);
3437
3438     alignPanel.paintAlignment(true, true);
3439   }
3440
3441   /**
3442    * Show the PID threshold slider panel
3443    */
3444   @Override
3445   protected void modifyPID_actionPerformed()
3446   {
3447     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3448             alignPanel.getViewName());
3449     SliderPanel.showPIDSlider();
3450   }
3451
3452   /**
3453    * Show the Conservation slider panel
3454    */
3455   @Override
3456   protected void modifyConservation_actionPerformed()
3457   {
3458     SliderPanel.setConservationSlider(alignPanel,
3459             viewport.getResidueShading(), alignPanel.getViewName());
3460     SliderPanel.showConservationSlider();
3461   }
3462
3463   /**
3464    * Action on selecting or deselecting (Colour) By Conservation
3465    */
3466   @Override
3467   public void conservationMenuItem_actionPerformed(boolean selected)
3468   {
3469     modifyConservation.setEnabled(selected);
3470     viewport.setConservationSelected(selected);
3471     viewport.getResidueShading().setConservationApplied(selected);
3472
3473     changeColour(viewport.getGlobalColourScheme());
3474     if (selected)
3475     {
3476       modifyConservation_actionPerformed();
3477     }
3478     else
3479     {
3480       SliderPanel.hideConservationSlider();
3481     }
3482   }
3483
3484   /**
3485    * Action on selecting or deselecting (Colour) Above PID Threshold
3486    */
3487   @Override
3488   public void abovePIDThreshold_actionPerformed(boolean selected)
3489   {
3490     modifyPID.setEnabled(selected);
3491     viewport.setAbovePIDThreshold(selected);
3492     if (!selected)
3493     {
3494       viewport.getResidueShading().setThreshold(0,
3495               viewport.isIgnoreGapsConsensus());
3496     }
3497
3498     changeColour(viewport.getGlobalColourScheme());
3499     if (selected)
3500     {
3501       modifyPID_actionPerformed();
3502     }
3503     else
3504     {
3505       SliderPanel.hidePIDSlider();
3506     }
3507   }
3508
3509   /**
3510    * DOCUMENT ME!
3511    *
3512    * @param e
3513    *          DOCUMENT ME!
3514    */
3515   @Override
3516   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3517   {
3518     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3519     AlignmentSorter.sortByPID(viewport.getAlignment(),
3520             viewport.getAlignment().getSequenceAt(0));
3521     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3522             viewport.getAlignment()));
3523     alignPanel.paintAlignment(true, false);
3524   }
3525
3526   /**
3527    * DOCUMENT ME!
3528    *
3529    * @param e
3530    *          DOCUMENT ME!
3531    */
3532   @Override
3533   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3534   {
3535     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3536     AlignmentSorter.sortByID(viewport.getAlignment());
3537     addHistoryItem(
3538             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3539     alignPanel.paintAlignment(true, false);
3540   }
3541
3542   /**
3543    * DOCUMENT ME!
3544    *
3545    * @param e
3546    *          DOCUMENT ME!
3547    */
3548   @Override
3549   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3550   {
3551     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3552     AlignmentSorter.sortByLength(viewport.getAlignment());
3553     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3554             viewport.getAlignment()));
3555     alignPanel.paintAlignment(true, false);
3556   }
3557
3558   /**
3559    * DOCUMENT ME!
3560    *
3561    * @param e
3562    *          DOCUMENT ME!
3563    */
3564   @Override
3565   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3566   {
3567     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3568     AlignmentSorter.sortByGroup(viewport.getAlignment());
3569     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3570             viewport.getAlignment()));
3571
3572     alignPanel.paintAlignment(true, false);
3573   }
3574
3575   /**
3576    * DOCUMENT ME!
3577    *
3578    * @param e
3579    *          DOCUMENT ME!
3580    */
3581   @Override
3582   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3583   {
3584     new RedundancyPanel(alignPanel, this);
3585   }
3586
3587   /**
3588    * DOCUMENT ME!
3589    *
3590    * @param e
3591    *          DOCUMENT ME!
3592    */
3593   @Override
3594   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3595   {
3596     if ((viewport.getSelectionGroup() == null)
3597             || (viewport.getSelectionGroup().getSize() < 2))
3598     {
3599       JvOptionPane.showInternalMessageDialog(this,
3600               MessageManager.getString(
3601                       "label.you_must_select_least_two_sequences"),
3602               MessageManager.getString("label.invalid_selection"),
3603               JvOptionPane.WARNING_MESSAGE);
3604     }
3605     else
3606     {
3607       JInternalFrame frame = new JInternalFrame();
3608       frame.setContentPane(new PairwiseAlignPanel(viewport));
3609       Desktop.addInternalFrame(frame,
3610               MessageManager.getString("action.pairwise_alignment"), 600,
3611               500);
3612     }
3613   }
3614
3615   @Override
3616   public void autoCalculate_actionPerformed(ActionEvent e)
3617   {
3618     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3619     if (viewport.autoCalculateConsensus)
3620     {
3621       viewport.firePropertyChange("alignment", null,
3622               viewport.getAlignment().getSequences());
3623     }
3624   }
3625
3626   @Override
3627   public void sortByTreeOption_actionPerformed(ActionEvent e)
3628   {
3629     viewport.sortByTree = sortByTree.isSelected();
3630   }
3631
3632   @Override
3633   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3634   {
3635     viewport.followSelection = listenToViewSelections.isSelected();
3636   }
3637
3638   /**
3639    * Constructs a tree panel and adds it to the desktop
3640    *
3641    * @param type
3642    *          tree type (NJ or AV)
3643    * @param modelName
3644    *          name of score model used to compute the tree
3645    * @param options
3646    *          parameters for the distance or similarity calculation
3647    */
3648   void newTreePanel(String type, String modelName,
3649           SimilarityParamsI options)
3650   {
3651     String frameTitle = "";
3652     TreePanel tp;
3653
3654     boolean onSelection = false;
3655     if (viewport.getSelectionGroup() != null
3656             && viewport.getSelectionGroup().getSize() > 0)
3657     {
3658       SequenceGroup sg = viewport.getSelectionGroup();
3659
3660       /* Decide if the selection is a column region */
3661       for (SequenceI _s : sg.getSequences())
3662       {
3663         if (_s.getLength() < sg.getEndRes())
3664         {
3665           JvOptionPane.showMessageDialog(Desktop.desktop,
3666                   MessageManager.getString(
3667                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3668                   MessageManager.getString(
3669                           "label.sequences_selection_not_aligned"),
3670                   JvOptionPane.WARNING_MESSAGE);
3671
3672           return;
3673         }
3674       }
3675       onSelection = true;
3676     }
3677     else
3678     {
3679       if (viewport.getAlignment().getHeight() < 2)
3680       {
3681         return;
3682       }
3683     }
3684
3685     tp = new TreePanel(alignPanel, type, modelName, options);
3686     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3687
3688     frameTitle += " from ";
3689
3690     if (viewport.getViewName() != null)
3691     {
3692       frameTitle += viewport.getViewName() + " of ";
3693     }
3694
3695     frameTitle += this.title;
3696
3697     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3698   }
3699
3700   /**
3701    * DOCUMENT ME!
3702    *
3703    * @param title
3704    *          DOCUMENT ME!
3705    * @param order
3706    *          DOCUMENT ME!
3707    */
3708   public void addSortByOrderMenuItem(String title,
3709           final AlignmentOrder order)
3710   {
3711     final JMenuItem item = new JMenuItem(MessageManager
3712             .formatMessage("action.by_title_param", new Object[]
3713             { title }));
3714     sort.add(item);
3715     item.addActionListener(new java.awt.event.ActionListener()
3716     {
3717       @Override
3718       public void actionPerformed(ActionEvent e)
3719       {
3720         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3721
3722         // TODO: JBPNote - have to map order entries to curent SequenceI
3723         // pointers
3724         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3725
3726         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3727                 viewport.getAlignment()));
3728
3729         alignPanel.paintAlignment(true, false);
3730       }
3731     });
3732   }
3733
3734   /**
3735    * Add a new sort by annotation score menu item
3736    *
3737    * @param sort
3738    *          the menu to add the option to
3739    * @param scoreLabel
3740    *          the label used to retrieve scores for each sequence on the
3741    *          alignment
3742    */
3743   public void addSortByAnnotScoreMenuItem(JMenu sort,
3744           final String scoreLabel)
3745   {
3746     final JMenuItem item = new JMenuItem(scoreLabel);
3747     sort.add(item);
3748     item.addActionListener(new java.awt.event.ActionListener()
3749     {
3750       @Override
3751       public void actionPerformed(ActionEvent e)
3752       {
3753         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3754         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3755                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3756         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3757                 viewport.getAlignment()));
3758         alignPanel.paintAlignment(true, false);
3759       }
3760     });
3761   }
3762
3763   /**
3764    * last hash for alignment's annotation array - used to minimise cost of
3765    * rebuild.
3766    */
3767   protected int _annotationScoreVectorHash;
3768
3769   /**
3770    * search the alignment and rebuild the sort by annotation score submenu the
3771    * last alignment annotation vector hash is stored to minimize cost of
3772    * rebuilding in subsequence calls.
3773    *
3774    */
3775   @Override
3776   public void buildSortByAnnotationScoresMenu()
3777   {
3778     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3779     {
3780       return;
3781     }
3782
3783     if (viewport.getAlignment().getAlignmentAnnotation()
3784             .hashCode() != _annotationScoreVectorHash)
3785     {
3786       sortByAnnotScore.removeAll();
3787       // almost certainly a quicker way to do this - but we keep it simple
3788       Hashtable scoreSorts = new Hashtable();
3789       AlignmentAnnotation aann[];
3790       for (SequenceI sqa : viewport.getAlignment().getSequences())
3791       {
3792         aann = sqa.getAnnotation();
3793         for (int i = 0; aann != null && i < aann.length; i++)
3794         {
3795           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3796           {
3797             scoreSorts.put(aann[i].label, aann[i].label);
3798           }
3799         }
3800       }
3801       Enumeration labels = scoreSorts.keys();
3802       while (labels.hasMoreElements())
3803       {
3804         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3805                 (String) labels.nextElement());
3806       }
3807       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3808       scoreSorts.clear();
3809
3810       _annotationScoreVectorHash = viewport.getAlignment()
3811               .getAlignmentAnnotation().hashCode();
3812     }
3813   }
3814
3815   /**
3816    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3817    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3818    * call. Listeners are added to remove the menu item when the treePanel is
3819    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3820    * modified.
3821    */
3822   @Override
3823   public void buildTreeSortMenu()
3824   {
3825     sortByTreeMenu.removeAll();
3826
3827     List<Component> comps = PaintRefresher.components
3828             .get(viewport.getSequenceSetId());
3829     List<TreePanel> treePanels = new ArrayList<>();
3830     for (Component comp : comps)
3831     {
3832       if (comp instanceof TreePanel)
3833       {
3834         treePanels.add((TreePanel) comp);
3835       }
3836     }
3837
3838     if (treePanels.size() < 1)
3839     {
3840       sortByTreeMenu.setVisible(false);
3841       return;
3842     }
3843
3844     sortByTreeMenu.setVisible(true);
3845
3846     for (final TreePanel tp : treePanels)
3847     {
3848       final JMenuItem item = new JMenuItem(tp.getTitle());
3849       item.addActionListener(new java.awt.event.ActionListener()
3850       {
3851         @Override
3852         public void actionPerformed(ActionEvent e)
3853         {
3854           tp.sortByTree_actionPerformed();
3855           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3856
3857         }
3858       });
3859
3860       sortByTreeMenu.add(item);
3861     }
3862   }
3863
3864   public boolean sortBy(AlignmentOrder alorder, String undoname)
3865   {
3866     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3867     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3868     if (undoname != null)
3869     {
3870       addHistoryItem(new OrderCommand(undoname, oldOrder,
3871               viewport.getAlignment()));
3872     }
3873     alignPanel.paintAlignment(true, false);
3874     return true;
3875   }
3876
3877   /**
3878    * Work out whether the whole set of sequences or just the selected set will
3879    * be submitted for multiple alignment.
3880    *
3881    */
3882   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3883   {
3884     // Now, check we have enough sequences
3885     AlignmentView msa = null;
3886
3887     if ((viewport.getSelectionGroup() != null)
3888             && (viewport.getSelectionGroup().getSize() > 1))
3889     {
3890       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3891       // some common interface!
3892       /*
3893        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3894        * SequenceI[sz = seqs.getSize(false)];
3895        *
3896        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3897        * seqs.getSequenceAt(i); }
3898        */
3899       msa = viewport.getAlignmentView(true);
3900     }
3901     else if (viewport.getSelectionGroup() != null
3902             && viewport.getSelectionGroup().getSize() == 1)
3903     {
3904       int option = JvOptionPane.showConfirmDialog(this,
3905               MessageManager.getString("warn.oneseq_msainput_selection"),
3906               MessageManager.getString("label.invalid_selection"),
3907               JvOptionPane.OK_CANCEL_OPTION);
3908       if (option == JvOptionPane.OK_OPTION)
3909       {
3910         msa = viewport.getAlignmentView(false);
3911       }
3912     }
3913     else
3914     {
3915       msa = viewport.getAlignmentView(false);
3916     }
3917     return msa;
3918   }
3919
3920   /**
3921    * Decides what is submitted to a secondary structure prediction service: the
3922    * first sequence in the alignment, or in the current selection, or, if the
3923    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3924    * region or the whole alignment. (where the first sequence in the set is the
3925    * one that the prediction will be for).
3926    */
3927   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3928   {
3929     AlignmentView seqs = null;
3930
3931     if ((viewport.getSelectionGroup() != null)
3932             && (viewport.getSelectionGroup().getSize() > 0))
3933     {
3934       seqs = viewport.getAlignmentView(true);
3935     }
3936     else
3937     {
3938       seqs = viewport.getAlignmentView(false);
3939     }
3940     // limit sequences - JBPNote in future - could spawn multiple prediction
3941     // jobs
3942     // TODO: viewport.getAlignment().isAligned is a global state - the local
3943     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3944     if (!viewport.getAlignment().isAligned(false))
3945     {
3946       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3947       // TODO: if seqs.getSequences().length>1 then should really have warned
3948       // user!
3949
3950     }
3951     return seqs;
3952   }
3953
3954   /**
3955    * DOCUMENT ME!
3956    *
3957    * @param e
3958    *          DOCUMENT ME!
3959    */
3960   @Override
3961   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3962   {
3963     // Pick the tree file
3964     JalviewFileChooser chooser = new JalviewFileChooser(
3965             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3966     chooser.setFileView(new JalviewFileView());
3967     chooser.setDialogTitle(
3968             MessageManager.getString("label.select_newick_like_tree_file"));
3969     chooser.setToolTipText(
3970             MessageManager.getString("label.load_tree_file"));
3971
3972     chooser.setResponseHandler(0,new Runnable()
3973     {
3974       @Override
3975       public void run()
3976       {
3977         String filePath = chooser.getSelectedFile().getPath();
3978         Cache.setProperty("LAST_DIRECTORY", filePath);
3979         NewickFile fin = null;
3980         try
3981         {
3982           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
3983                   DataSourceType.FILE));
3984           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3985         } catch (Exception ex)
3986         {
3987           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3988                   MessageManager
3989                           .getString("label.problem_reading_tree_file"),
3990                   JvOptionPane.WARNING_MESSAGE);
3991           ex.printStackTrace();
3992         }
3993         if (fin != null && fin.hasWarningMessage())
3994         {
3995           JvOptionPane.showMessageDialog(Desktop.desktop,
3996                   fin.getWarningMessage(),
3997                   MessageManager.getString(
3998                           "label.possible_problem_with_tree_file"),
3999                   JvOptionPane.WARNING_MESSAGE);
4000         }
4001       }
4002     });
4003     chooser.showOpenDialog(this);
4004   }
4005
4006   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4007   {
4008     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4009   }
4010
4011   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4012           int h, int x, int y)
4013   {
4014     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4015   }
4016
4017   /**
4018    * Add a treeviewer for the tree extracted from a Newick file object to the
4019    * current alignment view
4020    *
4021    * @param nf
4022    *          the tree
4023    * @param title
4024    *          tree viewer title
4025    * @param input
4026    *          Associated alignment input data (or null)
4027    * @param w
4028    *          width
4029    * @param h
4030    *          height
4031    * @param x
4032    *          position
4033    * @param y
4034    *          position
4035    * @return TreePanel handle
4036    */
4037   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4038           AlignmentView input, int w, int h, int x, int y)
4039   {
4040     TreePanel tp = null;
4041
4042     try
4043     {
4044       nf.parse();
4045
4046       if (nf.getTree() != null)
4047       {
4048         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4049
4050         tp.setSize(w, h);
4051
4052         if (x > 0 && y > 0)
4053         {
4054           tp.setLocation(x, y);
4055         }
4056
4057         Desktop.addInternalFrame(tp, treeTitle, w, h);
4058       }
4059     } catch (Exception ex)
4060     {
4061       ex.printStackTrace();
4062     }
4063
4064     return tp;
4065   }
4066
4067   private boolean buildingMenu = false;
4068
4069   /**
4070    * Generates menu items and listener event actions for web service clients
4071    *
4072    */
4073   public void BuildWebServiceMenu()
4074   {
4075     while (buildingMenu)
4076     {
4077       try
4078       {
4079         System.err.println("Waiting for building menu to finish.");
4080         Thread.sleep(10);
4081       } catch (Exception e)
4082       {
4083       }
4084     }
4085     final AlignFrame me = this;
4086     buildingMenu = true;
4087     new Thread(new Runnable()
4088     {
4089       @Override
4090       public void run()
4091       {
4092         final List<JMenuItem> legacyItems = new ArrayList<>();
4093         try
4094         {
4095           // System.err.println("Building ws menu again "
4096           // + Thread.currentThread());
4097           // TODO: add support for context dependent disabling of services based
4098           // on
4099           // alignment and current selection
4100           // TODO: add additional serviceHandle parameter to specify abstract
4101           // handler
4102           // class independently of AbstractName
4103           // TODO: add in rediscovery GUI function to restart discoverer
4104           // TODO: group services by location as well as function and/or
4105           // introduce
4106           // object broker mechanism.
4107           final Vector<JMenu> wsmenu = new Vector<>();
4108           final IProgressIndicator af = me;
4109
4110           /*
4111            * do not i18n these strings - they are hard-coded in class
4112            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4113            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4114            */
4115           final JMenu msawsmenu = new JMenu("Alignment");
4116           final JMenu secstrmenu = new JMenu(
4117                   "Secondary Structure Prediction");
4118           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4119           final JMenu analymenu = new JMenu("Analysis");
4120           final JMenu dismenu = new JMenu("Protein Disorder");
4121           // JAL-940 - only show secondary structure prediction services from
4122           // the legacy server
4123           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4124               // &&
4125           Discoverer.services != null && (Discoverer.services.size() > 0))
4126           {
4127             // TODO: refactor to allow list of AbstractName/Handler bindings to
4128             // be
4129             // stored or retrieved from elsewhere
4130             // No MSAWS used any more:
4131             // Vector msaws = null; // (Vector)
4132             // Discoverer.services.get("MsaWS");
4133             Vector secstrpr = (Vector) Discoverer.services
4134                     .get("SecStrPred");
4135             if (secstrpr != null)
4136             {
4137               // Add any secondary structure prediction services
4138               for (int i = 0, j = secstrpr.size(); i < j; i++)
4139               {
4140                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4141                         .get(i);
4142                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4143                         .getServiceClient(sh);
4144                 int p = secstrmenu.getItemCount();
4145                 impl.attachWSMenuEntry(secstrmenu, me);
4146                 int q = secstrmenu.getItemCount();
4147                 for (int litm = p; litm < q; litm++)
4148                 {
4149                   legacyItems.add(secstrmenu.getItem(litm));
4150                 }
4151               }
4152             }
4153           }
4154
4155           // Add all submenus in the order they should appear on the web
4156           // services menu
4157           wsmenu.add(msawsmenu);
4158           wsmenu.add(secstrmenu);
4159           wsmenu.add(dismenu);
4160           wsmenu.add(analymenu);
4161           // No search services yet
4162           // wsmenu.add(seqsrchmenu);
4163
4164           javax.swing.SwingUtilities.invokeLater(new Runnable()
4165           {
4166             @Override
4167             public void run()
4168             {
4169               try
4170               {
4171                 webService.removeAll();
4172                 // first, add discovered services onto the webservices menu
4173                 if (wsmenu.size() > 0)
4174                 {
4175                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4176                   {
4177                     webService.add(wsmenu.get(i));
4178                   }
4179                 }
4180                 else
4181                 {
4182                   webService.add(me.webServiceNoServices);
4183                 }
4184                 // TODO: move into separate menu builder class.
4185                 boolean new_sspred = false;
4186                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4187                 {
4188                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4189                   if (jws2servs != null)
4190                   {
4191                     if (jws2servs.hasServices())
4192                     {
4193                       jws2servs.attachWSMenuEntry(webService, me);
4194                       for (Jws2Instance sv : jws2servs.getServices())
4195                       {
4196                         if (sv.description.toLowerCase().contains("jpred"))
4197                         {
4198                           for (JMenuItem jmi : legacyItems)
4199                           {
4200                             jmi.setVisible(false);
4201                           }
4202                         }
4203                       }
4204
4205                     }
4206                     if (jws2servs.isRunning())
4207                     {
4208                       JMenuItem tm = new JMenuItem(
4209                               "Still discovering JABA Services");
4210                       tm.setEnabled(false);
4211                       webService.add(tm);
4212                     }
4213                   }
4214                 }
4215                 build_urlServiceMenu(me.webService);
4216                 build_fetchdbmenu(webService);
4217                 for (JMenu item : wsmenu)
4218                 {
4219                   if (item.getItemCount() == 0)
4220                   {
4221                     item.setEnabled(false);
4222                   }
4223                   else
4224                   {
4225                     item.setEnabled(true);
4226                   }
4227                 }
4228               } catch (Exception e)
4229               {
4230                 Cache.log.debug(
4231                         "Exception during web service menu building process.",
4232                         e);
4233               }
4234             }
4235           });
4236         } catch (Exception e)
4237         {
4238         }
4239         buildingMenu = false;
4240       }
4241     }).start();
4242
4243   }
4244
4245   /**
4246    * construct any groupURL type service menu entries.
4247    *
4248    * @param webService
4249    */
4250   private void build_urlServiceMenu(JMenu webService)
4251   {
4252     // TODO: remove this code when 2.7 is released
4253     // DEBUG - alignmentView
4254     /*
4255      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4256      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4257      *
4258      * @Override public void actionPerformed(ActionEvent e) {
4259      * jalview.datamodel.AlignmentView
4260      * .testSelectionViews(af.viewport.getAlignment(),
4261      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4262      *
4263      * }); webService.add(testAlView);
4264      */
4265     // TODO: refactor to RestClient discoverer and merge menu entries for
4266     // rest-style services with other types of analysis/calculation service
4267     // SHmmr test client - still being implemented.
4268     // DEBUG - alignmentView
4269
4270     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4271             .getRestClients())
4272     {
4273       client.attachWSMenuEntry(
4274               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4275               this);
4276     }
4277   }
4278
4279   /**
4280    * Searches the alignment sequences for xRefs and builds the Show
4281    * Cross-References menu (formerly called Show Products), with database
4282    * sources for which cross-references are found (protein sources for a
4283    * nucleotide alignment and vice versa)
4284    *
4285    * @return true if Show Cross-references menu should be enabled
4286    */
4287   public boolean canShowProducts()
4288   {
4289     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4290     AlignmentI dataset = viewport.getAlignment().getDataset();
4291
4292     showProducts.removeAll();
4293     final boolean dna = viewport.getAlignment().isNucleotide();
4294
4295     if (seqs == null || seqs.length == 0)
4296     {
4297       // nothing to see here.
4298       return false;
4299     }
4300
4301     boolean showp = false;
4302     try
4303     {
4304       List<String> ptypes = new CrossRef(seqs, dataset)
4305               .findXrefSourcesForSequences(dna);
4306
4307       for (final String source : ptypes)
4308       {
4309         showp = true;
4310         final AlignFrame af = this;
4311         JMenuItem xtype = new JMenuItem(source);
4312         xtype.addActionListener(new ActionListener()
4313         {
4314           @Override
4315           public void actionPerformed(ActionEvent e)
4316           {
4317             showProductsFor(af.viewport.getSequenceSelection(), dna,
4318                     source);
4319           }
4320         });
4321         showProducts.add(xtype);
4322       }
4323       showProducts.setVisible(showp);
4324       showProducts.setEnabled(showp);
4325     } catch (Exception e)
4326     {
4327       Cache.log.warn(
4328               "canShowProducts threw an exception - please report to help@jalview.org",
4329               e);
4330       return false;
4331     }
4332     return showp;
4333   }
4334
4335   /**
4336    * Finds and displays cross-references for the selected sequences (protein
4337    * products for nucleotide sequences, dna coding sequences for peptides).
4338    *
4339    * @param sel
4340    *          the sequences to show cross-references for
4341    * @param dna
4342    *          true if from a nucleotide alignment (so showing proteins)
4343    * @param source
4344    *          the database to show cross-references for
4345    */
4346   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4347           final String source)
4348   {
4349     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4350             .start();
4351   }
4352
4353   /**
4354    * Construct and display a new frame containing the translation of this
4355    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4356    */
4357   @Override
4358   public void showTranslation_actionPerformed(ActionEvent e)
4359   {
4360     AlignmentI al = null;
4361     try
4362     {
4363       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4364
4365       al = dna.translateCdna();
4366     } catch (Exception ex)
4367     {
4368       jalview.bin.Cache.log.error(
4369               "Exception during translation. Please report this !", ex);
4370       final String msg = MessageManager.getString(
4371               "label.error_when_translating_sequences_submit_bug_report");
4372       final String errorTitle = MessageManager
4373               .getString("label.implementation_error")
4374               + MessageManager.getString("label.translation_failed");
4375       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4376               JvOptionPane.ERROR_MESSAGE);
4377       return;
4378     }
4379     if (al == null || al.getHeight() == 0)
4380     {
4381       final String msg = MessageManager.getString(
4382               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4383       final String errorTitle = MessageManager
4384               .getString("label.translation_failed");
4385       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4386               JvOptionPane.WARNING_MESSAGE);
4387     }
4388     else
4389     {
4390       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4391       af.setFileFormat(this.currentFileFormat);
4392       final String newTitle = MessageManager
4393               .formatMessage("label.translation_of_params", new Object[]
4394               { this.getTitle() });
4395       af.setTitle(newTitle);
4396       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4397       {
4398         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4399         viewport.openSplitFrame(af, new Alignment(seqs));
4400       }
4401       else
4402       {
4403         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4404                 DEFAULT_HEIGHT);
4405       }
4406     }
4407   }
4408
4409   /**
4410    * Set the file format
4411    *
4412    * @param format
4413    */
4414   public void setFileFormat(FileFormatI format)
4415   {
4416     this.currentFileFormat = format;
4417   }
4418
4419   /**
4420    * Try to load a features file onto the alignment.
4421    *
4422    * @param file
4423    *          contents or path to retrieve file or a File object
4424    * @param sourceType
4425    *          access mode of file (see jalview.io.AlignFile)
4426    * @return true if features file was parsed correctly.
4427    */
4428   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4429   {
4430     // BH 2018
4431     return avc.parseFeaturesFile(file, sourceType,
4432             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4433
4434   }
4435
4436   @Override
4437   public void refreshFeatureUI(boolean enableIfNecessary)
4438   {
4439     // note - currently this is only still here rather than in the controller
4440     // because of the featureSettings hard reference that is yet to be
4441     // abstracted
4442     if (enableIfNecessary)
4443     {
4444       viewport.setShowSequenceFeatures(true);
4445       showSeqFeatures.setSelected(true);
4446     }
4447
4448   }
4449
4450   @Override
4451   public void dragEnter(DropTargetDragEvent evt)
4452   {
4453   }
4454
4455   @Override
4456   public void dragExit(DropTargetEvent evt)
4457   {
4458   }
4459
4460   @Override
4461   public void dragOver(DropTargetDragEvent evt)
4462   {
4463   }
4464
4465   @Override
4466   public void dropActionChanged(DropTargetDragEvent evt)
4467   {
4468   }
4469
4470   @Override
4471   public void drop(DropTargetDropEvent evt)
4472   {
4473     // JAL-1552 - acceptDrop required before getTransferable call for
4474     // Java's Transferable for native dnd
4475     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4476     Transferable t = evt.getTransferable();
4477
4478     final AlignFrame thisaf = this;
4479     final List<Object> 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       new Thread(new Runnable()
4492       {
4493         @Override
4494         public void run()
4495         {
4496           try
4497           {
4498             // check to see if any of these files have names matching sequences
4499             // in
4500             // the alignment
4501             SequenceIdMatcher idm = new SequenceIdMatcher(
4502                     viewport.getAlignment().getSequencesArray());
4503             /**
4504              * Object[] { String,SequenceI}
4505              */
4506             ArrayList<Object[]> filesmatched = new ArrayList<>();
4507             ArrayList<Object> filesnotmatched = new ArrayList<>();
4508             for (int i = 0; i < files.size(); i++)
4509             {
4510               // BH 2018
4511               Object file = files.get(i);
4512               String fileName = file.toString();
4513               String pdbfn = "";
4514               DataSourceType protocol = (file instanceof File
4515                       ? DataSourceType.FILE
4516                       : FormatAdapter.checkProtocol(fileName));
4517               if (protocol == DataSourceType.FILE)
4518               {
4519                 File fl = (file instanceof File ? (File) file
4520                         : new File(fileName));
4521                 pdbfn = fl.getName();
4522               }
4523               else if (protocol == DataSourceType.URL)
4524               {
4525                 URL url = new URL(fileName);
4526                 pdbfn = url.getFile();
4527               }
4528               if (pdbfn.length() > 0)
4529               {
4530                 // attempt to find a match in the alignment
4531                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4532                 int l = 0, c = pdbfn.indexOf(".");
4533                 while (mtch == null && c != -1)
4534                 {
4535                   do
4536                   {
4537                     l = c;
4538                   } while ((c = pdbfn.indexOf(".", l)) > l);
4539                   if (l > -1)
4540                   {
4541                     pdbfn = pdbfn.substring(0, l);
4542                   }
4543                   mtch = idm.findAllIdMatches(pdbfn);
4544                 }
4545                 if (mtch != null)
4546                 {
4547                   FileFormatI type;
4548                   try
4549                   {
4550                     type = new IdentifyFile().identify(file, protocol);
4551                   } catch (Exception ex)
4552                   {
4553                     type = null;
4554                   }
4555                   if (type != null && type.isStructureFile())
4556                   {
4557                     filesmatched.add(new Object[] { file, protocol, mtch });
4558                     continue;
4559                   }
4560                 }
4561                 // File wasn't named like one of the sequences or wasn't a PDB
4562                 // file.
4563                 filesnotmatched.add(file);
4564               }
4565             }
4566             int assocfiles = 0;
4567             if (filesmatched.size() > 0)
4568             {
4569               boolean autoAssociate = Cache
4570                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4571               if (!autoAssociate)
4572               {
4573                 String msg = MessageManager.formatMessage(
4574                         "label.automatically_associate_structure_files_with_sequences_same_name",
4575                         new Object[]
4576                         { Integer.valueOf(filesmatched.size())
4577                                 .toString() });
4578                 String ttl = MessageManager.getString(
4579                         "label.automatically_associate_structure_files_by_name");
4580                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4581                         ttl, JvOptionPane.YES_NO_OPTION);
4582                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4583               }
4584               if (autoAssociate)
4585               {
4586                 for (Object[] fm : filesmatched)
4587                 {
4588                   // try and associate
4589                   // TODO: may want to set a standard ID naming formalism for
4590                   // associating PDB files which have no IDs.
4591                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4592                   {
4593                     PDBEntry pe = new AssociatePdbFileWithSeq()
4594                             .associatePdbWithSeq(fm[0].toString(),
4595                                     (DataSourceType) fm[1], toassoc, false,
4596                                     Desktop.instance);
4597                     if (pe != null)
4598                     {
4599                       System.err.println("Associated file : "
4600                               + (fm[0].toString()) + " with "
4601                               + toassoc.getDisplayId(true));
4602                       assocfiles++;
4603                     }
4604                   }
4605                   // TODO: do we need to update overview ? only if features are
4606                   // shown I guess
4607                   alignPanel.paintAlignment(true, false);
4608                 }
4609               }
4610               else
4611               {
4612                 /*
4613                  * add declined structures as sequences
4614                  */
4615                 for (Object[] o : filesmatched)
4616                 {
4617                   filesnotmatched.add(o[0]);
4618                 }
4619               }
4620             }
4621             if (filesnotmatched.size() > 0)
4622             {
4623               if (assocfiles > 0 && (Cache.getDefault(
4624                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4625                       || JvOptionPane.showConfirmDialog(thisaf,
4626                               "<html>" + MessageManager.formatMessage(
4627                                       "label.ignore_unmatched_dropped_files_info",
4628                                       new Object[]
4629                                       { Integer.valueOf(
4630                                               filesnotmatched.size())
4631                                               .toString() })
4632                                       + "</html>",
4633                               MessageManager.getString(
4634                                       "label.ignore_unmatched_dropped_files"),
4635                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4636               {
4637                 return;
4638               }
4639               for (Object fn : filesnotmatched)
4640               {
4641                 loadJalviewDataFile(fn, null, null, null);
4642               }
4643
4644             }
4645           } catch (Exception ex)
4646           {
4647             ex.printStackTrace();
4648           }
4649         }
4650       }).start();
4651     }
4652   }
4653
4654   /**
4655    * Attempt to load a "dropped" file or URL string, by testing in turn for
4656    * <ul>
4657    * <li>an Annotation file</li>
4658    * <li>a JNet file</li>
4659    * <li>a features file</li>
4660    * <li>else try to interpret as an alignment file</li>
4661    * </ul>
4662    *
4663    * @param file
4664    *          either a filename or a URL string.
4665    */
4666   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4667           FileFormatI format, SequenceI assocSeq)
4668   {
4669     // BH 2018 was String file
4670     try
4671     {
4672       if (sourceType == null)
4673       {
4674         sourceType = FormatAdapter.checkProtocol(file);
4675       }
4676       // if the file isn't identified, or not positively identified as some
4677       // other filetype (PFAM is default unidentified alignment file type) then
4678       // try to parse as annotation.
4679       boolean isAnnotation = (format == null
4680               || FileFormat.Pfam.equals(format))
4681                       ? new AnnotationFile().annotateAlignmentView(viewport,
4682                               file, sourceType)
4683                       : false;
4684
4685       if (!isAnnotation)
4686       {
4687         // first see if its a T-COFFEE score file
4688         TCoffeeScoreFile tcf = null;
4689         try
4690         {
4691           tcf = new TCoffeeScoreFile(file, sourceType);
4692           if (tcf.isValid())
4693           {
4694             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4695             {
4696               buildColourMenu();
4697               changeColour(
4698                       new TCoffeeColourScheme(viewport.getAlignment()));
4699               isAnnotation = true;
4700               setStatus(MessageManager.getString(
4701                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4702             }
4703             else
4704             {
4705               // some problem - if no warning its probable that the ID matching
4706               // process didn't work
4707               JvOptionPane.showMessageDialog(Desktop.desktop,
4708                       tcf.getWarningMessage() == null
4709                               ? MessageManager.getString(
4710                                       "label.check_file_matches_sequence_ids_alignment")
4711                               : tcf.getWarningMessage(),
4712                       MessageManager.getString(
4713                               "label.problem_reading_tcoffee_score_file"),
4714                       JvOptionPane.WARNING_MESSAGE);
4715             }
4716           }
4717           else
4718           {
4719             tcf = null;
4720           }
4721         } catch (Exception x)
4722         {
4723           Cache.log.debug(
4724                   "Exception when processing data source as T-COFFEE score file",
4725                   x);
4726           tcf = null;
4727         }
4728         if (tcf == null)
4729         {
4730           // try to see if its a JNet 'concise' style annotation file *before*
4731           // we
4732           // try to parse it as a features file
4733           if (format == null)
4734           {
4735             format = new IdentifyFile().identify(file, sourceType);
4736           }
4737           if (FileFormat.ScoreMatrix == format)
4738           {
4739             ScoreMatrixFile sm = new ScoreMatrixFile(
4740                     new FileParse(file, sourceType));
4741             sm.parse();
4742             // todo: i18n this message
4743             setStatus(MessageManager.formatMessage(
4744                     "label.successfully_loaded_matrix",
4745                     sm.getMatrixName()));
4746           }
4747           else if (FileFormat.Jnet.equals(format))
4748           {
4749             JPredFile predictions = new JPredFile(file, sourceType);
4750             new JnetAnnotationMaker();
4751             JnetAnnotationMaker.add_annotation(predictions,
4752                     viewport.getAlignment(), 0, false);
4753             viewport.getAlignment().setupJPredAlignment();
4754             isAnnotation = true;
4755           }
4756           // else if (IdentifyFile.FeaturesFile.equals(format))
4757           else if (FileFormat.Features.equals(format))
4758           {
4759             if (parseFeaturesFile(file, sourceType))
4760             {
4761               alignPanel.paintAlignment(true, true);
4762             }
4763           }
4764           else
4765           {
4766             new FileLoader().LoadFile(viewport, file, sourceType, format);
4767           }
4768         }
4769       }
4770       if (isAnnotation)
4771       {
4772
4773         alignPanel.adjustAnnotationHeight();
4774         viewport.updateSequenceIdColours();
4775         buildSortByAnnotationScoresMenu();
4776         alignPanel.paintAlignment(true, true);
4777       }
4778     } catch (Exception ex)
4779     {
4780       ex.printStackTrace();
4781     } catch (OutOfMemoryError oom)
4782     {
4783       try
4784       {
4785         System.gc();
4786       } catch (Exception x)
4787       {
4788       }
4789       new OOMWarning(
4790               "loading data "
4791                       + (sourceType != null
4792                               ? (sourceType == DataSourceType.PASTE
4793                                       ? "from clipboard."
4794                                       : "using " + sourceType + " from "
4795                                               + file)
4796                               : ".")
4797                       + (format != null
4798                               ? "(parsing as '" + format + "' file)"
4799                               : ""),
4800               oom, Desktop.desktop);
4801     }
4802   }
4803
4804   /**
4805    * Method invoked by the ChangeListener on the tabbed pane, in other words
4806    * when a different tabbed pane is selected by the user or programmatically.
4807    */
4808   @Override
4809   public void tabSelectionChanged(int index)
4810   {
4811     if (index > -1)
4812     {
4813       alignPanel = alignPanels.get(index);
4814       viewport = alignPanel.av;
4815       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4816       setMenusFromViewport(viewport);
4817     }
4818
4819     /*
4820      * 'focus' any colour slider that is open to the selected viewport
4821      */
4822     if (viewport.getConservationSelected())
4823     {
4824       SliderPanel.setConservationSlider(alignPanel,
4825               viewport.getResidueShading(), alignPanel.getViewName());
4826     }
4827     else
4828     {
4829       SliderPanel.hideConservationSlider();
4830     }
4831     if (viewport.getAbovePIDThreshold())
4832     {
4833       SliderPanel.setPIDSliderSource(alignPanel,
4834               viewport.getResidueShading(), alignPanel.getViewName());
4835     }
4836     else
4837     {
4838       SliderPanel.hidePIDSlider();
4839     }
4840
4841     /*
4842      * If there is a frame linked to this one in a SplitPane, switch it to the
4843      * same view tab index. No infinite recursion of calls should happen, since
4844      * tabSelectionChanged() should not get invoked on setting the selected
4845      * index to an unchanged value. Guard against setting an invalid index
4846      * before the new view peer tab has been created.
4847      */
4848     final AlignViewportI peer = viewport.getCodingComplement();
4849     if (peer != null)
4850     {
4851       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4852               .getAlignPanel().alignFrame;
4853       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4854       {
4855         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4856       }
4857     }
4858   }
4859
4860   /**
4861    * On right mouse click on view tab, prompt for and set new view name.
4862    */
4863   @Override
4864   public void tabbedPane_mousePressed(MouseEvent e)
4865   {
4866     if (e.isPopupTrigger())
4867     {
4868       String msg = MessageManager.getString("label.enter_view_name");
4869       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4870       String reply = JvOptionPane.showInputDialog(msg, ttl);
4871
4872       if (reply != null)
4873       {
4874         viewport.setViewName(reply);
4875         // TODO warn if reply is in getExistingViewNames()?
4876         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4877       }
4878     }
4879   }
4880
4881   public AlignViewport getCurrentView()
4882   {
4883     return viewport;
4884   }
4885
4886   /**
4887    * Open the dialog for regex description parsing.
4888    */
4889   @Override
4890   protected void extractScores_actionPerformed(ActionEvent e)
4891   {
4892     ParseProperties pp = new jalview.analysis.ParseProperties(
4893             viewport.getAlignment());
4894     // TODO: verify regex and introduce GUI dialog for version 2.5
4895     // if (pp.getScoresFromDescription("col", "score column ",
4896     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4897     // true)>0)
4898     if (pp.getScoresFromDescription("description column",
4899             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4900     {
4901       buildSortByAnnotationScoresMenu();
4902     }
4903   }
4904
4905   /*
4906    * (non-Javadoc)
4907    *
4908    * @see
4909    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4910    * )
4911    */
4912   @Override
4913   protected void showDbRefs_actionPerformed(ActionEvent e)
4914   {
4915     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4916   }
4917
4918   /*
4919    * (non-Javadoc)
4920    *
4921    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4922    * ActionEvent)
4923    */
4924   @Override
4925   protected void showNpFeats_actionPerformed(ActionEvent e)
4926   {
4927     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4928   }
4929
4930   /**
4931    * find the viewport amongst the tabs in this alignment frame and close that
4932    * tab
4933    *
4934    * @param av
4935    */
4936   public boolean closeView(AlignViewportI av)
4937   {
4938     if (viewport == av)
4939     {
4940       this.closeMenuItem_actionPerformed(false);
4941       return true;
4942     }
4943     Component[] comp = tabbedPane.getComponents();
4944     for (int i = 0; comp != null && i < comp.length; i++)
4945     {
4946       if (comp[i] instanceof AlignmentPanel)
4947       {
4948         if (((AlignmentPanel) comp[i]).av == av)
4949         {
4950           // close the view.
4951           closeView((AlignmentPanel) comp[i]);
4952           return true;
4953         }
4954       }
4955     }
4956     return false;
4957   }
4958
4959   protected void build_fetchdbmenu(JMenu webService)
4960   {
4961     // Temporary hack - DBRef Fetcher always top level ws entry.
4962     // TODO We probably want to store a sequence database checklist in
4963     // preferences and have checkboxes.. rather than individual sources selected
4964     // here
4965     final JMenu rfetch = new JMenu(
4966             MessageManager.getString("action.fetch_db_references"));
4967     rfetch.setToolTipText(MessageManager.getString(
4968             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4969     webService.add(rfetch);
4970
4971     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4972             MessageManager.getString("option.trim_retrieved_seqs"));
4973     trimrs.setToolTipText(
4974             MessageManager.getString("label.trim_retrieved_sequences"));
4975     trimrs.setSelected(
4976             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4977     trimrs.addActionListener(new ActionListener()
4978     {
4979       @Override
4980       public void actionPerformed(ActionEvent e)
4981       {
4982         trimrs.setSelected(trimrs.isSelected());
4983         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4984                 Boolean.valueOf(trimrs.isSelected()).toString());
4985       };
4986     });
4987     rfetch.add(trimrs);
4988     JMenuItem fetchr = new JMenuItem(
4989             MessageManager.getString("label.standard_databases"));
4990     fetchr.setToolTipText(
4991             MessageManager.getString("label.fetch_embl_uniprot"));
4992     fetchr.addActionListener(new ActionListener()
4993     {
4994
4995       @Override
4996       public void actionPerformed(ActionEvent e)
4997       {
4998         new Thread(new Runnable()
4999         {
5000           @Override
5001           public void run()
5002           {
5003             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5004                     .getAlignment().isNucleotide();
5005             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5006                     alignPanel.av.getSequenceSelection(),
5007                     alignPanel.alignFrame, null,
5008                     alignPanel.alignFrame.featureSettings, isNucleotide);
5009             dbRefFetcher.addListener(new FetchFinishedListenerI()
5010             {
5011               @Override
5012               public void finished()
5013               {
5014                 AlignFrame.this.setMenusForViewport();
5015               }
5016             });
5017             dbRefFetcher.fetchDBRefs(false);
5018           }
5019         }).start();
5020
5021       }
5022
5023     });
5024     rfetch.add(fetchr);
5025     new Thread(new Runnable()
5026     {
5027       @Override
5028       public void run()
5029       {
5030         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5031                 .getSequenceFetcherSingleton();
5032         javax.swing.SwingUtilities.invokeLater(new Runnable()
5033         {
5034           @Override
5035           public void run()
5036           {
5037             String[] dbclasses = sf.getNonAlignmentSources();
5038             List<DbSourceProxy> otherdb;
5039             JMenu dfetch = new JMenu();
5040             JMenu ifetch = new JMenu();
5041             JMenuItem fetchr = null;
5042             int comp = 0, icomp = 0, mcomp = 15;
5043             String mname = null;
5044             int dbi = 0;
5045             for (String dbclass : dbclasses)
5046             {
5047               otherdb = sf.getSourceProxy(dbclass);
5048               // add a single entry for this class, or submenu allowing 'fetch
5049               // all' or pick one
5050               if (otherdb == null || otherdb.size() < 1)
5051               {
5052                 continue;
5053               }
5054               if (mname == null)
5055               {
5056                 mname = "From " + dbclass;
5057               }
5058               if (otherdb.size() == 1)
5059               {
5060                 final DbSourceProxy[] dassource = otherdb
5061                         .toArray(new DbSourceProxy[0]);
5062                 DbSourceProxy src = otherdb.get(0);
5063                 fetchr = new JMenuItem(src.getDbSource());
5064                 fetchr.addActionListener(new ActionListener()
5065                 {
5066
5067                   @Override
5068                   public void actionPerformed(ActionEvent e)
5069                   {
5070                     new Thread(new Runnable()
5071                     {
5072
5073                       @Override
5074                       public void run()
5075                       {
5076                         boolean isNucleotide = alignPanel.alignFrame
5077                                 .getViewport().getAlignment()
5078                                 .isNucleotide();
5079                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5080                                 alignPanel.av.getSequenceSelection(),
5081                                 alignPanel.alignFrame, dassource,
5082                                 alignPanel.alignFrame.featureSettings,
5083                                 isNucleotide);
5084                         dbRefFetcher
5085                                 .addListener(new FetchFinishedListenerI()
5086                                 {
5087                                   @Override
5088                                   public void finished()
5089                                   {
5090                                     AlignFrame.this.setMenusForViewport();
5091                                   }
5092                                 });
5093                         dbRefFetcher.fetchDBRefs(false);
5094                       }
5095                     }).start();
5096                   }
5097
5098                 });
5099                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5100                         MessageManager.formatMessage(
5101                                 "label.fetch_retrieve_from", new Object[]
5102                                 { src.getDbName() })));
5103                 dfetch.add(fetchr);
5104                 comp++;
5105               }
5106               else
5107               {
5108                 final DbSourceProxy[] dassource = otherdb
5109                         .toArray(new DbSourceProxy[0]);
5110                 // fetch all entry
5111                 DbSourceProxy src = otherdb.get(0);
5112                 fetchr = new JMenuItem(MessageManager
5113                         .formatMessage("label.fetch_all_param", new Object[]
5114                         { src.getDbSource() }));
5115                 fetchr.addActionListener(new ActionListener()
5116                 {
5117                   @Override
5118                   public void actionPerformed(ActionEvent e)
5119                   {
5120                     new Thread(new Runnable()
5121                     {
5122
5123                       @Override
5124                       public void run()
5125                       {
5126                         boolean isNucleotide = alignPanel.alignFrame
5127                                 .getViewport().getAlignment()
5128                                 .isNucleotide();
5129                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5130                                 alignPanel.av.getSequenceSelection(),
5131                                 alignPanel.alignFrame, dassource,
5132                                 alignPanel.alignFrame.featureSettings,
5133                                 isNucleotide);
5134                         dbRefFetcher
5135                                 .addListener(new FetchFinishedListenerI()
5136                                 {
5137                                   @Override
5138                                   public void finished()
5139                                   {
5140                                     AlignFrame.this.setMenusForViewport();
5141                                   }
5142                                 });
5143                         dbRefFetcher.fetchDBRefs(false);
5144                       }
5145                     }).start();
5146                   }
5147                 });
5148
5149                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5150                         MessageManager.formatMessage(
5151                                 "label.fetch_retrieve_from_all_sources",
5152                                 new Object[]
5153                                 { Integer.valueOf(otherdb.size())
5154                                         .toString(),
5155                                     src.getDbSource(), src.getDbName() })));
5156                 dfetch.add(fetchr);
5157                 comp++;
5158                 // and then build the rest of the individual menus
5159                 ifetch = new JMenu(MessageManager.formatMessage(
5160                         "label.source_from_db_source", new Object[]
5161                         { src.getDbSource() }));
5162                 icomp = 0;
5163                 String imname = null;
5164                 int i = 0;
5165                 for (DbSourceProxy sproxy : otherdb)
5166                 {
5167                   String dbname = sproxy.getDbName();
5168                   String sname = dbname.length() > 5
5169                           ? dbname.substring(0, 5) + "..."
5170                           : dbname;
5171                   String msname = dbname.length() > 10
5172                           ? dbname.substring(0, 10) + "..."
5173                           : dbname;
5174                   if (imname == null)
5175                   {
5176                     imname = MessageManager
5177                             .formatMessage("label.from_msname", new Object[]
5178                             { sname });
5179                   }
5180                   fetchr = new JMenuItem(msname);
5181                   final DbSourceProxy[] dassrc = { sproxy };
5182                   fetchr.addActionListener(new ActionListener()
5183                   {
5184
5185                     @Override
5186                     public void actionPerformed(ActionEvent e)
5187                     {
5188                       new Thread(new Runnable()
5189                       {
5190
5191                         @Override
5192                         public void run()
5193                         {
5194                           boolean isNucleotide = alignPanel.alignFrame
5195                                   .getViewport().getAlignment()
5196                                   .isNucleotide();
5197                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5198                                   alignPanel.av.getSequenceSelection(),
5199                                   alignPanel.alignFrame, dassrc,
5200                                   alignPanel.alignFrame.featureSettings,
5201                                   isNucleotide);
5202                           dbRefFetcher
5203                                   .addListener(new FetchFinishedListenerI()
5204                                   {
5205                                     @Override
5206                                     public void finished()
5207                                     {
5208                                       AlignFrame.this.setMenusForViewport();
5209                                     }
5210                                   });
5211                           dbRefFetcher.fetchDBRefs(false);
5212                         }
5213                       }).start();
5214                     }
5215
5216                   });
5217                   fetchr.setToolTipText(
5218                           "<html>" + MessageManager.formatMessage(
5219                                   "label.fetch_retrieve_from", new Object[]
5220                                   { dbname }));
5221                   ifetch.add(fetchr);
5222                   ++i;
5223                   if (++icomp >= mcomp || i == (otherdb.size()))
5224                   {
5225                     ifetch.setText(MessageManager.formatMessage(
5226                             "label.source_to_target", imname, sname));
5227                     dfetch.add(ifetch);
5228                     ifetch = new JMenu();
5229                     imname = null;
5230                     icomp = 0;
5231                     comp++;
5232                   }
5233                 }
5234               }
5235               ++dbi;
5236               if (comp >= mcomp || dbi >= (dbclasses.length))
5237               {
5238                 dfetch.setText(MessageManager.formatMessage(
5239                         "label.source_to_target", mname, dbclass));
5240                 rfetch.add(dfetch);
5241                 dfetch = new JMenu();
5242                 mname = null;
5243                 comp = 0;
5244               }
5245             }
5246           }
5247         });
5248       }
5249     }).start();
5250
5251   }
5252
5253   /**
5254    * Left justify the whole alignment.
5255    */
5256   @Override
5257   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5258   {
5259     AlignmentI al = viewport.getAlignment();
5260     al.justify(false);
5261     viewport.firePropertyChange("alignment", null, al);
5262   }
5263
5264   /**
5265    * Right justify the whole alignment.
5266    */
5267   @Override
5268   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5269   {
5270     AlignmentI al = viewport.getAlignment();
5271     al.justify(true);
5272     viewport.firePropertyChange("alignment", null, al);
5273   }
5274
5275   @Override
5276   public void setShowSeqFeatures(boolean b)
5277   {
5278     showSeqFeatures.setSelected(b);
5279     viewport.setShowSequenceFeatures(b);
5280   }
5281
5282   /*
5283    * (non-Javadoc)
5284    *
5285    * @see
5286    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5287    * awt.event.ActionEvent)
5288    */
5289   @Override
5290   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5291   {
5292     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5293     alignPanel.paintAlignment(false, false);
5294   }
5295
5296   /*
5297    * (non-Javadoc)
5298    *
5299    * @see
5300    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5301    * .ActionEvent)
5302    */
5303   @Override
5304   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5305   {
5306     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5307     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5308
5309   }
5310
5311   /*
5312    * (non-Javadoc)
5313    *
5314    * @see
5315    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5316    * .event.ActionEvent)
5317    */
5318   @Override
5319   protected void showGroupConservation_actionPerformed(ActionEvent e)
5320   {
5321     viewport.setShowGroupConservation(showGroupConservation.getState());
5322     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5323   }
5324
5325   /*
5326    * (non-Javadoc)
5327    *
5328    * @see
5329    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5330    * .event.ActionEvent)
5331    */
5332   @Override
5333   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5334   {
5335     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5336     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5337   }
5338
5339   /*
5340    * (non-Javadoc)
5341    *
5342    * @see
5343    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5344    * .event.ActionEvent)
5345    */
5346   @Override
5347   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5348   {
5349     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5350     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5351   }
5352
5353   @Override
5354   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5355   {
5356     showSequenceLogo.setState(true);
5357     viewport.setShowSequenceLogo(true);
5358     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5359     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5360   }
5361
5362   @Override
5363   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5364   {
5365     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5366   }
5367
5368   /*
5369    * (non-Javadoc)
5370    *
5371    * @see
5372    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5373    * .event.ActionEvent)
5374    */
5375   @Override
5376   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5377   {
5378     if (avc.makeGroupsFromSelection())
5379     {
5380       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5381       alignPanel.updateAnnotation();
5382       alignPanel.paintAlignment(true, true);
5383     }
5384   }
5385
5386   public void clearAlignmentSeqRep()
5387   {
5388     // TODO refactor alignmentseqrep to controller
5389     if (viewport.getAlignment().hasSeqrep())
5390     {
5391       viewport.getAlignment().setSeqrep(null);
5392       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5393       alignPanel.updateAnnotation();
5394       alignPanel.paintAlignment(true, true);
5395     }
5396   }
5397
5398   @Override
5399   protected void createGroup_actionPerformed(ActionEvent e)
5400   {
5401     if (avc.createGroup())
5402     {
5403       if (applyAutoAnnotationSettings.isSelected())
5404       {
5405         alignPanel.updateAnnotation(true, false);
5406       }
5407       alignPanel.alignmentChanged();
5408     }
5409   }
5410
5411   @Override
5412   protected void unGroup_actionPerformed(ActionEvent e)
5413   {
5414     if (avc.unGroup())
5415     {
5416       alignPanel.alignmentChanged();
5417     }
5418   }
5419
5420   /**
5421    * make the given alignmentPanel the currently selected tab
5422    *
5423    * @param alignmentPanel
5424    */
5425   public void setDisplayedView(AlignmentPanel alignmentPanel)
5426   {
5427     if (!viewport.getSequenceSetId()
5428             .equals(alignmentPanel.av.getSequenceSetId()))
5429     {
5430       throw new Error(MessageManager.getString(
5431               "error.implementation_error_cannot_show_view_alignment_frame"));
5432     }
5433     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5434             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5435     {
5436       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5437     }
5438   }
5439
5440   /**
5441    * Action on selection of menu options to Show or Hide annotations.
5442    *
5443    * @param visible
5444    * @param forSequences
5445    *          update sequence-related annotations
5446    * @param forAlignment
5447    *          update non-sequence-related annotations
5448    */
5449   @Override
5450   protected void setAnnotationsVisibility(boolean visible,
5451           boolean forSequences, boolean forAlignment)
5452   {
5453     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5454             .getAlignmentAnnotation();
5455     if (anns == null)
5456     {
5457       return;
5458     }
5459     for (AlignmentAnnotation aa : anns)
5460     {
5461       /*
5462        * don't display non-positional annotations on an alignment
5463        */
5464       if (aa.annotations == null)
5465       {
5466         continue;
5467       }
5468       boolean apply = (aa.sequenceRef == null && forAlignment)
5469               || (aa.sequenceRef != null && forSequences);
5470       if (apply)
5471       {
5472         aa.visible = visible;
5473       }
5474     }
5475     alignPanel.validateAnnotationDimensions(true);
5476     alignPanel.alignmentChanged();
5477   }
5478
5479   /**
5480    * Store selected annotation sort order for the view and repaint.
5481    */
5482   @Override
5483   protected void sortAnnotations_actionPerformed()
5484   {
5485     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5486     this.alignPanel.av
5487             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5488     alignPanel.paintAlignment(false, false);
5489   }
5490
5491   /**
5492    *
5493    * @return alignment panels in this alignment frame
5494    */
5495   public List<? extends AlignmentViewPanel> getAlignPanels()
5496   {
5497     // alignPanels is never null
5498     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5499     return alignPanels;
5500   }
5501
5502   /**
5503    * Open a new alignment window, with the cDNA associated with this (protein)
5504    * alignment, aligned as is the protein.
5505    */
5506   protected void viewAsCdna_actionPerformed()
5507   {
5508     // TODO no longer a menu action - refactor as required
5509     final AlignmentI alignment = getViewport().getAlignment();
5510     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5511     if (mappings == null)
5512     {
5513       return;
5514     }
5515     List<SequenceI> cdnaSeqs = new ArrayList<>();
5516     for (SequenceI aaSeq : alignment.getSequences())
5517     {
5518       for (AlignedCodonFrame acf : mappings)
5519       {
5520         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5521         if (dnaSeq != null)
5522         {
5523           /*
5524            * There is a cDNA mapping for this protein sequence - add to new
5525            * alignment. It will share the same dataset sequence as other mapped
5526            * cDNA (no new mappings need to be created).
5527            */
5528           final Sequence newSeq = new Sequence(dnaSeq);
5529           newSeq.setDatasetSequence(dnaSeq);
5530           cdnaSeqs.add(newSeq);
5531         }
5532       }
5533     }
5534     if (cdnaSeqs.size() == 0)
5535     {
5536       // show a warning dialog no mapped cDNA
5537       return;
5538     }
5539     AlignmentI cdna = new Alignment(
5540             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5541     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5542             AlignFrame.DEFAULT_HEIGHT);
5543     cdna.alignAs(alignment);
5544     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5545             + this.title;
5546     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5547             AlignFrame.DEFAULT_HEIGHT);
5548   }
5549
5550   /**
5551    * Set visibility of dna/protein complement view (available when shown in a
5552    * split frame).
5553    *
5554    * @param show
5555    */
5556   @Override
5557   protected void showComplement_actionPerformed(boolean show)
5558   {
5559     SplitContainerI sf = getSplitViewContainer();
5560     if (sf != null)
5561     {
5562       sf.setComplementVisible(this, show);
5563     }
5564   }
5565
5566   /**
5567    * Generate the reverse (optionally complemented) of the selected sequences,
5568    * and add them to the alignment
5569    */
5570   @Override
5571   protected void showReverse_actionPerformed(boolean complement)
5572   {
5573     AlignmentI al = null;
5574     try
5575     {
5576       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5577       al = dna.reverseCdna(complement);
5578       viewport.addAlignment(al, "");
5579       addHistoryItem(new EditCommand(
5580               MessageManager.getString("label.add_sequences"), Action.PASTE,
5581               al.getSequencesArray(), 0, al.getWidth(),
5582               viewport.getAlignment()));
5583     } catch (Exception ex)
5584     {
5585       System.err.println(ex.getMessage());
5586       return;
5587     }
5588   }
5589
5590   /**
5591    * Try to run a script in the Groovy console, having first ensured that this
5592    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5593    * be targeted at this alignment.
5594    */
5595   @Override
5596   protected void runGroovy_actionPerformed()
5597   {
5598     Jalview.setCurrentAlignFrame(this);
5599     groovy.ui.Console console = Desktop.getGroovyConsole();
5600     if (console != null)
5601     {
5602       try
5603       {
5604         console.runScript();
5605       } catch (Exception ex)
5606       {
5607         System.err.println((ex.toString()));
5608         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5609                 MessageManager.getString("label.couldnt_run_groovy_script"),
5610                 MessageManager.getString("label.groovy_support_failed"),
5611                 JvOptionPane.ERROR_MESSAGE);
5612       }
5613     }
5614     else
5615     {
5616       System.err.println("Can't run Groovy script as console not found");
5617     }
5618   }
5619
5620   /**
5621    * Hides columns containing (or not containing) a specified feature, provided
5622    * that would not leave all columns hidden
5623    *
5624    * @param featureType
5625    * @param columnsContaining
5626    * @return
5627    */
5628   public boolean hideFeatureColumns(String featureType,
5629           boolean columnsContaining)
5630   {
5631     boolean notForHiding = avc.markColumnsContainingFeatures(
5632             columnsContaining, false, false, featureType);
5633     if (notForHiding)
5634     {
5635       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5636               false, featureType))
5637       {
5638         getViewport().hideSelectedColumns();
5639         return true;
5640       }
5641     }
5642     return false;
5643   }
5644
5645   @Override
5646   protected void selectHighlightedColumns_actionPerformed(
5647           ActionEvent actionEvent)
5648   {
5649     // include key modifier check in case user selects from menu
5650     avc.markHighlightedColumns(
5651             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5652             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5653                     | ActionEvent.CTRL_MASK)) != 0);
5654   }
5655
5656   /**
5657    * Rebuilds the Colour menu, including any user-defined colours which have
5658    * been loaded either on startup or during the session
5659    */
5660   public void buildColourMenu()
5661   {
5662     colourMenu.removeAll();
5663
5664     colourMenu.add(applyToAllGroups);
5665     colourMenu.add(textColour);
5666     colourMenu.addSeparator();
5667
5668     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5669             false);
5670
5671     colourMenu.addSeparator();
5672     colourMenu.add(conservationMenuItem);
5673     colourMenu.add(modifyConservation);
5674     colourMenu.add(abovePIDThreshold);
5675     colourMenu.add(modifyPID);
5676     colourMenu.add(annotationColour);
5677
5678     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5679     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5680   }
5681
5682   /**
5683    * Open a dialog (if not already open) that allows the user to select and
5684    * calculate PCA or Tree analysis
5685    */
5686   protected void openTreePcaDialog()
5687   {
5688     if (alignPanel.getCalculationDialog() == null)
5689     {
5690       new CalculationChooser(AlignFrame.this);
5691     }
5692   }
5693
5694   @Override
5695   protected void loadVcf_actionPerformed()
5696   {
5697     JalviewFileChooser chooser = new JalviewFileChooser(
5698             Cache.getProperty("LAST_DIRECTORY"));
5699     chooser.setFileView(new JalviewFileView());
5700     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5701     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5702     final AlignFrame us = this;
5703     chooser.setResponseHandler(0, new Runnable()
5704     {
5705       @Override
5706       public void run()
5707       {
5708         String choice = chooser.getSelectedFile().getPath();
5709         Cache.setProperty("LAST_DIRECTORY", choice);
5710         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5711         new VCFLoader(choice).loadVCF(seqs, us);
5712       };
5713     });
5714     chooser.showOpenDialog(null);
5715
5716   }
5717
5718 }
5719
5720 class PrintThread extends Thread
5721 {
5722   AlignmentPanel ap;
5723
5724   public PrintThread(AlignmentPanel ap)
5725   {
5726     this.ap = ap;
5727   }
5728
5729   static PageFormat pf;
5730
5731   @Override
5732   public void run()
5733   {
5734     PrinterJob printJob = PrinterJob.getPrinterJob();
5735
5736     if (pf != null)
5737     {
5738       printJob.setPrintable(ap, pf);
5739     }
5740     else
5741     {
5742       printJob.setPrintable(ap);
5743     }
5744
5745     if (printJob.printDialog())
5746     {
5747       try
5748       {
5749         printJob.print();
5750       } catch (Exception PrintException)
5751       {
5752         PrintException.printStackTrace();
5753       }
5754     }
5755   }
5756 }