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.dialogrunner.RunResponse;
  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     if (!Jalview.isHeadlessMode())
 342     {
 343       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 344     }
 345
 346     avc = new jalview.controller.AlignViewController(this, viewport,
 347             alignPanel);
 348     if (viewport.getAlignmentConservationAnnotation() == null)
 349     {
 350       // BLOSUM62Colour.setEnabled(false);
 351       conservationMenuItem.setEnabled(false);
 352       modifyConservation.setEnabled(false);
 353       // PIDColour.setEnabled(false);
 354       // abovePIDThreshold.setEnabled(false);
 355       // modifyPID.setEnabled(false);
 356     }
 357
 358     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 359             "No sort");
 360
 361     if (sortby.equals("Id"))
 362     {
 363       sortIDMenuItem_actionPerformed(null);
 364     }
 365     else if (sortby.equals("Pairwise Identity"))
 366     {
 367       sortPairwiseMenuItem_actionPerformed(null);
 368     }
 369
 370     this.alignPanel.av
 371             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 372
 373     setMenusFromViewport(viewport);
 374     buildSortByAnnotationScoresMenu();
 375     calculateTree.addActionListener(new ActionListener()
 376     {
 377
 378       @Override
 379       public void actionPerformed(ActionEvent e)
 380       {
 381         openTreePcaDialog();
 382       }
 383     });
 384     buildColourMenu();
 385
 386     if (Desktop.desktop != null)
 387     {
 388       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 389       /**
 390        * BH 2018 ignore service listeners
 391        *
 392        * @j2sNative
 393        *
 394        */
 395       {
 396         addServiceListeners();
 397       }
 398       setGUINucleotide();
 399     }
 400
 401     if (viewport.getWrapAlignment())
 402     {
 403       wrapMenuItem_actionPerformed(null);
 404     }
 405
 406     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 407     {
 408       this.overviewMenuItem_actionPerformed(null);
 409     }
 410
 411     addKeyListener();
 412
 413     final List<AlignmentPanel> selviews = new ArrayList<>();
 414     final List<AlignmentPanel> origview = new ArrayList<>();
 415     final String menuLabel = MessageManager
 416             .getString("label.copy_format_from");
 417     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 418             new ViewSetProvider()
 419             {
 420
 421               @Override
 422               public AlignmentPanel[] getAllAlignmentPanels()
 423               {
 424                 origview.clear();
 425                 origview.add(alignPanel);
 426                 // make an array of all alignment panels except for this one
 427                 List<AlignmentPanel> aps = new ArrayList<>(
 428                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 429                 aps.remove(AlignFrame.this.alignPanel);
 430                 return aps.toArray(new AlignmentPanel[aps.size()]);
 431               }
 432             }, selviews, new ItemListener()
 433             {
 434
 435               @Override
 436               public void itemStateChanged(ItemEvent e)
 437               {
 438                 if (origview.size() > 0)
 439                 {
 440                   final AlignmentPanel ap = origview.get(0);
 441
 442                   /*
 443                    * Copy the ViewStyle of the selected panel to 'this one'.
 444                    * Don't change value of 'scaleProteinAsCdna' unless copying
 445                    * from a SplitFrame.
 446                    */
 447                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 448                           .getViewStyle();
 449                   boolean fromSplitFrame = selviews.get(0)
 450                           .getAlignViewport().getCodingComplement() != null;
 451                   if (!fromSplitFrame)
 452                   {
 453                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 454                             .getViewStyle().isScaleProteinAsCdna());
 455                   }
 456                   ap.getAlignViewport().setViewStyle(vs);
 457
 458                   /*
 459                    * Also rescale ViewStyle of SplitFrame complement if there is
 460                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 461                    * the whole ViewStyle (allow cDNA protein to have different
 462                    * fonts)
 463                    */
 464                   AlignViewportI complement = ap.getAlignViewport()
 465                           .getCodingComplement();
 466                   if (complement != null && vs.isScaleProteinAsCdna())
 467                   {
 468                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 469                     ((SplitFrame) af.getSplitViewContainer())
 470                             .adjustLayout();
 471                     af.setMenusForViewport();
 472                   }
 473
 474                   ap.updateLayout();
 475                   ap.setSelected(true);
 476                   ap.alignFrame.setMenusForViewport();
 477
 478                 }
 479               }
 480             });
 481     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 482             .indexOf("devel") > -1
 483             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 484                     .indexOf("test") > -1)
 485     {
 486       formatMenu.add(vsel);
 487     }
 488     addFocusListener(new FocusAdapter()
 489     {
 490       @Override
 491       public void focusGained(FocusEvent e)
 492       {
 493         Jalview.setCurrentAlignFrame(AlignFrame.this);
 494       }
 495     });
 496
 497   }
 498
 499   /**
 500    * Change the filename and format for the alignment, and enable the 'reload'
 501    * button functionality.
 502    *
 503    * @param file
 504    *          valid filename
 505    * @param format
 506    *          format of file
 507    */
 508   public void setFileName(String file, FileFormatI format)
 509   {
 510     fileName = file;
 511     setFileFormat(format);
 512     reload.setEnabled(true);
 513   }
 514
 515   /**
 516    * JavaScript will have this, maybe others. More dependable than a file name
 517    * and maintains a reference to the actual bytes loaded.
 518    *
 519    * @param file
 520    */
 521   public void setFileObject(File file)
 522   {
 523     this.fileObject = file;
 524   }
 525
 526   /**
 527    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 528    * events
 529    */
 530   void addKeyListener()
 531   {
 532     addKeyListener(new KeyAdapter()
 533     {
 534       @Override
 535       public void keyPressed(KeyEvent evt)
 536       {
 537         if (viewport.cursorMode
 538                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 539                         && evt.getKeyCode() <= KeyEvent.VK_9)
 540                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 541                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 542                 && Character.isDigit(evt.getKeyChar()))
 543         {
 544           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 545         }
 546
 547         switch (evt.getKeyCode())
 548         {
 549
 550         case 27: // escape key
 551           deselectAllSequenceMenuItem_actionPerformed(null);
 552
 553           break;
 554
 555         case KeyEvent.VK_DOWN:
 556           if (evt.isAltDown() || !viewport.cursorMode)
 557           {
 558             moveSelectedSequences(false);
 559           }
 560           if (viewport.cursorMode)
 561           {
 562             alignPanel.getSeqPanel().moveCursor(0, 1);
 563           }
 564           break;
 565
 566         case KeyEvent.VK_UP:
 567           if (evt.isAltDown() || !viewport.cursorMode)
 568           {
 569             moveSelectedSequences(true);
 570           }
 571           if (viewport.cursorMode)
 572           {
 573             alignPanel.getSeqPanel().moveCursor(0, -1);
 574           }
 575
 576           break;
 577
 578         case KeyEvent.VK_LEFT:
 579           if (evt.isAltDown() || !viewport.cursorMode)
 580           {
 581             slideSequences(false,
 582                     alignPanel.getSeqPanel().getKeyboardNo1());
 583           }
 584           else
 585           {
 586             alignPanel.getSeqPanel().moveCursor(-1, 0);
 587           }
 588
 589           break;
 590
 591         case KeyEvent.VK_RIGHT:
 592           if (evt.isAltDown() || !viewport.cursorMode)
 593           {
 594             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 595           }
 596           else
 597           {
 598             alignPanel.getSeqPanel().moveCursor(1, 0);
 599           }
 600           break;
 601
 602         case KeyEvent.VK_SPACE:
 603           if (viewport.cursorMode)
 604           {
 605             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 606                     || evt.isShiftDown() || evt.isAltDown());
 607           }
 608           break;
 609
 610         // case KeyEvent.VK_A:
 611         // if (viewport.cursorMode)
 612         // {
 613         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 614         // //System.out.println("A");
 615         // }
 616         // break;
 617         /*
 618          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 619          * System.out.println("closing bracket"); } break;
 620          */
 621         case KeyEvent.VK_DELETE:
 622         case KeyEvent.VK_BACK_SPACE:
 623           if (!viewport.cursorMode)
 624           {
 625             cut_actionPerformed(null);
 626           }
 627           else
 628           {
 629             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 630                     || evt.isShiftDown() || evt.isAltDown());
 631           }
 632
 633           break;
 634
 635         case KeyEvent.VK_S:
 636           if (viewport.cursorMode)
 637           {
 638             alignPanel.getSeqPanel().setCursorRow();
 639           }
 640           break;
 641         case KeyEvent.VK_C:
 642           if (viewport.cursorMode && !evt.isControlDown())
 643           {
 644             alignPanel.getSeqPanel().setCursorColumn();
 645           }
 646           break;
 647         case KeyEvent.VK_P:
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().setCursorPosition();
 651           }
 652           break;
 653
 654         case KeyEvent.VK_ENTER:
 655         case KeyEvent.VK_COMMA:
 656           if (viewport.cursorMode)
 657           {
 658             alignPanel.getSeqPanel().setCursorRowAndColumn();
 659           }
 660           break;
 661
 662         case KeyEvent.VK_Q:
 663           if (viewport.cursorMode)
 664           {
 665             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 666           }
 667           break;
 668         case KeyEvent.VK_M:
 669           if (viewport.cursorMode)
 670           {
 671             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 672           }
 673           break;
 674
 675         case KeyEvent.VK_F2:
 676           viewport.cursorMode = !viewport.cursorMode;
 677           setStatus(MessageManager
 678                   .formatMessage("label.keyboard_editing_mode", new String[]
 679                   { (viewport.cursorMode ? "on" : "off") }));
 680           if (viewport.cursorMode)
 681           {
 682             ViewportRanges ranges = viewport.getRanges();
 683             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 684                     .getStartRes();
 685             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 686                     .getStartSeq();
 687           }
 688           alignPanel.getSeqPanel().seqCanvas.repaint();
 689           break;
 690
 691         case KeyEvent.VK_F1:
 692           try
 693           {
 694             Help.showHelpWindow();
 695           } catch (Exception ex)
 696           {
 697             ex.printStackTrace();
 698           }
 699           break;
 700         case KeyEvent.VK_H:
 701         {
 702           boolean toggleSeqs = !evt.isControlDown();
 703           boolean toggleCols = !evt.isShiftDown();
 704           toggleHiddenRegions(toggleSeqs, toggleCols);
 705           break;
 706         }
 707         case KeyEvent.VK_B:
 708         {
 709           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 710           boolean modifyExisting = true; // always modify, don't clear
 711                                          // evt.isShiftDown();
 712           boolean invertHighlighted = evt.isAltDown();
 713           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 714                   toggleSel);
 715           break;
 716         }
 717         case KeyEvent.VK_PAGE_UP:
 718           viewport.getRanges().pageUp();
 719           break;
 720         case KeyEvent.VK_PAGE_DOWN:
 721           viewport.getRanges().pageDown();
 722           break;
 723         }
 724       }
 725
 726       @Override
 727       public void keyReleased(KeyEvent evt)
 728       {
 729         switch (evt.getKeyCode())
 730         {
 731         case KeyEvent.VK_LEFT:
 732           if (evt.isAltDown() || !viewport.cursorMode)
 733           {
 734             viewport.firePropertyChange("alignment", null,
 735                     viewport.getAlignment().getSequences());
 736           }
 737           break;
 738
 739         case KeyEvent.VK_RIGHT:
 740           if (evt.isAltDown() || !viewport.cursorMode)
 741           {
 742             viewport.firePropertyChange("alignment", null,
 743                     viewport.getAlignment().getSequences());
 744           }
 745           break;
 746         }
 747       }
 748     });
 749   }
 750
 751   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 752   {
 753     ap.alignFrame = this;
 754     avc = new jalview.controller.AlignViewController(this, viewport,
 755             alignPanel);
 756
 757     alignPanels.add(ap);
 758
 759     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 760
 761     int aSize = alignPanels.size();
 762
 763     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 764
 765     if (aSize == 1 && ap.av.viewName == null)
 766     {
 767       this.getContentPane().add(ap, BorderLayout.CENTER);
 768     }
 769     else
 770     {
 771       if (aSize == 2)
 772       {
 773         setInitialTabVisible();
 774       }
 775
 776       expandViews.setEnabled(true);
 777       gatherViews.setEnabled(true);
 778       tabbedPane.addTab(ap.av.viewName, ap);
 779
 780       ap.setVisible(false);
 781     }
 782
 783     if (newPanel)
 784     {
 785       if (ap.av.isPadGaps())
 786       {
 787         ap.av.getAlignment().padGaps();
 788       }
 789       ap.av.updateConservation(ap);
 790       ap.av.updateConsensus(ap);
 791       ap.av.updateStrucConsensus(ap);
 792     }
 793   }
 794
 795   public void setInitialTabVisible()
 796   {
 797     expandViews.setEnabled(true);
 798     gatherViews.setEnabled(true);
 799     tabbedPane.setVisible(true);
 800     AlignmentPanel first = alignPanels.get(0);
 801     tabbedPane.addTab(first.av.viewName, first);
 802     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 803   }
 804
 805   public AlignViewport getViewport()
 806   {
 807     return viewport;
 808   }
 809
 810   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 811   private void addServiceListeners()
 812   {
 813     final java.beans.PropertyChangeListener thisListener;
 814     Desktop.instance.addJalviewPropertyChangeListener("services",
 815             thisListener = new java.beans.PropertyChangeListener()
 816             {
 817               @Override
 818               public void propertyChange(PropertyChangeEvent evt)
 819               {
 820                 // // System.out.println("Discoverer property change.");
 821                 // if (evt.getPropertyName().equals("services"))
 822                 {
 823                   SwingUtilities.invokeLater(new Runnable()
 824                   {
 825
 826                     @Override
 827                     public void run()
 828                     {
 829                       System.err.println(
 830                               "Rebuild WS Menu for service change");
 831                       BuildWebServiceMenu();
 832                     }
 833
 834                   });
 835                 }
 836               }
 837             });
 838     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 839     {
 840       @Override
 841       public void internalFrameClosed(
 842               javax.swing.event.InternalFrameEvent evt)
 843       {
 844         // System.out.println("deregistering discoverer listener");
 845         Desktop.instance.removeJalviewPropertyChangeListener("services",
 846                 thisListener);
 847         closeMenuItem_actionPerformed(true);
 848       };
 849     });
 850     // Finally, build the menu once to get current service state
 851     new Thread(new Runnable()
 852     {
 853       @Override
 854       public void run()
 855       {
 856         BuildWebServiceMenu();
 857       }
 858     }).start();
 859   }
 860
 861   /**
 862    * Configure menu items that vary according to whether the alignment is
 863    * nucleotide or protein
 864    */
 865   public void setGUINucleotide()
 866   {
 867     AlignmentI al = getViewport().getAlignment();
 868     boolean nucleotide = al.isNucleotide();
 869
 870     loadVcf.setVisible(nucleotide);
 871     showTranslation.setVisible(nucleotide);
 872     showReverse.setVisible(nucleotide);
 873     showReverseComplement.setVisible(nucleotide);
 874     conservationMenuItem.setEnabled(!nucleotide);
 875     modifyConservation
 876             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 877     showGroupConservation.setEnabled(!nucleotide);
 878
 879     showComplementMenuItem
 880             .setText(nucleotide ? MessageManager.getString("label.protein")
 881                     : MessageManager.getString("label.nucleotide"));
 882   }
 883
 884   /**
 885    * set up menus for the current viewport. This may be called after any
 886    * operation that affects the data in the current view (selection changed,
 887    * etc) to update the menus to reflect the new state.
 888    */
 889   @Override
 890   public void setMenusForViewport()
 891   {
 892     setMenusFromViewport(viewport);
 893   }
 894
 895   /**
 896    * Need to call this method when tabs are selected for multiple views, or when
 897    * loading from Jalview2XML.java
 898    *
 899    * @param av
 900    *          AlignViewport
 901    */
 902   void setMenusFromViewport(AlignViewport av)
 903   {
 904     padGapsMenuitem.setSelected(av.isPadGaps());
 905     colourTextMenuItem.setSelected(av.isShowColourText());
 906     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 907     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 908     conservationMenuItem.setSelected(av.getConservationSelected());
 909     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 910     seqLimits.setSelected(av.getShowJVSuffix());
 911     idRightAlign.setSelected(av.isRightAlignIds());
 912     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 913     renderGapsMenuItem.setSelected(av.isRenderGaps());
 914     wrapMenuItem.setSelected(av.getWrapAlignment());
 915     scaleAbove.setVisible(av.getWrapAlignment());
 916     scaleLeft.setVisible(av.getWrapAlignment());
 917     scaleRight.setVisible(av.getWrapAlignment());
 918     annotationPanelMenuItem.setState(av.isShowAnnotation());
 919     /*
 920      * Show/hide annotations only enabled if annotation panel is shown
 921      */
 922     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 923     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 924     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 925     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 926     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 927     viewTextMenuItem.setSelected(av.getShowText());
 928     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 929     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 930     showGroupConservation.setSelected(av.isShowGroupConservation());
 931     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 932     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 933     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 934
 935     ColourMenuHelper.setColourSelected(colourMenu,
 936             av.getGlobalColourScheme());
 937
 938     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 939     hiddenMarkers.setState(av.getShowHiddenMarkers());
 940     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 941     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 942     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 943     autoCalculate.setSelected(av.autoCalculateConsensus);
 944     sortByTree.setSelected(av.sortByTree);
 945     listenToViewSelections.setSelected(av.followSelection);
 946
 947     showProducts.setEnabled(canShowProducts());
 948     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 949
 950     updateEditMenuBar();
 951   }
 952
 953   /**
 954    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 955    *
 956    * @param b
 957    */
 958   public void setGroovyEnabled(boolean b)
 959   {
 960     runGroovy.setEnabled(b);
 961   }
 962
 963   private IProgressIndicator progressBar;
 964
 965   /*
 966    * (non-Javadoc)
 967    *
 968    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 969    */
 970   @Override
 971   public void setProgressBar(String message, long id)
 972   {
 973     progressBar.setProgressBar(message, id);
 974   }
 975
 976   @Override
 977   public void registerHandler(final long id,
 978           final IProgressIndicatorHandler handler)
 979   {
 980     progressBar.registerHandler(id, handler);
 981   }
 982
 983   /**
 984    *
 985    * @return true if any progress bars are still active
 986    */
 987   @Override
 988   public boolean operationInProgress()
 989   {
 990     return progressBar.operationInProgress();
 991   }
 992
 993   @Override
 994   public void setStatus(String text)
 995   {
 996     statusBar.setText(text);
 997   }
 998
 999   /*
1000    * Added so Castor Mapping file can obtain Jalview Version
1001    */
1002   public String getVersion()
1003   {
1004     return jalview.bin.Cache.getProperty("VERSION");
1005   }
1006
1007   public FeatureRenderer getFeatureRenderer()
1008   {
1009     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1010   }
1011
1012   @Override
1013   public void fetchSequence_actionPerformed(ActionEvent e)
1014   {
1015     new jalview.gui.SequenceFetcher(this);
1016   }
1017
1018   @Override
1019   public void addFromFile_actionPerformed(ActionEvent e)
1020   {
1021     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1022   }
1023
1024   @Override
1025   public void reload_actionPerformed(ActionEvent e)
1026   {
1027     if (fileName != null)
1028     {
1029       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1030       // originating file's format
1031       // TODO: work out how to recover feature settings for correct view(s) when
1032       // file is reloaded.
1033       if (FileFormat.Jalview.equals(currentFileFormat))
1034       {
1035         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1036         for (int i = 0; i < frames.length; i++)
1037         {
1038           if (frames[i] instanceof AlignFrame && frames[i] != this
1039                   && ((AlignFrame) frames[i]).fileName != null
1040                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1041           {
1042             try
1043             {
1044               frames[i].setSelected(true);
1045               Desktop.instance.closeAssociatedWindows();
1046             } catch (java.beans.PropertyVetoException ex)
1047             {
1048             }
1049           }
1050
1051         }
1052         Desktop.instance.closeAssociatedWindows();
1053
1054         FileLoader loader = new FileLoader();
1055         DataSourceType protocol = fileName.startsWith("http:")
1056                 ? DataSourceType.URL
1057                 : DataSourceType.FILE;
1058         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1059       }
1060       else
1061       {
1062         Rectangle bounds = this.getBounds();
1063
1064         FileLoader loader = new FileLoader();
1065
1066         AlignFrame newframe = null;
1067
1068         if (fileObject == null)
1069         {
1070
1071           DataSourceType protocol = (fileName.startsWith("http:")
1072                   ? DataSourceType.URL
1073                   : DataSourceType.FILE);
1074           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1075                   currentFileFormat);
1076         }
1077         else
1078         {
1079           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1080                   DataSourceType.FILE, currentFileFormat);
1081         }
1082
1083         newframe.setBounds(bounds);
1084         if (featureSettings != null && featureSettings.isShowing())
1085         {
1086           final Rectangle fspos = featureSettings.frame.getBounds();
1087           // TODO: need a 'show feature settings' function that takes bounds -
1088           // need to refactor Desktop.addFrame
1089           newframe.featureSettings_actionPerformed(null);
1090           final FeatureSettings nfs = newframe.featureSettings;
1091           SwingUtilities.invokeLater(new Runnable()
1092           {
1093             @Override
1094             public void run()
1095             {
1096               nfs.frame.setBounds(fspos);
1097             }
1098           });
1099           this.featureSettings.close();
1100           this.featureSettings = null;
1101         }
1102         this.closeMenuItem_actionPerformed(true);
1103       }
1104     }
1105   }
1106
1107   @Override
1108   public void addFromText_actionPerformed(ActionEvent e)
1109   {
1110     Desktop.instance
1111             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1112   }
1113
1114   @Override
1115   public void addFromURL_actionPerformed(ActionEvent e)
1116   {
1117     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1118   }
1119
1120   @Override
1121   public void save_actionPerformed(ActionEvent e)
1122   {
1123     if (fileName == null || (currentFileFormat == null)
1124             || fileName.startsWith("http"))
1125     {
1126       saveAs_actionPerformed();
1127     }
1128     else
1129     {
1130       saveAlignment(fileName, currentFileFormat);
1131     }
1132   }
1133
1134   /**
1135    * Saves the alignment to a file with a name chosen by the user, if necessary
1136    * warning if a file would be overwritten
1137    */
1138   @Override
1139   public void saveAs_actionPerformed()
1140   {
1141     String format = currentFileFormat == null ? null
1142             : currentFileFormat.getName();
1143     JalviewFileChooser chooser = JalviewFileChooser
1144             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1145
1146     chooser.setFileView(new JalviewFileView());
1147     chooser.setDialogTitle(
1148             MessageManager.getString("label.save_alignment_to_file"));
1149     chooser.setToolTipText(MessageManager.getString("action.save"));
1150
1151     int value = chooser.showSaveDialog(this);
1152
1153     if (value != JalviewFileChooser.APPROVE_OPTION)
1154     {
1155       return;
1156     }
1157     currentFileFormat = chooser.getSelectedFormat();
1158     // todo is this (2005) test now obsolete - value is never null?
1159     while (currentFileFormat == null)
1160     {
1161       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1162               MessageManager
1163                       .getString("label.select_file_format_before_saving"),
1164               MessageManager.getString("label.file_format_not_specified"),
1165               JvOptionPane.WARNING_MESSAGE);
1166       currentFileFormat = chooser.getSelectedFormat();
1167       value = chooser.showSaveDialog(this);
1168       if (value != JalviewFileChooser.APPROVE_OPTION)
1169       {
1170         return;
1171       }
1172     }
1173
1174     fileName = chooser.getSelectedFile().getPath();
1175
1176     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1177     Cache.setProperty("LAST_DIRECTORY", fileName);
1178     saveAlignment(fileName, currentFileFormat);
1179   }
1180
1181   boolean lastSaveSuccessful = false;
1182
1183   FileFormatI lastFormatSaved;
1184
1185   String lastFilenameSaved;
1186
1187   /**
1188    * Raise a dialog or status message for the last call to saveAlignment.
1189    *
1190    * @return true if last call to saveAlignment(file, format) was successful.
1191    */
1192   public boolean isSaveAlignmentSuccessful()
1193   {
1194
1195     if (!lastSaveSuccessful)
1196     {
1197       JvOptionPane.showInternalMessageDialog(this, MessageManager
1198               .formatMessage("label.couldnt_save_file", new Object[]
1199               { lastFilenameSaved }),
1200               MessageManager.getString("label.error_saving_file"),
1201               JvOptionPane.WARNING_MESSAGE);
1202     }
1203     else
1204     {
1205
1206       setStatus(MessageManager.formatMessage(
1207               "label.successfully_saved_to_file_in_format", new Object[]
1208               { lastFilenameSaved, lastFormatSaved }));
1209
1210     }
1211     return lastSaveSuccessful;
1212   }
1213
1214   /**
1215    * Saves the alignment to the specified file path, in the specified format,
1216    * which may be an alignment format, or Jalview project format. If the
1217    * alignment has hidden regions, or the format is one capable of including
1218    * non-sequence data (features, annotations, groups), then the user may be
1219    * prompted to specify what to include in the output.
1220    *
1221    * @param file
1222    * @param format
1223    */
1224   public void saveAlignment(String file, FileFormatI format)
1225   {
1226     lastSaveSuccessful = false;
1227     lastFilenameSaved = file;
1228     lastFormatSaved = format;
1229
1230     if (FileFormat.Jalview.equals(format))
1231     {
1232       String shortName = title;
1233       if (shortName.indexOf(File.separatorChar) > -1)
1234       {
1235         shortName = shortName.substring(
1236                 shortName.lastIndexOf(File.separatorChar) + 1);
1237       }
1238       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1239               shortName);
1240       return;
1241     }
1242
1243     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1244     RunResponse cancelAction = new RunResponse(JvOptionPane.CANCEL_OPTION)
1245     {
1246       @Override
1247       public void run()
1248       {
1249         lastSaveSuccessful = false;
1250       }
1251     };
1252     RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
1253     {
1254       @Override
1255       public void run()
1256       {
1257         // todo defer this to inside formatSequences (or later)
1258         AlignmentExportData exportData = viewport
1259                 .getAlignExportData(options);
1260         String output = new FormatAdapter(alignPanel, options)
1261                 .formatSequences(format, exportData.getAlignment(),
1262                         exportData.getOmitHidden(),
1263                         exportData.getStartEndPostions(),
1264                         viewport.getAlignment().getHiddenColumns());
1265         if (output == null)
1266         {
1267           lastSaveSuccessful = false;
1268         }
1269         else
1270         {
1271           try
1272           {
1273             PrintWriter out = new PrintWriter(new FileWriter(file));
1274             out.print(output);
1275             out.close();
1276             AlignFrame.this.setTitle(file);
1277             setStatus(MessageManager.formatMessage(
1278                     "label.successfully_saved_to_file_in_format",
1279                     new Object[]
1280                     { fileName, format.getName() }));
1281           } catch (Exception ex)
1282           {
1283             lastSaveSuccessful = false;
1284             ex.printStackTrace();
1285           }
1286         }
1287       }
1288     };
1289
1290     /*
1291      * show dialog with export options if applicable; else just do it
1292      */
1293     if (AlignExportOptions.isNeeded(viewport, format))
1294     {
1295       AlignExportOptions choices = new AlignExportOptions(
1296               alignPanel.getAlignViewport(), format, options);
1297       choices.setResponseAction(outputAction);
1298       choices.setResponseAction(cancelAction);
1299       choices.showDialog();
1300     }
1301     else
1302     {
1303       outputAction.run();
1304     }
1305   }
1306
1307   /**
1308    * Outputs the alignment to textbox in the requested format, if necessary
1309    * first prompting the user for whether to include hidden regions or
1310    * non-sequence data
1311    *
1312    * @param fileFormatName
1313    */
1314   @Override
1315   protected void outputText_actionPerformed(String fileFormatName)
1316   {
1317     FileFormatI fileFormat = FileFormats.getInstance()
1318             .forName(fileFormatName);
1319     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1320     RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
1321     {
1322       @Override
1323       public void run()
1324       {
1325         // todo defer this to inside formatSequences (or later)
1326         AlignmentExportData exportData = viewport
1327                 .getAlignExportData(options);
1328         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1329         cap.setForInput(null);
1330         try
1331         {
1332           FileFormatI format = fileFormat;
1333           cap.setText(new FormatAdapter(alignPanel, options)
1334                   .formatSequences(format, exportData.getAlignment(),
1335                           exportData.getOmitHidden(),
1336                           exportData.getStartEndPostions(),
1337                           viewport.getAlignment().getHiddenColumns()));
1338           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1339                   "label.alignment_output_command", new Object[]
1340                   { fileFormat.getName() }), 600, 500);
1341         } catch (OutOfMemoryError oom)
1342         {
1343           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1344                   oom);
1345           cap.dispose();
1346         }
1347       }
1348     };
1349
1350     /*
1351      * show dialog with export options if applicable; else just do it
1352      */
1353     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1354     {
1355       AlignExportOptions choices = new AlignExportOptions(
1356               alignPanel.getAlignViewport(), fileFormat, options);
1357       choices.setResponseAction(outputAction);
1358       choices.showDialog();
1359     }
1360     else
1361     {
1362       outputAction.run();
1363     }
1364   }
1365
1366   /**
1367    * DOCUMENT ME!
1368    *
1369    * @param e
1370    *          DOCUMENT ME!
1371    */
1372   @Override
1373   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1374   {
1375     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1376     htmlSVG.exportHTML(null);
1377   }
1378
1379   @Override
1380   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1381   {
1382     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1383     bjs.exportHTML(null);
1384   }
1385
1386   public void createImageMap(File file, String image)
1387   {
1388     alignPanel.makePNGImageMap(file, image);
1389   }
1390
1391   /**
1392    * Creates a PNG image of the alignment and writes it to the given file. If
1393    * the file is null, the user is prompted to choose a file.
1394    *
1395    * @param f
1396    */
1397   @Override
1398   public void createPNG(File f)
1399   {
1400     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1401   }
1402
1403   /**
1404    * Creates an EPS 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 createEPS(File f)
1411   {
1412     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1413   }
1414
1415   /**
1416    * Creates an SVG 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 createSVG(File f)
1423   {
1424     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1425   }
1426
1427   @Override
1428   public void pageSetup_actionPerformed(ActionEvent e)
1429   {
1430     PrinterJob printJob = PrinterJob.getPrinterJob();
1431     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1432   }
1433
1434   /**
1435    * DOCUMENT ME!
1436    *
1437    * @param e
1438    *          DOCUMENT ME!
1439    */
1440   @Override
1441   public void printMenuItem_actionPerformed(ActionEvent e)
1442   {
1443     // Putting in a thread avoids Swing painting problems
1444     PrintThread thread = new PrintThread(alignPanel);
1445     thread.start();
1446   }
1447
1448   @Override
1449   public void exportFeatures_actionPerformed(ActionEvent e)
1450   {
1451     new AnnotationExporter(alignPanel).exportFeatures();
1452   }
1453
1454   @Override
1455   public void exportAnnotations_actionPerformed(ActionEvent e)
1456   {
1457     new AnnotationExporter(alignPanel).exportAnnotations();
1458   }
1459
1460   @Override
1461   public void associatedData_actionPerformed(ActionEvent e)
1462   {
1463     final JalviewFileChooser chooser = new JalviewFileChooser(
1464             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1465     chooser.setFileView(new JalviewFileView());
1466     chooser.setDialogTitle(
1467             MessageManager.getString("label.load_jalview_annotations"));
1468     chooser.setToolTipText(
1469             MessageManager.getString("label.load_jalview_annotations"));
1470     chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1471     {
1472
1473       @Override
1474       public void run()
1475       {
1476         String choice = chooser.getSelectedFile().getPath();
1477         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1478         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1479       }
1480
1481     });
1482
1483     chooser.openDialog(this);
1484   }
1485
1486   /**
1487    * Close the current view or all views in the alignment frame. If the frame
1488    * only contains one view then the alignment will be removed from memory.
1489    *
1490    * @param closeAllTabs
1491    */
1492   @Override
1493   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1494   {
1495     if (alignPanels != null && alignPanels.size() < 2)
1496     {
1497       closeAllTabs = true;
1498     }
1499
1500     try
1501     {
1502       if (alignPanels != null)
1503       {
1504         if (closeAllTabs)
1505         {
1506           if (this.isClosed())
1507           {
1508             // really close all the windows - otherwise wait till
1509             // setClosed(true) is called
1510             for (int i = 0; i < alignPanels.size(); i++)
1511             {
1512               AlignmentPanel ap = alignPanels.get(i);
1513               ap.closePanel();
1514             }
1515           }
1516         }
1517         else
1518         {
1519           closeView(alignPanel);
1520         }
1521       }
1522
1523       if (closeAllTabs)
1524       {
1525         /*
1526          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1527          * be called recursively, with the frame now in 'closed' state
1528          */
1529         this.setClosed(true);
1530       }
1531     } catch (Exception ex)
1532     {
1533       ex.printStackTrace();
1534     }
1535   }
1536
1537   /**
1538    * Close the specified panel and close up tabs appropriately.
1539    *
1540    * @param panelToClose
1541    */
1542   public void closeView(AlignmentPanel panelToClose)
1543   {
1544     int index = tabbedPane.getSelectedIndex();
1545     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1546     alignPanels.remove(panelToClose);
1547     panelToClose.closePanel();
1548     panelToClose = null;
1549
1550     tabbedPane.removeTabAt(closedindex);
1551     tabbedPane.validate();
1552
1553     if (index > closedindex || index == tabbedPane.getTabCount())
1554     {
1555       // modify currently selected tab index if necessary.
1556       index--;
1557     }
1558
1559     this.tabSelectionChanged(index);
1560   }
1561
1562   /**
1563    * DOCUMENT ME!
1564    */
1565   void updateEditMenuBar()
1566   {
1567
1568     if (viewport.getHistoryList().size() > 0)
1569     {
1570       undoMenuItem.setEnabled(true);
1571       CommandI command = viewport.getHistoryList().peek();
1572       undoMenuItem.setText(MessageManager
1573               .formatMessage("label.undo_command", new Object[]
1574               { command.getDescription() }));
1575     }
1576     else
1577     {
1578       undoMenuItem.setEnabled(false);
1579       undoMenuItem.setText(MessageManager.getString("action.undo"));
1580     }
1581
1582     if (viewport.getRedoList().size() > 0)
1583     {
1584       redoMenuItem.setEnabled(true);
1585
1586       CommandI command = viewport.getRedoList().peek();
1587       redoMenuItem.setText(MessageManager
1588               .formatMessage("label.redo_command", new Object[]
1589               { command.getDescription() }));
1590     }
1591     else
1592     {
1593       redoMenuItem.setEnabled(false);
1594       redoMenuItem.setText(MessageManager.getString("action.redo"));
1595     }
1596   }
1597
1598   @Override
1599   public void addHistoryItem(CommandI command)
1600   {
1601     if (command.getSize() > 0)
1602     {
1603       viewport.addToHistoryList(command);
1604       viewport.clearRedoList();
1605       updateEditMenuBar();
1606       viewport.updateHiddenColumns();
1607       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1608       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609       // viewport.getColumnSelection()
1610       // .getHiddenColumns().size() > 0);
1611     }
1612   }
1613
1614   /**
1615    *
1616    * @return alignment objects for all views
1617    */
1618   AlignmentI[] getViewAlignments()
1619   {
1620     if (alignPanels != null)
1621     {
1622       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1623       int i = 0;
1624       for (AlignmentPanel ap : alignPanels)
1625       {
1626         als[i++] = ap.av.getAlignment();
1627       }
1628       return als;
1629     }
1630     if (viewport != null)
1631     {
1632       return new AlignmentI[] { viewport.getAlignment() };
1633     }
1634     return null;
1635   }
1636
1637   /**
1638    * DOCUMENT ME!
1639    *
1640    * @param e
1641    *          DOCUMENT ME!
1642    */
1643   @Override
1644   protected void undoMenuItem_actionPerformed(ActionEvent e)
1645   {
1646     if (viewport.getHistoryList().isEmpty())
1647     {
1648       return;
1649     }
1650     CommandI command = viewport.getHistoryList().pop();
1651     viewport.addToRedoList(command);
1652     command.undoCommand(getViewAlignments());
1653
1654     AlignmentViewport originalSource = getOriginatingSource(command);
1655     updateEditMenuBar();
1656
1657     if (originalSource != null)
1658     {
1659       if (originalSource != viewport)
1660       {
1661         Cache.log.warn(
1662                 "Implementation worry: mismatch of viewport origin for undo");
1663       }
1664       originalSource.updateHiddenColumns();
1665       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666       // null
1667       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1668       // viewport.getColumnSelection()
1669       // .getHiddenColumns().size() > 0);
1670       originalSource.firePropertyChange("alignment", null,
1671               originalSource.getAlignment().getSequences());
1672     }
1673   }
1674
1675   /**
1676    * DOCUMENT ME!
1677    *
1678    * @param e
1679    *          DOCUMENT ME!
1680    */
1681   @Override
1682   protected void redoMenuItem_actionPerformed(ActionEvent e)
1683   {
1684     if (viewport.getRedoList().size() < 1)
1685     {
1686       return;
1687     }
1688
1689     CommandI command = viewport.getRedoList().pop();
1690     viewport.addToHistoryList(command);
1691     command.doCommand(getViewAlignments());
1692
1693     AlignmentViewport originalSource = getOriginatingSource(command);
1694     updateEditMenuBar();
1695
1696     if (originalSource != null)
1697     {
1698
1699       if (originalSource != viewport)
1700       {
1701         Cache.log.warn(
1702                 "Implementation worry: mismatch of viewport origin for redo");
1703       }
1704       originalSource.updateHiddenColumns();
1705       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1706       // null
1707       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1708       // viewport.getColumnSelection()
1709       // .getHiddenColumns().size() > 0);
1710       originalSource.firePropertyChange("alignment", null,
1711               originalSource.getAlignment().getSequences());
1712     }
1713   }
1714
1715   AlignmentViewport getOriginatingSource(CommandI command)
1716   {
1717     AlignmentViewport originalSource = null;
1718     // For sequence removal and addition, we need to fire
1719     // the property change event FROM the viewport where the
1720     // original alignment was altered
1721     AlignmentI al = null;
1722     if (command instanceof EditCommand)
1723     {
1724       EditCommand editCommand = (EditCommand) command;
1725       al = editCommand.getAlignment();
1726       List<Component> comps = PaintRefresher.components
1727               .get(viewport.getSequenceSetId());
1728
1729       for (Component comp : comps)
1730       {
1731         if (comp instanceof AlignmentPanel)
1732         {
1733           if (al == ((AlignmentPanel) comp).av.getAlignment())
1734           {
1735             originalSource = ((AlignmentPanel) comp).av;
1736             break;
1737           }
1738         }
1739       }
1740     }
1741
1742     if (originalSource == null)
1743     {
1744       // The original view is closed, we must validate
1745       // the current view against the closed view first
1746       if (al != null)
1747       {
1748         PaintRefresher.validateSequences(al, viewport.getAlignment());
1749       }
1750
1751       originalSource = viewport;
1752     }
1753
1754     return originalSource;
1755   }
1756
1757   /**
1758    * DOCUMENT ME!
1759    *
1760    * @param up
1761    *          DOCUMENT ME!
1762    */
1763   public void moveSelectedSequences(boolean up)
1764   {
1765     SequenceGroup sg = viewport.getSelectionGroup();
1766
1767     if (sg == null)
1768     {
1769       return;
1770     }
1771     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1772             viewport.getHiddenRepSequences(), up);
1773     alignPanel.paintAlignment(true, false);
1774   }
1775
1776   synchronized void slideSequences(boolean right, int size)
1777   {
1778     List<SequenceI> sg = new ArrayList<>();
1779     if (viewport.cursorMode)
1780     {
1781       sg.add(viewport.getAlignment()
1782               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1783     }
1784     else if (viewport.getSelectionGroup() != null
1785             && viewport.getSelectionGroup().getSize() != viewport
1786                     .getAlignment().getHeight())
1787     {
1788       sg = viewport.getSelectionGroup()
1789               .getSequences(viewport.getHiddenRepSequences());
1790     }
1791
1792     if (sg.size() < 1)
1793     {
1794       return;
1795     }
1796
1797     List<SequenceI> invertGroup = new ArrayList<>();
1798
1799     for (SequenceI seq : viewport.getAlignment().getSequences())
1800     {
1801       if (!sg.contains(seq))
1802       {
1803         invertGroup.add(seq);
1804       }
1805     }
1806
1807     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1808
1809     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1810     for (int i = 0; i < invertGroup.size(); i++)
1811     {
1812       seqs2[i] = invertGroup.get(i);
1813     }
1814
1815     SlideSequencesCommand ssc;
1816     if (right)
1817     {
1818       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1819               viewport.getGapCharacter());
1820     }
1821     else
1822     {
1823       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1824               viewport.getGapCharacter());
1825     }
1826
1827     int groupAdjustment = 0;
1828     if (ssc.getGapsInsertedBegin() && right)
1829     {
1830       if (viewport.cursorMode)
1831       {
1832         alignPanel.getSeqPanel().moveCursor(size, 0);
1833       }
1834       else
1835       {
1836         groupAdjustment = size;
1837       }
1838     }
1839     else if (!ssc.getGapsInsertedBegin() && !right)
1840     {
1841       if (viewport.cursorMode)
1842       {
1843         alignPanel.getSeqPanel().moveCursor(-size, 0);
1844       }
1845       else
1846       {
1847         groupAdjustment = -size;
1848       }
1849     }
1850
1851     if (groupAdjustment != 0)
1852     {
1853       viewport.getSelectionGroup().setStartRes(
1854               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1855       viewport.getSelectionGroup().setEndRes(
1856               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1857     }
1858
1859     /*
1860      * just extend the last slide command if compatible; but not if in
1861      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1862      */
1863     boolean appendHistoryItem = false;
1864     Deque<CommandI> historyList = viewport.getHistoryList();
1865     boolean inSplitFrame = getSplitViewContainer() != null;
1866     if (!inSplitFrame && historyList != null && historyList.size() > 0
1867             && historyList.peek() instanceof SlideSequencesCommand)
1868     {
1869       appendHistoryItem = ssc.appendSlideCommand(
1870               (SlideSequencesCommand) historyList.peek());
1871     }
1872
1873     if (!appendHistoryItem)
1874     {
1875       addHistoryItem(ssc);
1876     }
1877
1878     repaint();
1879   }
1880
1881   /**
1882    * DOCUMENT ME!
1883    *
1884    * @param e
1885    *          DOCUMENT ME!
1886    */
1887   @Override
1888   protected void copy_actionPerformed(ActionEvent e)
1889   {
1890     if (viewport.getSelectionGroup() == null)
1891     {
1892       return;
1893     }
1894     // TODO: preserve the ordering of displayed alignment annotation in any
1895     // internal paste (particularly sequence associated annotation)
1896     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1897     String[] omitHidden = null;
1898
1899     if (viewport.hasHiddenColumns())
1900     {
1901       omitHidden = viewport.getViewAsString(true);
1902     }
1903
1904     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1905             seqs, omitHidden, null);
1906
1907     StringSelection ss = new StringSelection(output);
1908
1909     try
1910     {
1911       jalview.gui.Desktop.internalCopy = true;
1912       // Its really worth setting the clipboard contents
1913       // to empty before setting the large StringSelection!!
1914       Toolkit.getDefaultToolkit().getSystemClipboard()
1915               .setContents(new StringSelection(""), null);
1916
1917       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1918               Desktop.instance);
1919     } catch (OutOfMemoryError er)
1920     {
1921       new OOMWarning("copying region", er);
1922       return;
1923     }
1924
1925     HiddenColumns hiddenColumns = null;
1926     if (viewport.hasHiddenColumns())
1927     {
1928       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1929       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1930
1931       // create new HiddenColumns object with copy of hidden regions
1932       // between startRes and endRes, offset by startRes
1933       hiddenColumns = new HiddenColumns(
1934               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1935               hiddenCutoff, hiddenOffset);
1936     }
1937
1938     Desktop.jalviewClipboard = new Object[] { seqs,
1939         viewport.getAlignment().getDataset(), hiddenColumns };
1940     setStatus(MessageManager.formatMessage(
1941             "label.copied_sequences_to_clipboard", new Object[]
1942             { Integer.valueOf(seqs.length).toString() }));
1943   }
1944
1945   /**
1946    * DOCUMENT ME!
1947    *
1948    * @param e
1949    *          DOCUMENT ME!
1950    */
1951   @Override
1952   protected void pasteNew_actionPerformed(ActionEvent e)
1953   {
1954     paste(true);
1955   }
1956
1957   /**
1958    * DOCUMENT ME!
1959    *
1960    * @param e
1961    *          DOCUMENT ME!
1962    */
1963   @Override
1964   protected void pasteThis_actionPerformed(ActionEvent e)
1965   {
1966     paste(false);
1967   }
1968
1969   /**
1970    * Paste contents of Jalview clipboard
1971    *
1972    * @param newAlignment
1973    *          true to paste to a new alignment, otherwise add to this.
1974    */
1975   void paste(boolean newAlignment)
1976   {
1977     boolean externalPaste = true;
1978     try
1979     {
1980       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1981       Transferable contents = c.getContents(this);
1982
1983       if (contents == null)
1984       {
1985         return;
1986       }
1987
1988       String str;
1989       FileFormatI format;
1990       try
1991       {
1992         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1993         if (str.length() < 1)
1994         {
1995           return;
1996         }
1997
1998         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1999
2000       } catch (OutOfMemoryError er)
2001       {
2002         new OOMWarning("Out of memory pasting sequences!!", er);
2003         return;
2004       }
2005
2006       SequenceI[] sequences;
2007       boolean annotationAdded = false;
2008       AlignmentI alignment = null;
2009
2010       if (Desktop.jalviewClipboard != null)
2011       {
2012         // The clipboard was filled from within Jalview, we must use the
2013         // sequences
2014         // And dataset from the copied alignment
2015         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2016         // be doubly sure that we create *new* sequence objects.
2017         sequences = new SequenceI[newseq.length];
2018         for (int i = 0; i < newseq.length; i++)
2019         {
2020           sequences[i] = new Sequence(newseq[i]);
2021         }
2022         alignment = new Alignment(sequences);
2023         externalPaste = false;
2024       }
2025       else
2026       {
2027         // parse the clipboard as an alignment.
2028         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2029                 format);
2030         sequences = alignment.getSequencesArray();
2031       }
2032
2033       int alwidth = 0;
2034       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2035       int fgroup = -1;
2036
2037       if (newAlignment)
2038       {
2039
2040         if (Desktop.jalviewClipboard != null)
2041         {
2042           // dataset is inherited
2043           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2044         }
2045         else
2046         {
2047           // new dataset is constructed
2048           alignment.setDataset(null);
2049         }
2050         alwidth = alignment.getWidth() + 1;
2051       }
2052       else
2053       {
2054         AlignmentI pastedal = alignment; // preserve pasted alignment object
2055         // Add pasted sequences and dataset into existing alignment.
2056         alignment = viewport.getAlignment();
2057         alwidth = alignment.getWidth() + 1;
2058         // decide if we need to import sequences from an existing dataset
2059         boolean importDs = Desktop.jalviewClipboard != null
2060                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2061         // importDs==true instructs us to copy over new dataset sequences from
2062         // an existing alignment
2063         Vector newDs = (importDs) ? new Vector() : null; // used to create
2064         // minimum dataset set
2065
2066         for (int i = 0; i < sequences.length; i++)
2067         {
2068           if (importDs)
2069           {
2070             newDs.addElement(null);
2071           }
2072           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2073           // paste
2074           if (importDs && ds != null)
2075           {
2076             if (!newDs.contains(ds))
2077             {
2078               newDs.setElementAt(ds, i);
2079               ds = new Sequence(ds);
2080               // update with new dataset sequence
2081               sequences[i].setDatasetSequence(ds);
2082             }
2083             else
2084             {
2085               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2086             }
2087           }
2088           else
2089           {
2090             // copy and derive new dataset sequence
2091             sequences[i] = sequences[i].deriveSequence();
2092             alignment.getDataset()
2093                     .addSequence(sequences[i].getDatasetSequence());
2094             // TODO: avoid creation of duplicate dataset sequences with a
2095             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2096           }
2097           alignment.addSequence(sequences[i]); // merges dataset
2098         }
2099         if (newDs != null)
2100         {
2101           newDs.clear(); // tidy up
2102         }
2103         if (alignment.getAlignmentAnnotation() != null)
2104         {
2105           for (AlignmentAnnotation alan : alignment
2106                   .getAlignmentAnnotation())
2107           {
2108             if (alan.graphGroup > fgroup)
2109             {
2110               fgroup = alan.graphGroup;
2111             }
2112           }
2113         }
2114         if (pastedal.getAlignmentAnnotation() != null)
2115         {
2116           // Add any annotation attached to alignment.
2117           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2118           for (int i = 0; i < alann.length; i++)
2119           {
2120             annotationAdded = true;
2121             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2122             {
2123               AlignmentAnnotation newann = new AlignmentAnnotation(
2124                       alann[i]);
2125               if (newann.graphGroup > -1)
2126               {
2127                 if (newGraphGroups.size() <= newann.graphGroup
2128                         || newGraphGroups.get(newann.graphGroup) == null)
2129                 {
2130                   for (int q = newGraphGroups
2131                           .size(); q <= newann.graphGroup; q++)
2132                   {
2133                     newGraphGroups.add(q, null);
2134                   }
2135                   newGraphGroups.set(newann.graphGroup,
2136                           new Integer(++fgroup));
2137                 }
2138                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2139                         .intValue();
2140               }
2141
2142               newann.padAnnotation(alwidth);
2143               alignment.addAnnotation(newann);
2144             }
2145           }
2146         }
2147       }
2148       if (!newAlignment)
2149       {
2150         // /////
2151         // ADD HISTORY ITEM
2152         //
2153         addHistoryItem(new EditCommand(
2154                 MessageManager.getString("label.add_sequences"),
2155                 Action.PASTE, sequences, 0, alignment.getWidth(),
2156                 alignment));
2157       }
2158       // Add any annotations attached to sequences
2159       for (int i = 0; i < sequences.length; i++)
2160       {
2161         if (sequences[i].getAnnotation() != null)
2162         {
2163           AlignmentAnnotation newann;
2164           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2165           {
2166             annotationAdded = true;
2167             newann = sequences[i].getAnnotation()[a];
2168             newann.adjustForAlignment();
2169             newann.padAnnotation(alwidth);
2170             if (newann.graphGroup > -1)
2171             {
2172               if (newann.graphGroup > -1)
2173               {
2174                 if (newGraphGroups.size() <= newann.graphGroup
2175                         || newGraphGroups.get(newann.graphGroup) == null)
2176                 {
2177                   for (int q = newGraphGroups
2178                           .size(); q <= newann.graphGroup; q++)
2179                   {
2180                     newGraphGroups.add(q, null);
2181                   }
2182                   newGraphGroups.set(newann.graphGroup,
2183                           new Integer(++fgroup));
2184                 }
2185                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2186                         .intValue();
2187               }
2188             }
2189             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2190             // was
2191             // duplicated
2192             // earlier
2193             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2194                     a);
2195           }
2196         }
2197       }
2198       if (!newAlignment)
2199       {
2200
2201         // propagate alignment changed.
2202         viewport.getRanges().setEndSeq(alignment.getHeight());
2203         if (annotationAdded)
2204         {
2205           // Duplicate sequence annotation in all views.
2206           AlignmentI[] alview = this.getViewAlignments();
2207           for (int i = 0; i < sequences.length; i++)
2208           {
2209             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2210             if (sann == null)
2211             {
2212               continue;
2213             }
2214             for (int avnum = 0; avnum < alview.length; avnum++)
2215             {
2216               if (alview[avnum] != alignment)
2217               {
2218                 // duplicate in a view other than the one with input focus
2219                 int avwidth = alview[avnum].getWidth() + 1;
2220                 // this relies on sann being preserved after we
2221                 // modify the sequence's annotation array for each duplication
2222                 for (int a = 0; a < sann.length; a++)
2223                 {
2224                   AlignmentAnnotation newann = new AlignmentAnnotation(
2225                           sann[a]);
2226                   sequences[i].addAlignmentAnnotation(newann);
2227                   newann.padAnnotation(avwidth);
2228                   alview[avnum].addAnnotation(newann); // annotation was
2229                   // duplicated earlier
2230                   // TODO JAL-1145 graphGroups are not updated for sequence
2231                   // annotation added to several views. This may cause
2232                   // strangeness
2233                   alview[avnum].setAnnotationIndex(newann, a);
2234                 }
2235               }
2236             }
2237           }
2238           buildSortByAnnotationScoresMenu();
2239         }
2240         viewport.firePropertyChange("alignment", null,
2241                 alignment.getSequences());
2242         if (alignPanels != null)
2243         {
2244           for (AlignmentPanel ap : alignPanels)
2245           {
2246             ap.validateAnnotationDimensions(false);
2247           }
2248         }
2249         else
2250         {
2251           alignPanel.validateAnnotationDimensions(false);
2252         }
2253
2254       }
2255       else
2256       {
2257         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2258                 DEFAULT_HEIGHT);
2259         String newtitle = new String("Copied sequences");
2260
2261         if (Desktop.jalviewClipboard != null
2262                 && Desktop.jalviewClipboard[2] != null)
2263         {
2264           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2265           af.viewport.setHiddenColumns(hc);
2266         }
2267
2268         // >>>This is a fix for the moment, until a better solution is
2269         // found!!<<<
2270         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2271                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2272                         .getFeatureRenderer());
2273
2274         // TODO: maintain provenance of an alignment, rather than just make the
2275         // title a concatenation of operations.
2276         if (!externalPaste)
2277         {
2278           if (title.startsWith("Copied sequences"))
2279           {
2280             newtitle = title;
2281           }
2282           else
2283           {
2284             newtitle = newtitle.concat("- from " + title);
2285           }
2286         }
2287         else
2288         {
2289           newtitle = new String("Pasted sequences");
2290         }
2291
2292         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2293                 DEFAULT_HEIGHT);
2294
2295       }
2296
2297     } catch (Exception ex)
2298     {
2299       ex.printStackTrace();
2300       System.out.println("Exception whilst pasting: " + ex);
2301       // could be anything being pasted in here
2302     }
2303
2304   }
2305
2306   @Override
2307   protected void expand_newalign(ActionEvent e)
2308   {
2309     try
2310     {
2311       AlignmentI alignment = AlignmentUtils
2312               .expandContext(getViewport().getAlignment(), -1);
2313       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2314               DEFAULT_HEIGHT);
2315       String newtitle = new String("Flanking alignment");
2316
2317       if (Desktop.jalviewClipboard != null
2318               && Desktop.jalviewClipboard[2] != null)
2319       {
2320         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2321         af.viewport.setHiddenColumns(hc);
2322       }
2323
2324       // >>>This is a fix for the moment, until a better solution is
2325       // found!!<<<
2326       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2327               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2328                       .getFeatureRenderer());
2329
2330       // TODO: maintain provenance of an alignment, rather than just make the
2331       // title a concatenation of operations.
2332       {
2333         if (title.startsWith("Copied sequences"))
2334         {
2335           newtitle = title;
2336         }
2337         else
2338         {
2339           newtitle = newtitle.concat("- from " + title);
2340         }
2341       }
2342
2343       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2344
2345     } catch (Exception ex)
2346     {
2347       ex.printStackTrace();
2348       System.out.println("Exception whilst pasting: " + ex);
2349       // could be anything being pasted in here
2350     } catch (OutOfMemoryError oom)
2351     {
2352       new OOMWarning("Viewing flanking region of alignment", oom);
2353     }
2354   }
2355
2356   /**
2357    * DOCUMENT ME!
2358    *
2359    * @param e
2360    *          DOCUMENT ME!
2361    */
2362   @Override
2363   protected void cut_actionPerformed(ActionEvent e)
2364   {
2365     copy_actionPerformed(null);
2366     delete_actionPerformed(null);
2367   }
2368
2369   /**
2370    * DOCUMENT ME!
2371    *
2372    * @param e
2373    *          DOCUMENT ME!
2374    */
2375   @Override
2376   protected void delete_actionPerformed(ActionEvent evt)
2377   {
2378
2379     SequenceGroup sg = viewport.getSelectionGroup();
2380     if (sg == null)
2381     {
2382       return;
2383     }
2384
2385     /*
2386      * If the cut affects all sequences, warn, remove highlighted columns
2387      */
2388     if (sg.getSize() == viewport.getAlignment().getHeight())
2389     {
2390       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2391               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2392       if (isEntireAlignWidth)
2393       {
2394         int confirm = JvOptionPane.showConfirmDialog(this,
2395                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2396                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2397                 JvOptionPane.OK_CANCEL_OPTION);
2398
2399         if (confirm == JvOptionPane.CANCEL_OPTION
2400                 || confirm == JvOptionPane.CLOSED_OPTION)
2401         {
2402           return;
2403         }
2404       }
2405       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2406               sg.getEndRes() + 1);
2407     }
2408     SequenceI[] cut = sg.getSequences()
2409             .toArray(new SequenceI[sg.getSize()]);
2410
2411     addHistoryItem(new EditCommand(
2412             MessageManager.getString("label.cut_sequences"), Action.CUT,
2413             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2414             viewport.getAlignment()));
2415
2416     viewport.setSelectionGroup(null);
2417     viewport.sendSelection();
2418     viewport.getAlignment().deleteGroup(sg);
2419
2420     viewport.firePropertyChange("alignment", null,
2421             viewport.getAlignment().getSequences());
2422     if (viewport.getAlignment().getHeight() < 1)
2423     {
2424       try
2425       {
2426         this.setClosed(true);
2427       } catch (Exception ex)
2428       {
2429       }
2430     }
2431   }
2432
2433   /**
2434    * DOCUMENT ME!
2435    *
2436    * @param e
2437    *          DOCUMENT ME!
2438    */
2439   @Override
2440   protected void deleteGroups_actionPerformed(ActionEvent e)
2441   {
2442     if (avc.deleteGroups())
2443     {
2444       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2445       alignPanel.updateAnnotation();
2446       alignPanel.paintAlignment(true, true);
2447     }
2448   }
2449
2450   /**
2451    * DOCUMENT ME!
2452    *
2453    * @param e
2454    *          DOCUMENT ME!
2455    */
2456   @Override
2457   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2458   {
2459     SequenceGroup sg = new SequenceGroup();
2460
2461     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2462     {
2463       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2464     }
2465
2466     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2467     viewport.setSelectionGroup(sg);
2468     viewport.sendSelection();
2469     // JAL-2034 - should delegate to
2470     // alignPanel to decide if overview needs
2471     // updating.
2472     alignPanel.paintAlignment(false, false);
2473     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2474   }
2475
2476   /**
2477    * DOCUMENT ME!
2478    *
2479    * @param e
2480    *          DOCUMENT ME!
2481    */
2482   @Override
2483   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2484   {
2485     if (viewport.cursorMode)
2486     {
2487       alignPanel.getSeqPanel().keyboardNo1 = null;
2488       alignPanel.getSeqPanel().keyboardNo2 = null;
2489     }
2490     viewport.setSelectionGroup(null);
2491     viewport.getColumnSelection().clear();
2492     viewport.setSelectionGroup(null);
2493     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2494     // JAL-2034 - should delegate to
2495     // alignPanel to decide if overview needs
2496     // updating.
2497     alignPanel.paintAlignment(false, false);
2498     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2499     viewport.sendSelection();
2500   }
2501
2502   /**
2503    * DOCUMENT ME!
2504    *
2505    * @param e
2506    *          DOCUMENT ME!
2507    */
2508   @Override
2509   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2510   {
2511     SequenceGroup sg = viewport.getSelectionGroup();
2512
2513     if (sg == null)
2514     {
2515       selectAllSequenceMenuItem_actionPerformed(null);
2516
2517       return;
2518     }
2519
2520     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2521     {
2522       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2523     }
2524     // JAL-2034 - should delegate to
2525     // alignPanel to decide if overview needs
2526     // updating.
2527
2528     alignPanel.paintAlignment(true, false);
2529     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2530     viewport.sendSelection();
2531   }
2532
2533   @Override
2534   public void invertColSel_actionPerformed(ActionEvent e)
2535   {
2536     viewport.invertColumnSelection();
2537     alignPanel.paintAlignment(true, false);
2538     viewport.sendSelection();
2539   }
2540
2541   /**
2542    * DOCUMENT ME!
2543    *
2544    * @param e
2545    *          DOCUMENT ME!
2546    */
2547   @Override
2548   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2549   {
2550     trimAlignment(true);
2551   }
2552
2553   /**
2554    * DOCUMENT ME!
2555    *
2556    * @param e
2557    *          DOCUMENT ME!
2558    */
2559   @Override
2560   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2561   {
2562     trimAlignment(false);
2563   }
2564
2565   void trimAlignment(boolean trimLeft)
2566   {
2567     ColumnSelection colSel = viewport.getColumnSelection();
2568     int column;
2569
2570     if (!colSel.isEmpty())
2571     {
2572       if (trimLeft)
2573       {
2574         column = colSel.getMin();
2575       }
2576       else
2577       {
2578         column = colSel.getMax();
2579       }
2580
2581       SequenceI[] seqs;
2582       if (viewport.getSelectionGroup() != null)
2583       {
2584         seqs = viewport.getSelectionGroup()
2585                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2586       }
2587       else
2588       {
2589         seqs = viewport.getAlignment().getSequencesArray();
2590       }
2591
2592       TrimRegionCommand trimRegion;
2593       if (trimLeft)
2594       {
2595         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2596                 column, viewport.getAlignment());
2597         viewport.getRanges().setStartRes(0);
2598       }
2599       else
2600       {
2601         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2602                 column, viewport.getAlignment());
2603       }
2604
2605       setStatus(MessageManager
2606               .formatMessage("label.removed_columns", new String[]
2607               { Integer.valueOf(trimRegion.getSize()).toString() }));
2608
2609       addHistoryItem(trimRegion);
2610
2611       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2612       {
2613         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2614                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2615         {
2616           viewport.getAlignment().deleteGroup(sg);
2617         }
2618       }
2619
2620       viewport.firePropertyChange("alignment", null,
2621               viewport.getAlignment().getSequences());
2622     }
2623   }
2624
2625   /**
2626    * DOCUMENT ME!
2627    *
2628    * @param e
2629    *          DOCUMENT ME!
2630    */
2631   @Override
2632   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2633   {
2634     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2635
2636     SequenceI[] seqs;
2637     if (viewport.getSelectionGroup() != null)
2638     {
2639       seqs = viewport.getSelectionGroup()
2640               .getSequencesAsArray(viewport.getHiddenRepSequences());
2641       start = viewport.getSelectionGroup().getStartRes();
2642       end = viewport.getSelectionGroup().getEndRes();
2643     }
2644     else
2645     {
2646       seqs = viewport.getAlignment().getSequencesArray();
2647     }
2648
2649     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2650             "Remove Gapped Columns", seqs, start, end,
2651             viewport.getAlignment());
2652
2653     addHistoryItem(removeGapCols);
2654
2655     setStatus(MessageManager
2656             .formatMessage("label.removed_empty_columns", new Object[]
2657             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2658
2659     // This is to maintain viewport position on first residue
2660     // of first sequence
2661     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2662     ViewportRanges ranges = viewport.getRanges();
2663     int startRes = seq.findPosition(ranges.getStartRes());
2664     // ShiftList shifts;
2665     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2666     // edit.alColumnChanges=shifts.getInverse();
2667     // if (viewport.hasHiddenColumns)
2668     // viewport.getColumnSelection().compensateForEdits(shifts);
2669     ranges.setStartRes(seq.findIndex(startRes) - 1);
2670     viewport.firePropertyChange("alignment", null,
2671             viewport.getAlignment().getSequences());
2672
2673   }
2674
2675   /**
2676    * DOCUMENT ME!
2677    *
2678    * @param e
2679    *          DOCUMENT ME!
2680    */
2681   @Override
2682   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2683   {
2684     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2685
2686     SequenceI[] seqs;
2687     if (viewport.getSelectionGroup() != null)
2688     {
2689       seqs = viewport.getSelectionGroup()
2690               .getSequencesAsArray(viewport.getHiddenRepSequences());
2691       start = viewport.getSelectionGroup().getStartRes();
2692       end = viewport.getSelectionGroup().getEndRes();
2693     }
2694     else
2695     {
2696       seqs = viewport.getAlignment().getSequencesArray();
2697     }
2698
2699     // This is to maintain viewport position on first residue
2700     // of first sequence
2701     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2702     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2703
2704     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2705             viewport.getAlignment()));
2706
2707     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2708
2709     viewport.firePropertyChange("alignment", null,
2710             viewport.getAlignment().getSequences());
2711
2712   }
2713
2714   /**
2715    * DOCUMENT ME!
2716    *
2717    * @param e
2718    *          DOCUMENT ME!
2719    */
2720   @Override
2721   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2722   {
2723     viewport.setPadGaps(padGapsMenuitem.isSelected());
2724     viewport.firePropertyChange("alignment", null,
2725             viewport.getAlignment().getSequences());
2726   }
2727
2728   /**
2729    * DOCUMENT ME!
2730    *
2731    * @param e
2732    *          DOCUMENT ME!
2733    */
2734   @Override
2735   public void findMenuItem_actionPerformed(ActionEvent e)
2736   {
2737     new Finder();
2738   }
2739
2740   /**
2741    * Create a new view of the current alignment.
2742    */
2743   @Override
2744   public void newView_actionPerformed(ActionEvent e)
2745   {
2746     newView(null, true);
2747   }
2748
2749   /**
2750    * Creates and shows a new view of the current alignment.
2751    *
2752    * @param viewTitle
2753    *          title of newly created view; if null, one will be generated
2754    * @param copyAnnotation
2755    *          if true then duplicate all annnotation, groups and settings
2756    * @return new alignment panel, already displayed.
2757    */
2758   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2759   {
2760     /*
2761      * Create a new AlignmentPanel (with its own, new Viewport)
2762      */
2763     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2764     if (!copyAnnotation)
2765     {
2766       /*
2767        * remove all groups and annotation except for the automatic stuff
2768        */
2769       newap.av.getAlignment().deleteAllGroups();
2770       newap.av.getAlignment().deleteAllAnnotations(false);
2771     }
2772
2773     newap.av.setGatherViewsHere(false);
2774
2775     if (viewport.viewName == null)
2776     {
2777       viewport.viewName = MessageManager
2778               .getString("label.view_name_original");
2779     }
2780
2781     /*
2782      * Views share the same edits undo and redo stacks
2783      */
2784     newap.av.setHistoryList(viewport.getHistoryList());
2785     newap.av.setRedoList(viewport.getRedoList());
2786
2787     /*
2788      * Views share the same mappings; need to deregister any new mappings
2789      * created by copyAlignPanel, and register the new reference to the shared
2790      * mappings
2791      */
2792     newap.av.replaceMappings(viewport.getAlignment());
2793
2794     /*
2795      * start up cDNA consensus (if applicable) now mappings are in place
2796      */
2797     if (newap.av.initComplementConsensus())
2798     {
2799       newap.refresh(true); // adjust layout of annotations
2800     }
2801
2802     newap.av.viewName = getNewViewName(viewTitle);
2803
2804     addAlignmentPanel(newap, true);
2805     newap.alignmentChanged();
2806
2807     if (alignPanels.size() == 2)
2808     {
2809       viewport.setGatherViewsHere(true);
2810     }
2811     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2812     return newap;
2813   }
2814
2815   /**
2816    * Make a new name for the view, ensuring it is unique within the current
2817    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2818    * these now use viewId. Unique view names are still desirable for usability.)
2819    *
2820    * @param viewTitle
2821    * @return
2822    */
2823   protected String getNewViewName(String viewTitle)
2824   {
2825     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2826     boolean addFirstIndex = false;
2827     if (viewTitle == null || viewTitle.trim().length() == 0)
2828     {
2829       viewTitle = MessageManager.getString("action.view");
2830       addFirstIndex = true;
2831     }
2832     else
2833     {
2834       index = 1;// we count from 1 if given a specific name
2835     }
2836     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2837
2838     List<Component> comps = PaintRefresher.components
2839             .get(viewport.getSequenceSetId());
2840
2841     List<String> existingNames = getExistingViewNames(comps);
2842
2843     while (existingNames.contains(newViewName))
2844     {
2845       newViewName = viewTitle + " " + (++index);
2846     }
2847     return newViewName;
2848   }
2849
2850   /**
2851    * Returns a list of distinct view names found in the given list of
2852    * components. View names are held on the viewport of an AlignmentPanel.
2853    *
2854    * @param comps
2855    * @return
2856    */
2857   protected List<String> getExistingViewNames(List<Component> comps)
2858   {
2859     List<String> existingNames = new ArrayList<>();
2860     for (Component comp : comps)
2861     {
2862       if (comp instanceof AlignmentPanel)
2863       {
2864         AlignmentPanel ap = (AlignmentPanel) comp;
2865         if (!existingNames.contains(ap.av.viewName))
2866         {
2867           existingNames.add(ap.av.viewName);
2868         }
2869       }
2870     }
2871     return existingNames;
2872   }
2873
2874   /**
2875    * Explode tabbed views into separate windows.
2876    */
2877   @Override
2878   public void expandViews_actionPerformed(ActionEvent e)
2879   {
2880     Desktop.explodeViews(this);
2881   }
2882
2883   /**
2884    * Gather views in separate windows back into a tabbed presentation.
2885    */
2886   @Override
2887   public void gatherViews_actionPerformed(ActionEvent e)
2888   {
2889     Desktop.instance.gatherViews(this);
2890   }
2891
2892   /**
2893    * DOCUMENT ME!
2894    *
2895    * @param e
2896    *          DOCUMENT ME!
2897    */
2898   @Override
2899   public void font_actionPerformed(ActionEvent e)
2900   {
2901     new FontChooser(alignPanel);
2902   }
2903
2904   /**
2905    * DOCUMENT ME!
2906    *
2907    * @param e
2908    *          DOCUMENT ME!
2909    */
2910   @Override
2911   protected void seqLimit_actionPerformed(ActionEvent e)
2912   {
2913     viewport.setShowJVSuffix(seqLimits.isSelected());
2914
2915     alignPanel.getIdPanel().getIdCanvas()
2916             .setPreferredSize(alignPanel.calculateIdWidth());
2917     alignPanel.paintAlignment(true, false);
2918   }
2919
2920   @Override
2921   public void idRightAlign_actionPerformed(ActionEvent e)
2922   {
2923     viewport.setRightAlignIds(idRightAlign.isSelected());
2924     alignPanel.paintAlignment(false, false);
2925   }
2926
2927   @Override
2928   public void centreColumnLabels_actionPerformed(ActionEvent e)
2929   {
2930     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2931     alignPanel.paintAlignment(false, false);
2932   }
2933
2934   /*
2935    * (non-Javadoc)
2936    *
2937    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2938    */
2939   @Override
2940   protected void followHighlight_actionPerformed()
2941   {
2942     /*
2943      * Set the 'follow' flag on the Viewport (and scroll to position if now
2944      * true).
2945      */
2946     final boolean state = this.followHighlightMenuItem.getState();
2947     viewport.setFollowHighlight(state);
2948     if (state)
2949     {
2950       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2951     }
2952   }
2953
2954   /**
2955    * DOCUMENT ME!
2956    *
2957    * @param e
2958    *          DOCUMENT ME!
2959    */
2960   @Override
2961   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2962   {
2963     viewport.setColourText(colourTextMenuItem.isSelected());
2964     alignPanel.paintAlignment(false, false);
2965   }
2966
2967   /**
2968    * DOCUMENT ME!
2969    *
2970    * @param e
2971    *          DOCUMENT ME!
2972    */
2973   @Override
2974   public void wrapMenuItem_actionPerformed(ActionEvent e)
2975   {
2976     scaleAbove.setVisible(wrapMenuItem.isSelected());
2977     scaleLeft.setVisible(wrapMenuItem.isSelected());
2978     scaleRight.setVisible(wrapMenuItem.isSelected());
2979     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2980     alignPanel.updateLayout();
2981   }
2982
2983   @Override
2984   public void showAllSeqs_actionPerformed(ActionEvent e)
2985   {
2986     viewport.showAllHiddenSeqs();
2987   }
2988
2989   @Override
2990   public void showAllColumns_actionPerformed(ActionEvent e)
2991   {
2992     viewport.showAllHiddenColumns();
2993     alignPanel.paintAlignment(true, true);
2994     viewport.sendSelection();
2995   }
2996
2997   @Override
2998   public void hideSelSequences_actionPerformed(ActionEvent e)
2999   {
3000     viewport.hideAllSelectedSeqs();
3001   }
3002
3003   /**
3004    * called by key handler and the hide all/show all menu items
3005    *
3006    * @param toggleSeqs
3007    * @param toggleCols
3008    */
3009   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3010   {
3011
3012     boolean hide = false;
3013     SequenceGroup sg = viewport.getSelectionGroup();
3014     if (!toggleSeqs && !toggleCols)
3015     {
3016       // Hide everything by the current selection - this is a hack - we do the
3017       // invert and then hide
3018       // first check that there will be visible columns after the invert.
3019       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3020               && sg.getStartRes() <= sg.getEndRes()))
3021       {
3022         // now invert the sequence set, if required - empty selection implies
3023         // that no hiding is required.
3024         if (sg != null)
3025         {
3026           invertSequenceMenuItem_actionPerformed(null);
3027           sg = viewport.getSelectionGroup();
3028           toggleSeqs = true;
3029
3030         }
3031         viewport.expandColSelection(sg, true);
3032         // finally invert the column selection and get the new sequence
3033         // selection.
3034         invertColSel_actionPerformed(null);
3035         toggleCols = true;
3036       }
3037     }
3038
3039     if (toggleSeqs)
3040     {
3041       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3042       {
3043         hideSelSequences_actionPerformed(null);
3044         hide = true;
3045       }
3046       else if (!(toggleCols && viewport.hasSelectedColumns()))
3047       {
3048         showAllSeqs_actionPerformed(null);
3049       }
3050     }
3051
3052     if (toggleCols)
3053     {
3054       if (viewport.hasSelectedColumns())
3055       {
3056         hideSelColumns_actionPerformed(null);
3057         if (!toggleSeqs)
3058         {
3059           viewport.setSelectionGroup(sg);
3060         }
3061       }
3062       else if (!hide)
3063       {
3064         showAllColumns_actionPerformed(null);
3065       }
3066     }
3067   }
3068
3069   /*
3070    * (non-Javadoc)
3071    *
3072    * @see
3073    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3074    * event.ActionEvent)
3075    */
3076   @Override
3077   public void hideAllButSelection_actionPerformed(ActionEvent e)
3078   {
3079     toggleHiddenRegions(false, false);
3080     viewport.sendSelection();
3081   }
3082
3083   /*
3084    * (non-Javadoc)
3085    *
3086    * @see
3087    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3088    * .ActionEvent)
3089    */
3090   @Override
3091   public void hideAllSelection_actionPerformed(ActionEvent e)
3092   {
3093     SequenceGroup sg = viewport.getSelectionGroup();
3094     viewport.expandColSelection(sg, false);
3095     viewport.hideAllSelectedSeqs();
3096     viewport.hideSelectedColumns();
3097     alignPanel.paintAlignment(true, true);
3098     viewport.sendSelection();
3099   }
3100
3101   /*
3102    * (non-Javadoc)
3103    *
3104    * @see
3105    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3106    * ActionEvent)
3107    */
3108   @Override
3109   public void showAllhidden_actionPerformed(ActionEvent e)
3110   {
3111     viewport.showAllHiddenColumns();
3112     viewport.showAllHiddenSeqs();
3113     alignPanel.paintAlignment(true, true);
3114     viewport.sendSelection();
3115   }
3116
3117   @Override
3118   public void hideSelColumns_actionPerformed(ActionEvent e)
3119   {
3120     viewport.hideSelectedColumns();
3121     alignPanel.paintAlignment(true, true);
3122     viewport.sendSelection();
3123   }
3124
3125   @Override
3126   public void hiddenMarkers_actionPerformed(ActionEvent e)
3127   {
3128     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3129     repaint();
3130   }
3131
3132   /**
3133    * DOCUMENT ME!
3134    *
3135    * @param e
3136    *          DOCUMENT ME!
3137    */
3138   @Override
3139   protected void scaleAbove_actionPerformed(ActionEvent e)
3140   {
3141     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3142     // TODO: do we actually need to update overview for scale above change ?
3143     alignPanel.paintAlignment(true, false);
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   protected void scaleLeft_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3156     alignPanel.paintAlignment(true, false);
3157   }
3158
3159   /**
3160    * DOCUMENT ME!
3161    *
3162    * @param e
3163    *          DOCUMENT ME!
3164    */
3165   @Override
3166   protected void scaleRight_actionPerformed(ActionEvent e)
3167   {
3168     viewport.setScaleRightWrapped(scaleRight.isSelected());
3169     alignPanel.paintAlignment(true, false);
3170   }
3171
3172   /**
3173    * DOCUMENT ME!
3174    *
3175    * @param e
3176    *          DOCUMENT ME!
3177    */
3178   @Override
3179   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3180   {
3181     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3182     alignPanel.paintAlignment(false, false);
3183   }
3184
3185   /**
3186    * DOCUMENT ME!
3187    *
3188    * @param e
3189    *          DOCUMENT ME!
3190    */
3191   @Override
3192   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3193   {
3194     viewport.setShowText(viewTextMenuItem.isSelected());
3195     alignPanel.paintAlignment(false, false);
3196   }
3197
3198   /**
3199    * DOCUMENT ME!
3200    *
3201    * @param e
3202    *          DOCUMENT ME!
3203    */
3204   @Override
3205   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3206   {
3207     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3208     alignPanel.paintAlignment(false, false);
3209   }
3210
3211   public FeatureSettings featureSettings;
3212
3213   @Override
3214   public FeatureSettingsControllerI getFeatureSettingsUI()
3215   {
3216     return featureSettings;
3217   }
3218
3219   @Override
3220   public void featureSettings_actionPerformed(ActionEvent e)
3221   {
3222     if (featureSettings != null)
3223     {
3224       featureSettings.close();
3225       featureSettings = null;
3226     }
3227     if (!showSeqFeatures.isSelected())
3228     {
3229       // make sure features are actually displayed
3230       showSeqFeatures.setSelected(true);
3231       showSeqFeatures_actionPerformed(null);
3232     }
3233     featureSettings = new FeatureSettings(this);
3234   }
3235
3236   /**
3237    * Set or clear 'Show Sequence Features'
3238    *
3239    * @param evt
3240    *          DOCUMENT ME!
3241    */
3242   @Override
3243   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3244   {
3245     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3246     alignPanel.paintAlignment(true, true);
3247   }
3248
3249   /**
3250    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3251    * the annotations panel as a whole.
3252    *
3253    * The options to show/hide all annotations should be enabled when the panel
3254    * is shown, and disabled when the panel is hidden.
3255    *
3256    * @param e
3257    */
3258   @Override
3259   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3260   {
3261     final boolean setVisible = annotationPanelMenuItem.isSelected();
3262     viewport.setShowAnnotation(setVisible);
3263     this.showAllSeqAnnotations.setEnabled(setVisible);
3264     this.hideAllSeqAnnotations.setEnabled(setVisible);
3265     this.showAllAlAnnotations.setEnabled(setVisible);
3266     this.hideAllAlAnnotations.setEnabled(setVisible);
3267     alignPanel.updateLayout();
3268   }
3269
3270   @Override
3271   public void alignmentProperties()
3272   {
3273     JComponent pane;
3274     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3275
3276             .formatAsHtml();
3277     String content = MessageManager.formatMessage("label.html_content",
3278             new Object[]
3279             { contents.toString() });
3280     contents = null;
3281
3282     if (Jalview.isJS())
3283     {
3284       JLabel textLabel = new JLabel();
3285       textLabel.setText(content);
3286       textLabel.setBackground(Color.WHITE);
3287
3288       pane = new JPanel(new BorderLayout());
3289       ((JPanel) pane).setOpaque(true);
3290       pane.setBackground(Color.WHITE);
3291       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3292     }
3293     else
3294     {
3295       JEditorPane editPane = new JEditorPane("text/html", "");
3296       editPane.setEditable(false);
3297       editPane.setText(content);
3298       pane = editPane;
3299     }
3300
3301     JInternalFrame frame = new JInternalFrame();
3302
3303     frame.getContentPane().add(new JScrollPane(pane));
3304
3305     Desktop.addInternalFrame(frame, MessageManager
3306             .formatMessage("label.alignment_properties", new Object[]
3307             { getTitle() }), 500, 400);
3308   }
3309
3310   /**
3311    * DOCUMENT ME!
3312    *
3313    * @param e
3314    *          DOCUMENT ME!
3315    */
3316   @Override
3317   public void overviewMenuItem_actionPerformed(ActionEvent e)
3318   {
3319     if (alignPanel.overviewPanel != null)
3320     {
3321       return;
3322     }
3323
3324     JInternalFrame frame = new JInternalFrame();
3325     final OverviewPanel overview = new OverviewPanel(alignPanel);
3326     frame.setContentPane(overview);
3327     Desktop.addInternalFrame(frame, MessageManager
3328             .formatMessage("label.overview_params", new Object[]
3329             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3330             true, true);
3331     frame.pack();
3332     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3333     frame.addInternalFrameListener(
3334             new javax.swing.event.InternalFrameAdapter()
3335             {
3336               @Override
3337               public void internalFrameClosed(
3338                       javax.swing.event.InternalFrameEvent evt)
3339               {
3340                 overview.dispose();
3341                 alignPanel.setOverviewPanel(null);
3342               };
3343             });
3344     if (getKeyListeners().length > 0)
3345     {
3346       frame.addKeyListener(getKeyListeners()[0]);
3347     }
3348
3349     alignPanel.setOverviewPanel(overview);
3350   }
3351
3352   @Override
3353   public void textColour_actionPerformed()
3354   {
3355     new TextColourChooser().chooseColour(alignPanel, null);
3356   }
3357
3358   /*
3359    * public void covariationColour_actionPerformed() {
3360    * changeColour(new
3361    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3362    * ()[0])); }
3363    */
3364   @Override
3365   public void annotationColour_actionPerformed()
3366   {
3367     new AnnotationColourChooser(viewport, alignPanel);
3368   }
3369
3370   @Override
3371   public void annotationColumn_actionPerformed(ActionEvent e)
3372   {
3373     new AnnotationColumnChooser(viewport, alignPanel);
3374   }
3375
3376   /**
3377    * Action on the user checking or unchecking the option to apply the selected
3378    * colour scheme to all groups. If unchecked, groups may have their own
3379    * independent colour schemes.
3380    *
3381    * @param selected
3382    */
3383   @Override
3384   public void applyToAllGroups_actionPerformed(boolean selected)
3385   {
3386     viewport.setColourAppliesToAllGroups(selected);
3387   }
3388
3389   /**
3390    * Action on user selecting a colour from the colour menu
3391    *
3392    * @param name
3393    *          the name (not the menu item label!) of the colour scheme
3394    */
3395   @Override
3396   public void changeColour_actionPerformed(String name)
3397   {
3398     /*
3399      * 'User Defined' opens a panel to configure or load a
3400      * user-defined colour scheme
3401      */
3402     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3403     {
3404       new UserDefinedColours(alignPanel);
3405       return;
3406     }
3407
3408     /*
3409      * otherwise set the chosen colour scheme (or null for 'None')
3410      */
3411     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3412             viewport.getAlignment(), viewport.getHiddenRepSequences());
3413     changeColour(cs);
3414   }
3415
3416   /**
3417    * Actions on setting or changing the alignment colour scheme
3418    *
3419    * @param cs
3420    */
3421   @Override
3422   public void changeColour(ColourSchemeI cs)
3423   {
3424     // TODO: pull up to controller method
3425     ColourMenuHelper.setColourSelected(colourMenu, cs);
3426
3427     viewport.setGlobalColourScheme(cs);
3428
3429     alignPanel.paintAlignment(true, true);
3430   }
3431
3432   /**
3433    * Show the PID threshold slider panel
3434    */
3435   @Override
3436   protected void modifyPID_actionPerformed()
3437   {
3438     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3439             alignPanel.getViewName());
3440     SliderPanel.showPIDSlider();
3441   }
3442
3443   /**
3444    * Show the Conservation slider panel
3445    */
3446   @Override
3447   protected void modifyConservation_actionPerformed()
3448   {
3449     SliderPanel.setConservationSlider(alignPanel,
3450             viewport.getResidueShading(), alignPanel.getViewName());
3451     SliderPanel.showConservationSlider();
3452   }
3453
3454   /**
3455    * Action on selecting or deselecting (Colour) By Conservation
3456    */
3457   @Override
3458   public void conservationMenuItem_actionPerformed(boolean selected)
3459   {
3460     modifyConservation.setEnabled(selected);
3461     viewport.setConservationSelected(selected);
3462     viewport.getResidueShading().setConservationApplied(selected);
3463
3464     changeColour(viewport.getGlobalColourScheme());
3465     if (selected)
3466     {
3467       modifyConservation_actionPerformed();
3468     }
3469     else
3470     {
3471       SliderPanel.hideConservationSlider();
3472     }
3473   }
3474
3475   /**
3476    * Action on selecting or deselecting (Colour) Above PID Threshold
3477    */
3478   @Override
3479   public void abovePIDThreshold_actionPerformed(boolean selected)
3480   {
3481     modifyPID.setEnabled(selected);
3482     viewport.setAbovePIDThreshold(selected);
3483     if (!selected)
3484     {
3485       viewport.getResidueShading().setThreshold(0,
3486               viewport.isIgnoreGapsConsensus());
3487     }
3488
3489     changeColour(viewport.getGlobalColourScheme());
3490     if (selected)
3491     {
3492       modifyPID_actionPerformed();
3493     }
3494     else
3495     {
3496       SliderPanel.hidePIDSlider();
3497     }
3498   }
3499
3500   /**
3501    * DOCUMENT ME!
3502    *
3503    * @param e
3504    *          DOCUMENT ME!
3505    */
3506   @Override
3507   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3508   {
3509     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3510     AlignmentSorter.sortByPID(viewport.getAlignment(),
3511             viewport.getAlignment().getSequenceAt(0));
3512     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3513             viewport.getAlignment()));
3514     alignPanel.paintAlignment(true, false);
3515   }
3516
3517   /**
3518    * DOCUMENT ME!
3519    *
3520    * @param e
3521    *          DOCUMENT ME!
3522    */
3523   @Override
3524   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3525   {
3526     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3527     AlignmentSorter.sortByID(viewport.getAlignment());
3528     addHistoryItem(
3529             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3530     alignPanel.paintAlignment(true, false);
3531   }
3532
3533   /**
3534    * DOCUMENT ME!
3535    *
3536    * @param e
3537    *          DOCUMENT ME!
3538    */
3539   @Override
3540   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3541   {
3542     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3543     AlignmentSorter.sortByLength(viewport.getAlignment());
3544     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3545             viewport.getAlignment()));
3546     alignPanel.paintAlignment(true, false);
3547   }
3548
3549   /**
3550    * DOCUMENT ME!
3551    *
3552    * @param e
3553    *          DOCUMENT ME!
3554    */
3555   @Override
3556   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3557   {
3558     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3559     AlignmentSorter.sortByGroup(viewport.getAlignment());
3560     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3561             viewport.getAlignment()));
3562
3563     alignPanel.paintAlignment(true, false);
3564   }
3565
3566   /**
3567    * DOCUMENT ME!
3568    *
3569    * @param e
3570    *          DOCUMENT ME!
3571    */
3572   @Override
3573   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3574   {
3575     new RedundancyPanel(alignPanel, this);
3576   }
3577
3578   /**
3579    * DOCUMENT ME!
3580    *
3581    * @param e
3582    *          DOCUMENT ME!
3583    */
3584   @Override
3585   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3586   {
3587     if ((viewport.getSelectionGroup() == null)
3588             || (viewport.getSelectionGroup().getSize() < 2))
3589     {
3590       JvOptionPane.showInternalMessageDialog(this,
3591               MessageManager.getString(
3592                       "label.you_must_select_least_two_sequences"),
3593               MessageManager.getString("label.invalid_selection"),
3594               JvOptionPane.WARNING_MESSAGE);
3595     }
3596     else
3597     {
3598       JInternalFrame frame = new JInternalFrame();
3599       frame.setContentPane(new PairwiseAlignPanel(viewport));
3600       Desktop.addInternalFrame(frame,
3601               MessageManager.getString("action.pairwise_alignment"), 600,
3602               500);
3603     }
3604   }
3605
3606   @Override
3607   public void autoCalculate_actionPerformed(ActionEvent e)
3608   {
3609     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3610     if (viewport.autoCalculateConsensus)
3611     {
3612       viewport.firePropertyChange("alignment", null,
3613               viewport.getAlignment().getSequences());
3614     }
3615   }
3616
3617   @Override
3618   public void sortByTreeOption_actionPerformed(ActionEvent e)
3619   {
3620     viewport.sortByTree = sortByTree.isSelected();
3621   }
3622
3623   @Override
3624   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3625   {
3626     viewport.followSelection = listenToViewSelections.isSelected();
3627   }
3628
3629   /**
3630    * Constructs a tree panel and adds it to the desktop
3631    *
3632    * @param type
3633    *          tree type (NJ or AV)
3634    * @param modelName
3635    *          name of score model used to compute the tree
3636    * @param options
3637    *          parameters for the distance or similarity calculation
3638    */
3639   void newTreePanel(String type, String modelName,
3640           SimilarityParamsI options)
3641   {
3642     String frameTitle = "";
3643     TreePanel tp;
3644
3645     boolean onSelection = false;
3646     if (viewport.getSelectionGroup() != null
3647             && viewport.getSelectionGroup().getSize() > 0)
3648     {
3649       SequenceGroup sg = viewport.getSelectionGroup();
3650
3651       /* Decide if the selection is a column region */
3652       for (SequenceI _s : sg.getSequences())
3653       {
3654         if (_s.getLength() < sg.getEndRes())
3655         {
3656           JvOptionPane.showMessageDialog(Desktop.desktop,
3657                   MessageManager.getString(
3658                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3659                   MessageManager.getString(
3660                           "label.sequences_selection_not_aligned"),
3661                   JvOptionPane.WARNING_MESSAGE);
3662
3663           return;
3664         }
3665       }
3666       onSelection = true;
3667     }
3668     else
3669     {
3670       if (viewport.getAlignment().getHeight() < 2)
3671       {
3672         return;
3673       }
3674     }
3675
3676     tp = new TreePanel(alignPanel, type, modelName, options);
3677     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3678
3679     frameTitle += " from ";
3680
3681     if (viewport.viewName != null)
3682     {
3683       frameTitle += viewport.viewName + " of ";
3684     }
3685
3686     frameTitle += this.title;
3687
3688     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3689   }
3690
3691   /**
3692    * DOCUMENT ME!
3693    *
3694    * @param title
3695    *          DOCUMENT ME!
3696    * @param order
3697    *          DOCUMENT ME!
3698    */
3699   public void addSortByOrderMenuItem(String title,
3700           final AlignmentOrder order)
3701   {
3702     final JMenuItem item = new JMenuItem(MessageManager
3703             .formatMessage("action.by_title_param", new Object[]
3704             { title }));
3705     sort.add(item);
3706     item.addActionListener(new java.awt.event.ActionListener()
3707     {
3708       @Override
3709       public void actionPerformed(ActionEvent e)
3710       {
3711         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3712
3713         // TODO: JBPNote - have to map order entries to curent SequenceI
3714         // pointers
3715         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3716
3717         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3718                 viewport.getAlignment()));
3719
3720         alignPanel.paintAlignment(true, false);
3721       }
3722     });
3723   }
3724
3725   /**
3726    * Add a new sort by annotation score menu item
3727    *
3728    * @param sort
3729    *          the menu to add the option to
3730    * @param scoreLabel
3731    *          the label used to retrieve scores for each sequence on the
3732    *          alignment
3733    */
3734   public void addSortByAnnotScoreMenuItem(JMenu sort,
3735           final String scoreLabel)
3736   {
3737     final JMenuItem item = new JMenuItem(scoreLabel);
3738     sort.add(item);
3739     item.addActionListener(new java.awt.event.ActionListener()
3740     {
3741       @Override
3742       public void actionPerformed(ActionEvent e)
3743       {
3744         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3745         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3746                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3747         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3748                 viewport.getAlignment()));
3749         alignPanel.paintAlignment(true, false);
3750       }
3751     });
3752   }
3753
3754   /**
3755    * last hash for alignment's annotation array - used to minimise cost of
3756    * rebuild.
3757    */
3758   protected int _annotationScoreVectorHash;
3759
3760   /**
3761    * search the alignment and rebuild the sort by annotation score submenu the
3762    * last alignment annotation vector hash is stored to minimize cost of
3763    * rebuilding in subsequence calls.
3764    *
3765    */
3766   @Override
3767   public void buildSortByAnnotationScoresMenu()
3768   {
3769     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3770     {
3771       return;
3772     }
3773
3774     if (viewport.getAlignment().getAlignmentAnnotation()
3775             .hashCode() != _annotationScoreVectorHash)
3776     {
3777       sortByAnnotScore.removeAll();
3778       // almost certainly a quicker way to do this - but we keep it simple
3779       Hashtable scoreSorts = new Hashtable();
3780       AlignmentAnnotation aann[];
3781       for (SequenceI sqa : viewport.getAlignment().getSequences())
3782       {
3783         aann = sqa.getAnnotation();
3784         for (int i = 0; aann != null && i < aann.length; i++)
3785         {
3786           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3787           {
3788             scoreSorts.put(aann[i].label, aann[i].label);
3789           }
3790         }
3791       }
3792       Enumeration labels = scoreSorts.keys();
3793       while (labels.hasMoreElements())
3794       {
3795         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3796                 (String) labels.nextElement());
3797       }
3798       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3799       scoreSorts.clear();
3800
3801       _annotationScoreVectorHash = viewport.getAlignment()
3802               .getAlignmentAnnotation().hashCode();
3803     }
3804   }
3805
3806   /**
3807    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3808    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3809    * call. Listeners are added to remove the menu item when the treePanel is
3810    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3811    * modified.
3812    */
3813   @Override
3814   public void buildTreeSortMenu()
3815   {
3816     sortByTreeMenu.removeAll();
3817
3818     List<Component> comps = PaintRefresher.components
3819             .get(viewport.getSequenceSetId());
3820     List<TreePanel> treePanels = new ArrayList<>();
3821     for (Component comp : comps)
3822     {
3823       if (comp instanceof TreePanel)
3824       {
3825         treePanels.add((TreePanel) comp);
3826       }
3827     }
3828
3829     if (treePanels.size() < 1)
3830     {
3831       sortByTreeMenu.setVisible(false);
3832       return;
3833     }
3834
3835     sortByTreeMenu.setVisible(true);
3836
3837     for (final TreePanel tp : treePanels)
3838     {
3839       final JMenuItem item = new JMenuItem(tp.getTitle());
3840       item.addActionListener(new java.awt.event.ActionListener()
3841       {
3842         @Override
3843         public void actionPerformed(ActionEvent e)
3844         {
3845           tp.sortByTree_actionPerformed();
3846           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3847
3848         }
3849       });
3850
3851       sortByTreeMenu.add(item);
3852     }
3853   }
3854
3855   public boolean sortBy(AlignmentOrder alorder, String undoname)
3856   {
3857     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3858     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3859     if (undoname != null)
3860     {
3861       addHistoryItem(new OrderCommand(undoname, oldOrder,
3862               viewport.getAlignment()));
3863     }
3864     alignPanel.paintAlignment(true, false);
3865     return true;
3866   }
3867
3868   /**
3869    * Work out whether the whole set of sequences or just the selected set will
3870    * be submitted for multiple alignment.
3871    *
3872    */
3873   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3874   {
3875     // Now, check we have enough sequences
3876     AlignmentView msa = null;
3877
3878     if ((viewport.getSelectionGroup() != null)
3879             && (viewport.getSelectionGroup().getSize() > 1))
3880     {
3881       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3882       // some common interface!
3883       /*
3884        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3885        * SequenceI[sz = seqs.getSize(false)];
3886        *
3887        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3888        * seqs.getSequenceAt(i); }
3889        */
3890       msa = viewport.getAlignmentView(true);
3891     }
3892     else if (viewport.getSelectionGroup() != null
3893             && viewport.getSelectionGroup().getSize() == 1)
3894     {
3895       int option = JvOptionPane.showConfirmDialog(this,
3896               MessageManager.getString("warn.oneseq_msainput_selection"),
3897               MessageManager.getString("label.invalid_selection"),
3898               JvOptionPane.OK_CANCEL_OPTION);
3899       if (option == JvOptionPane.OK_OPTION)
3900       {
3901         msa = viewport.getAlignmentView(false);
3902       }
3903     }
3904     else
3905     {
3906       msa = viewport.getAlignmentView(false);
3907     }
3908     return msa;
3909   }
3910
3911   /**
3912    * Decides what is submitted to a secondary structure prediction service: the
3913    * first sequence in the alignment, or in the current selection, or, if the
3914    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3915    * region or the whole alignment. (where the first sequence in the set is the
3916    * one that the prediction will be for).
3917    */
3918   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3919   {
3920     AlignmentView seqs = null;
3921
3922     if ((viewport.getSelectionGroup() != null)
3923             && (viewport.getSelectionGroup().getSize() > 0))
3924     {
3925       seqs = viewport.getAlignmentView(true);
3926     }
3927     else
3928     {
3929       seqs = viewport.getAlignmentView(false);
3930     }
3931     // limit sequences - JBPNote in future - could spawn multiple prediction
3932     // jobs
3933     // TODO: viewport.getAlignment().isAligned is a global state - the local
3934     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3935     if (!viewport.getAlignment().isAligned(false))
3936     {
3937       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3938       // TODO: if seqs.getSequences().length>1 then should really have warned
3939       // user!
3940
3941     }
3942     return seqs;
3943   }
3944
3945   /**
3946    * DOCUMENT ME!
3947    *
3948    * @param e
3949    *          DOCUMENT ME!
3950    */
3951   @Override
3952   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3953   {
3954     // Pick the tree file
3955     JalviewFileChooser chooser = new JalviewFileChooser(
3956             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3957     chooser.setFileView(new JalviewFileView());
3958     chooser.setDialogTitle(
3959             MessageManager.getString("label.select_newick_like_tree_file"));
3960     chooser.setToolTipText(
3961             MessageManager.getString("label.load_tree_file"));
3962
3963     chooser.response(new jalview.util.dialogrunner.RunResponse(
3964             JalviewFileChooser.APPROVE_OPTION)
3965     {
3966       @Override
3967       public void run()
3968       {
3969         String filePath = chooser.getSelectedFile().getPath();
3970         Cache.setProperty("LAST_DIRECTORY", filePath);
3971         NewickFile fin = null;
3972         try
3973         {
3974           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
3975                   DataSourceType.FILE));
3976           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3977         } catch (Exception ex)
3978         {
3979           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3980                   MessageManager
3981                           .getString("label.problem_reading_tree_file"),
3982                   JvOptionPane.WARNING_MESSAGE);
3983           ex.printStackTrace();
3984         }
3985         if (fin != null && fin.hasWarningMessage())
3986         {
3987           JvOptionPane.showMessageDialog(Desktop.desktop,
3988                   fin.getWarningMessage(),
3989                   MessageManager.getString(
3990                           "label.possible_problem_with_tree_file"),
3991                   JvOptionPane.WARNING_MESSAGE);
3992         }
3993       }
3994     }).openDialog(this);
3995   }
3996
3997   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3998   {
3999     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4000   }
4001
4002   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4003           int h, int x, int y)
4004   {
4005     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4006   }
4007
4008   /**
4009    * Add a treeviewer for the tree extracted from a Newick file object to the
4010    * current alignment view
4011    *
4012    * @param nf
4013    *          the tree
4014    * @param title
4015    *          tree viewer title
4016    * @param input
4017    *          Associated alignment input data (or null)
4018    * @param w
4019    *          width
4020    * @param h
4021    *          height
4022    * @param x
4023    *          position
4024    * @param y
4025    *          position
4026    * @return TreePanel handle
4027    */
4028   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4029           AlignmentView input, int w, int h, int x, int y)
4030   {
4031     TreePanel tp = null;
4032
4033     try
4034     {
4035       nf.parse();
4036
4037       if (nf.getTree() != null)
4038       {
4039         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4040
4041         tp.setSize(w, h);
4042
4043         if (x > 0 && y > 0)
4044         {
4045           tp.setLocation(x, y);
4046         }
4047
4048         Desktop.addInternalFrame(tp, treeTitle, w, h);
4049       }
4050     } catch (Exception ex)
4051     {
4052       ex.printStackTrace();
4053     }
4054
4055     return tp;
4056   }
4057
4058   private boolean buildingMenu = false;
4059
4060   /**
4061    * Generates menu items and listener event actions for web service clients
4062    *
4063    */
4064   public void BuildWebServiceMenu()
4065   {
4066     while (buildingMenu)
4067     {
4068       try
4069       {
4070         System.err.println("Waiting for building menu to finish.");
4071         Thread.sleep(10);
4072       } catch (Exception e)
4073       {
4074       }
4075     }
4076     final AlignFrame me = this;
4077     buildingMenu = true;
4078     new Thread(new Runnable()
4079     {
4080       @Override
4081       public void run()
4082       {
4083         final List<JMenuItem> legacyItems = new ArrayList<>();
4084         try
4085         {
4086           // System.err.println("Building ws menu again "
4087           // + Thread.currentThread());
4088           // TODO: add support for context dependent disabling of services based
4089           // on
4090           // alignment and current selection
4091           // TODO: add additional serviceHandle parameter to specify abstract
4092           // handler
4093           // class independently of AbstractName
4094           // TODO: add in rediscovery GUI function to restart discoverer
4095           // TODO: group services by location as well as function and/or
4096           // introduce
4097           // object broker mechanism.
4098           final Vector<JMenu> wsmenu = new Vector<>();
4099           final IProgressIndicator af = me;
4100
4101           /*
4102            * do not i18n these strings - they are hard-coded in class
4103            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4104            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4105            */
4106           final JMenu msawsmenu = new JMenu("Alignment");
4107           final JMenu secstrmenu = new JMenu(
4108                   "Secondary Structure Prediction");
4109           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4110           final JMenu analymenu = new JMenu("Analysis");
4111           final JMenu dismenu = new JMenu("Protein Disorder");
4112           // JAL-940 - only show secondary structure prediction services from
4113           // the legacy server
4114           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4115               // &&
4116           Discoverer.services != null && (Discoverer.services.size() > 0))
4117           {
4118             // TODO: refactor to allow list of AbstractName/Handler bindings to
4119             // be
4120             // stored or retrieved from elsewhere
4121             // No MSAWS used any more:
4122             // Vector msaws = null; // (Vector)
4123             // Discoverer.services.get("MsaWS");
4124             Vector secstrpr = (Vector) Discoverer.services
4125                     .get("SecStrPred");
4126             if (secstrpr != null)
4127             {
4128               // Add any secondary structure prediction services
4129               for (int i = 0, j = secstrpr.size(); i < j; i++)
4130               {
4131                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4132                         .get(i);
4133                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4134                         .getServiceClient(sh);
4135                 int p = secstrmenu.getItemCount();
4136                 impl.attachWSMenuEntry(secstrmenu, me);
4137                 int q = secstrmenu.getItemCount();
4138                 for (int litm = p; litm < q; litm++)
4139                 {
4140                   legacyItems.add(secstrmenu.getItem(litm));
4141                 }
4142               }
4143             }
4144           }
4145
4146           // Add all submenus in the order they should appear on the web
4147           // services menu
4148           wsmenu.add(msawsmenu);
4149           wsmenu.add(secstrmenu);
4150           wsmenu.add(dismenu);
4151           wsmenu.add(analymenu);
4152           // No search services yet
4153           // wsmenu.add(seqsrchmenu);
4154
4155           javax.swing.SwingUtilities.invokeLater(new Runnable()
4156           {
4157             @Override
4158             public void run()
4159             {
4160               try
4161               {
4162                 webService.removeAll();
4163                 // first, add discovered services onto the webservices menu
4164                 if (wsmenu.size() > 0)
4165                 {
4166                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4167                   {
4168                     webService.add(wsmenu.get(i));
4169                   }
4170                 }
4171                 else
4172                 {
4173                   webService.add(me.webServiceNoServices);
4174                 }
4175                 // TODO: move into separate menu builder class.
4176                 boolean new_sspred = false;
4177                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4178                 {
4179                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4180                   if (jws2servs != null)
4181                   {
4182                     if (jws2servs.hasServices())
4183                     {
4184                       jws2servs.attachWSMenuEntry(webService, me);
4185                       for (Jws2Instance sv : jws2servs.getServices())
4186                       {
4187                         if (sv.description.toLowerCase().contains("jpred"))
4188                         {
4189                           for (JMenuItem jmi : legacyItems)
4190                           {
4191                             jmi.setVisible(false);
4192                           }
4193                         }
4194                       }
4195
4196                     }
4197                     if (jws2servs.isRunning())
4198                     {
4199                       JMenuItem tm = new JMenuItem(
4200                               "Still discovering JABA Services");
4201                       tm.setEnabled(false);
4202                       webService.add(tm);
4203                     }
4204                   }
4205                 }
4206                 build_urlServiceMenu(me.webService);
4207                 build_fetchdbmenu(webService);
4208                 for (JMenu item : wsmenu)
4209                 {
4210                   if (item.getItemCount() == 0)
4211                   {
4212                     item.setEnabled(false);
4213                   }
4214                   else
4215                   {
4216                     item.setEnabled(true);
4217                   }
4218                 }
4219               } catch (Exception e)
4220               {
4221                 Cache.log.debug(
4222                         "Exception during web service menu building process.",
4223                         e);
4224               }
4225             }
4226           });
4227         } catch (Exception e)
4228         {
4229         }
4230         buildingMenu = false;
4231       }
4232     }).start();
4233
4234   }
4235
4236   /**
4237    * construct any groupURL type service menu entries.
4238    *
4239    * @param webService
4240    */
4241   private void build_urlServiceMenu(JMenu webService)
4242   {
4243     // TODO: remove this code when 2.7 is released
4244     // DEBUG - alignmentView
4245     /*
4246      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4247      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4248      *
4249      * @Override public void actionPerformed(ActionEvent e) {
4250      * jalview.datamodel.AlignmentView
4251      * .testSelectionViews(af.viewport.getAlignment(),
4252      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4253      *
4254      * }); webService.add(testAlView);
4255      */
4256     // TODO: refactor to RestClient discoverer and merge menu entries for
4257     // rest-style services with other types of analysis/calculation service
4258     // SHmmr test client - still being implemented.
4259     // DEBUG - alignmentView
4260
4261     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4262             .getRestClients())
4263     {
4264       client.attachWSMenuEntry(
4265               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4266               this);
4267     }
4268   }
4269
4270   /**
4271    * Searches the alignment sequences for xRefs and builds the Show
4272    * Cross-References menu (formerly called Show Products), with database
4273    * sources for which cross-references are found (protein sources for a
4274    * nucleotide alignment and vice versa)
4275    *
4276    * @return true if Show Cross-references menu should be enabled
4277    */
4278   public boolean canShowProducts()
4279   {
4280     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4281     AlignmentI dataset = viewport.getAlignment().getDataset();
4282
4283     showProducts.removeAll();
4284     final boolean dna = viewport.getAlignment().isNucleotide();
4285
4286     if (seqs == null || seqs.length == 0)
4287     {
4288       // nothing to see here.
4289       return false;
4290     }
4291
4292     boolean showp = false;
4293     try
4294     {
4295       List<String> ptypes = new CrossRef(seqs, dataset)
4296               .findXrefSourcesForSequences(dna);
4297
4298       for (final String source : ptypes)
4299       {
4300         showp = true;
4301         final AlignFrame af = this;
4302         JMenuItem xtype = new JMenuItem(source);
4303         xtype.addActionListener(new ActionListener()
4304         {
4305           @Override
4306           public void actionPerformed(ActionEvent e)
4307           {
4308             showProductsFor(af.viewport.getSequenceSelection(), dna,
4309                     source);
4310           }
4311         });
4312         showProducts.add(xtype);
4313       }
4314       showProducts.setVisible(showp);
4315       showProducts.setEnabled(showp);
4316     } catch (Exception e)
4317     {
4318       Cache.log.warn(
4319               "canShowProducts threw an exception - please report to help@jalview.org",
4320               e);
4321       return false;
4322     }
4323     return showp;
4324   }
4325
4326   /**
4327    * Finds and displays cross-references for the selected sequences (protein
4328    * products for nucleotide sequences, dna coding sequences for peptides).
4329    *
4330    * @param sel
4331    *          the sequences to show cross-references for
4332    * @param dna
4333    *          true if from a nucleotide alignment (so showing proteins)
4334    * @param source
4335    *          the database to show cross-references for
4336    */
4337   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4338           final String source)
4339   {
4340     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4341             .start();
4342   }
4343
4344   /**
4345    * Construct and display a new frame containing the translation of this
4346    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4347    */
4348   @Override
4349   public void showTranslation_actionPerformed(ActionEvent e)
4350   {
4351     AlignmentI al = null;
4352     try
4353     {
4354       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4355
4356       al = dna.translateCdna();
4357     } catch (Exception ex)
4358     {
4359       jalview.bin.Cache.log.error(
4360               "Exception during translation. Please report this !", ex);
4361       final String msg = MessageManager.getString(
4362               "label.error_when_translating_sequences_submit_bug_report");
4363       final String errorTitle = MessageManager
4364               .getString("label.implementation_error")
4365               + MessageManager.getString("label.translation_failed");
4366       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4367               JvOptionPane.ERROR_MESSAGE);
4368       return;
4369     }
4370     if (al == null || al.getHeight() == 0)
4371     {
4372       final String msg = MessageManager.getString(
4373               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4374       final String errorTitle = MessageManager
4375               .getString("label.translation_failed");
4376       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4377               JvOptionPane.WARNING_MESSAGE);
4378     }
4379     else
4380     {
4381       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4382       af.setFileFormat(this.currentFileFormat);
4383       final String newTitle = MessageManager
4384               .formatMessage("label.translation_of_params", new Object[]
4385               { this.getTitle() });
4386       af.setTitle(newTitle);
4387       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4388       {
4389         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4390         viewport.openSplitFrame(af, new Alignment(seqs));
4391       }
4392       else
4393       {
4394         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4395                 DEFAULT_HEIGHT);
4396       }
4397     }
4398   }
4399
4400   /**
4401    * Set the file format
4402    *
4403    * @param format
4404    */
4405   public void setFileFormat(FileFormatI format)
4406   {
4407     this.currentFileFormat = format;
4408   }
4409
4410   /**
4411    * Try to load a features file onto the alignment.
4412    *
4413    * @param file
4414    *          contents or path to retrieve file or a File object
4415    * @param sourceType
4416    *          access mode of file (see jalview.io.AlignFile)
4417    * @return true if features file was parsed correctly.
4418    */
4419   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4420   {
4421     // BH 2018
4422     return avc.parseFeaturesFile(file, sourceType,
4423             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4424
4425   }
4426
4427   @Override
4428   public void refreshFeatureUI(boolean enableIfNecessary)
4429   {
4430     // note - currently this is only still here rather than in the controller
4431     // because of the featureSettings hard reference that is yet to be
4432     // abstracted
4433     if (enableIfNecessary)
4434     {
4435       viewport.setShowSequenceFeatures(true);
4436       showSeqFeatures.setSelected(true);
4437     }
4438
4439   }
4440
4441   @Override
4442   public void dragEnter(DropTargetDragEvent evt)
4443   {
4444   }
4445
4446   @Override
4447   public void dragExit(DropTargetEvent evt)
4448   {
4449   }
4450
4451   @Override
4452   public void dragOver(DropTargetDragEvent evt)
4453   {
4454   }
4455
4456   @Override
4457   public void dropActionChanged(DropTargetDragEvent evt)
4458   {
4459   }
4460
4461   @Override
4462   public void drop(DropTargetDropEvent evt)
4463   {
4464     // JAL-1552 - acceptDrop required before getTransferable call for
4465     // Java's Transferable for native dnd
4466     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4467     Transferable t = evt.getTransferable();
4468
4469     final AlignFrame thisaf = this;
4470     final List<Object> files = new ArrayList<>();
4471     List<DataSourceType> protocols = new ArrayList<>();
4472
4473     try
4474     {
4475       Desktop.transferFromDropTarget(files, protocols, evt, t);
4476     } catch (Exception e)
4477     {
4478       e.printStackTrace();
4479     }
4480     if (files != null)
4481     {
4482       new Thread(new Runnable()
4483       {
4484         @Override
4485         public void run()
4486         {
4487           try
4488           {
4489             // check to see if any of these files have names matching sequences
4490             // in
4491             // the alignment
4492             SequenceIdMatcher idm = new SequenceIdMatcher(
4493                     viewport.getAlignment().getSequencesArray());
4494             /**
4495              * Object[] { String,SequenceI}
4496              */
4497             ArrayList<Object[]> filesmatched = new ArrayList<>();
4498             ArrayList<Object> filesnotmatched = new ArrayList<>();
4499             for (int i = 0; i < files.size(); i++)
4500             {
4501               // BH 2018
4502               Object file = files.get(i);
4503               String fileName = file.toString();
4504               String pdbfn = "";
4505               DataSourceType protocol = (file instanceof File
4506                       ? DataSourceType.FILE
4507                       : FormatAdapter.checkProtocol(fileName));
4508               if (protocol == DataSourceType.FILE)
4509               {
4510                 File fl = (file instanceof File ? (File) file
4511                         : new File(fileName));
4512                 pdbfn = fl.getName();
4513               }
4514               else if (protocol == DataSourceType.URL)
4515               {
4516                 URL url = new URL(fileName);
4517                 pdbfn = url.getFile();
4518               }
4519               if (pdbfn.length() > 0)
4520               {
4521                 // attempt to find a match in the alignment
4522                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4523                 int l = 0, c = pdbfn.indexOf(".");
4524                 while (mtch == null && c != -1)
4525                 {
4526                   do
4527                   {
4528                     l = c;
4529                   } while ((c = pdbfn.indexOf(".", l)) > l);
4530                   if (l > -1)
4531                   {
4532                     pdbfn = pdbfn.substring(0, l);
4533                   }
4534                   mtch = idm.findAllIdMatches(pdbfn);
4535                 }
4536                 if (mtch != null)
4537                 {
4538                   FileFormatI type;
4539                   try
4540                   {
4541                     type = new IdentifyFile().identify(file, protocol);
4542                   } catch (Exception ex)
4543                   {
4544                     type = null;
4545                   }
4546                   if (type != null && type.isStructureFile())
4547                   {
4548                     filesmatched.add(new Object[] { file, protocol, mtch });
4549                     continue;
4550                   }
4551                 }
4552                 // File wasn't named like one of the sequences or wasn't a PDB
4553                 // file.
4554                 filesnotmatched.add(file);
4555               }
4556             }
4557             int assocfiles = 0;
4558             if (filesmatched.size() > 0)
4559             {
4560               boolean autoAssociate = Cache
4561                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4562               if (!autoAssociate)
4563               {
4564                 String msg = MessageManager.formatMessage(
4565                         "label.automatically_associate_structure_files_with_sequences_same_name",
4566                         new Object[]
4567                         { Integer.valueOf(filesmatched.size())
4568                                 .toString() });
4569                 String ttl = MessageManager.getString(
4570                         "label.automatically_associate_structure_files_by_name");
4571                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4572                         ttl, JvOptionPane.YES_NO_OPTION);
4573                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4574               }
4575               if (autoAssociate)
4576               {
4577                 for (Object[] fm : filesmatched)
4578                 {
4579                   // try and associate
4580                   // TODO: may want to set a standard ID naming formalism for
4581                   // associating PDB files which have no IDs.
4582                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4583                   {
4584                     PDBEntry pe = new AssociatePdbFileWithSeq()
4585                             .associatePdbWithSeq(fm[0].toString(),
4586                                     (DataSourceType) fm[1], toassoc, false,
4587                                     Desktop.instance);
4588                     if (pe != null)
4589                     {
4590                       System.err.println("Associated file : "
4591                               + (fm[0].toString()) + " with "
4592                               + toassoc.getDisplayId(true));
4593                       assocfiles++;
4594                     }
4595                   }
4596                   // TODO: do we need to update overview ? only if features are
4597                   // shown I guess
4598                   alignPanel.paintAlignment(true, false);
4599                 }
4600               }
4601               else
4602               {
4603                 /*
4604                  * add declined structures as sequences
4605                  */
4606                 for (Object[] o : filesmatched)
4607                 {
4608                   filesnotmatched.add(o[0]);
4609                 }
4610               }
4611             }
4612             if (filesnotmatched.size() > 0)
4613             {
4614               if (assocfiles > 0 && (Cache.getDefault(
4615                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4616                       || JvOptionPane.showConfirmDialog(thisaf,
4617                               "<html>" + MessageManager.formatMessage(
4618                                       "label.ignore_unmatched_dropped_files_info",
4619                                       new Object[]
4620                                       { Integer.valueOf(
4621                                               filesnotmatched.size())
4622                                               .toString() })
4623                                       + "</html>",
4624                               MessageManager.getString(
4625                                       "label.ignore_unmatched_dropped_files"),
4626                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4627               {
4628                 return;
4629               }
4630               for (Object fn : filesnotmatched)
4631               {
4632                 loadJalviewDataFile(fn, null, null, null);
4633               }
4634
4635             }
4636           } catch (Exception ex)
4637           {
4638             ex.printStackTrace();
4639           }
4640         }
4641       }).start();
4642     }
4643   }
4644
4645   /**
4646    * Attempt to load a "dropped" file or URL string, by testing in turn for
4647    * <ul>
4648    * <li>an Annotation file</li>
4649    * <li>a JNet file</li>
4650    * <li>a features file</li>
4651    * <li>else try to interpret as an alignment file</li>
4652    * </ul>
4653    *
4654    * @param file
4655    *          either a filename or a URL string.
4656    */
4657   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4658           FileFormatI format, SequenceI assocSeq)
4659   {
4660     // BH 2018 was String file
4661     try
4662     {
4663       if (sourceType == null)
4664       {
4665         sourceType = FormatAdapter.checkProtocol(file);
4666       }
4667       // if the file isn't identified, or not positively identified as some
4668       // other filetype (PFAM is default unidentified alignment file type) then
4669       // try to parse as annotation.
4670       boolean isAnnotation = (format == null
4671               || FileFormat.Pfam.equals(format))
4672                       ? new AnnotationFile().annotateAlignmentView(viewport,
4673                               file, sourceType)
4674                       : false;
4675
4676       if (!isAnnotation)
4677       {
4678         // first see if its a T-COFFEE score file
4679         TCoffeeScoreFile tcf = null;
4680         try
4681         {
4682           tcf = new TCoffeeScoreFile(file, sourceType);
4683           if (tcf.isValid())
4684           {
4685             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4686             {
4687               buildColourMenu();
4688               changeColour(
4689                       new TCoffeeColourScheme(viewport.getAlignment()));
4690               isAnnotation = true;
4691               setStatus(MessageManager.getString(
4692                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4693             }
4694             else
4695             {
4696               // some problem - if no warning its probable that the ID matching
4697               // process didn't work
4698               JvOptionPane.showMessageDialog(Desktop.desktop,
4699                       tcf.getWarningMessage() == null
4700                               ? MessageManager.getString(
4701                                       "label.check_file_matches_sequence_ids_alignment")
4702                               : tcf.getWarningMessage(),
4703                       MessageManager.getString(
4704                               "label.problem_reading_tcoffee_score_file"),
4705                       JvOptionPane.WARNING_MESSAGE);
4706             }
4707           }
4708           else
4709           {
4710             tcf = null;
4711           }
4712         } catch (Exception x)
4713         {
4714           Cache.log.debug(
4715                   "Exception when processing data source as T-COFFEE score file",
4716                   x);
4717           tcf = null;
4718         }
4719         if (tcf == null)
4720         {
4721           // try to see if its a JNet 'concise' style annotation file *before*
4722           // we
4723           // try to parse it as a features file
4724           if (format == null)
4725           {
4726             format = new IdentifyFile().identify(file, sourceType);
4727           }
4728           if (FileFormat.ScoreMatrix == format)
4729           {
4730             ScoreMatrixFile sm = new ScoreMatrixFile(
4731                     new FileParse(file, sourceType));
4732             sm.parse();
4733             // todo: i18n this message
4734             setStatus(MessageManager.formatMessage(
4735                     "label.successfully_loaded_matrix",
4736                     sm.getMatrixName()));
4737           }
4738           else if (FileFormat.Jnet.equals(format))
4739           {
4740             JPredFile predictions = new JPredFile(file, sourceType);
4741             new JnetAnnotationMaker();
4742             JnetAnnotationMaker.add_annotation(predictions,
4743                     viewport.getAlignment(), 0, false);
4744             viewport.getAlignment().setupJPredAlignment();
4745             isAnnotation = true;
4746           }
4747           // else if (IdentifyFile.FeaturesFile.equals(format))
4748           else if (FileFormat.Features.equals(format))
4749           {
4750             if (parseFeaturesFile(file, sourceType))
4751             {
4752               alignPanel.paintAlignment(true, true);
4753             }
4754           }
4755           else
4756           {
4757             new FileLoader().LoadFile(viewport, file, sourceType, format);
4758           }
4759         }
4760       }
4761       if (isAnnotation)
4762       {
4763
4764         alignPanel.adjustAnnotationHeight();
4765         viewport.updateSequenceIdColours();
4766         buildSortByAnnotationScoresMenu();
4767         alignPanel.paintAlignment(true, true);
4768       }
4769     } catch (Exception ex)
4770     {
4771       ex.printStackTrace();
4772     } catch (OutOfMemoryError oom)
4773     {
4774       try
4775       {
4776         System.gc();
4777       } catch (Exception x)
4778       {
4779       }
4780       new OOMWarning(
4781               "loading data "
4782                       + (sourceType != null
4783                               ? (sourceType == DataSourceType.PASTE
4784                                       ? "from clipboard."
4785                                       : "using " + sourceType + " from "
4786                                               + file)
4787                               : ".")
4788                       + (format != null
4789                               ? "(parsing as '" + format + "' file)"
4790                               : ""),
4791               oom, Desktop.desktop);
4792     }
4793   }
4794
4795   /**
4796    * Method invoked by the ChangeListener on the tabbed pane, in other words
4797    * when a different tabbed pane is selected by the user or programmatically.
4798    */
4799   @Override
4800   public void tabSelectionChanged(int index)
4801   {
4802     if (index > -1)
4803     {
4804       alignPanel = alignPanels.get(index);
4805       viewport = alignPanel.av;
4806       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4807       setMenusFromViewport(viewport);
4808     }
4809
4810     /*
4811      * 'focus' any colour slider that is open to the selected viewport
4812      */
4813     if (viewport.getConservationSelected())
4814     {
4815       SliderPanel.setConservationSlider(alignPanel,
4816               viewport.getResidueShading(), alignPanel.getViewName());
4817     }
4818     else
4819     {
4820       SliderPanel.hideConservationSlider();
4821     }
4822     if (viewport.getAbovePIDThreshold())
4823     {
4824       SliderPanel.setPIDSliderSource(alignPanel,
4825               viewport.getResidueShading(), alignPanel.getViewName());
4826     }
4827     else
4828     {
4829       SliderPanel.hidePIDSlider();
4830     }
4831
4832     /*
4833      * If there is a frame linked to this one in a SplitPane, switch it to the
4834      * same view tab index. No infinite recursion of calls should happen, since
4835      * tabSelectionChanged() should not get invoked on setting the selected
4836      * index to an unchanged value. Guard against setting an invalid index
4837      * before the new view peer tab has been created.
4838      */
4839     final AlignViewportI peer = viewport.getCodingComplement();
4840     if (peer != null)
4841     {
4842       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4843               .getAlignPanel().alignFrame;
4844       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4845       {
4846         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4847       }
4848     }
4849   }
4850
4851   /**
4852    * On right mouse click on view tab, prompt for and set new view name.
4853    */
4854   @Override
4855   public void tabbedPane_mousePressed(MouseEvent e)
4856   {
4857     if (e.isPopupTrigger())
4858     {
4859       String msg = MessageManager.getString("label.enter_view_name");
4860       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4861       String reply = JvOptionPane.showInputDialog(msg, ttl);
4862
4863       if (reply != null)
4864       {
4865         viewport.viewName = reply;
4866         // TODO warn if reply is in getExistingViewNames()?
4867         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4868       }
4869     }
4870   }
4871
4872   public AlignViewport getCurrentView()
4873   {
4874     return viewport;
4875   }
4876
4877   /**
4878    * Open the dialog for regex description parsing.
4879    */
4880   @Override
4881   protected void extractScores_actionPerformed(ActionEvent e)
4882   {
4883     ParseProperties pp = new jalview.analysis.ParseProperties(
4884             viewport.getAlignment());
4885     // TODO: verify regex and introduce GUI dialog for version 2.5
4886     // if (pp.getScoresFromDescription("col", "score column ",
4887     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4888     // true)>0)
4889     if (pp.getScoresFromDescription("description column",
4890             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4891     {
4892       buildSortByAnnotationScoresMenu();
4893     }
4894   }
4895
4896   /*
4897    * (non-Javadoc)
4898    *
4899    * @see
4900    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4901    * )
4902    */
4903   @Override
4904   protected void showDbRefs_actionPerformed(ActionEvent e)
4905   {
4906     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4907   }
4908
4909   /*
4910    * (non-Javadoc)
4911    *
4912    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4913    * ActionEvent)
4914    */
4915   @Override
4916   protected void showNpFeats_actionPerformed(ActionEvent e)
4917   {
4918     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4919   }
4920
4921   /**
4922    * find the viewport amongst the tabs in this alignment frame and close that
4923    * tab
4924    *
4925    * @param av
4926    */
4927   public boolean closeView(AlignViewportI av)
4928   {
4929     if (viewport == av)
4930     {
4931       this.closeMenuItem_actionPerformed(false);
4932       return true;
4933     }
4934     Component[] comp = tabbedPane.getComponents();
4935     for (int i = 0; comp != null && i < comp.length; i++)
4936     {
4937       if (comp[i] instanceof AlignmentPanel)
4938       {
4939         if (((AlignmentPanel) comp[i]).av == av)
4940         {
4941           // close the view.
4942           closeView((AlignmentPanel) comp[i]);
4943           return true;
4944         }
4945       }
4946     }
4947     return false;
4948   }
4949
4950   protected void build_fetchdbmenu(JMenu webService)
4951   {
4952     // Temporary hack - DBRef Fetcher always top level ws entry.
4953     // TODO We probably want to store a sequence database checklist in
4954     // preferences and have checkboxes.. rather than individual sources selected
4955     // here
4956     final JMenu rfetch = new JMenu(
4957             MessageManager.getString("action.fetch_db_references"));
4958     rfetch.setToolTipText(MessageManager.getString(
4959             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4960     webService.add(rfetch);
4961
4962     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4963             MessageManager.getString("option.trim_retrieved_seqs"));
4964     trimrs.setToolTipText(
4965             MessageManager.getString("label.trim_retrieved_sequences"));
4966     trimrs.setSelected(
4967             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4968     trimrs.addActionListener(new ActionListener()
4969     {
4970       @Override
4971       public void actionPerformed(ActionEvent e)
4972       {
4973         trimrs.setSelected(trimrs.isSelected());
4974         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4975                 Boolean.valueOf(trimrs.isSelected()).toString());
4976       };
4977     });
4978     rfetch.add(trimrs);
4979     JMenuItem fetchr = new JMenuItem(
4980             MessageManager.getString("label.standard_databases"));
4981     fetchr.setToolTipText(
4982             MessageManager.getString("label.fetch_embl_uniprot"));
4983     fetchr.addActionListener(new ActionListener()
4984     {
4985
4986       @Override
4987       public void actionPerformed(ActionEvent e)
4988       {
4989         new Thread(new Runnable()
4990         {
4991           @Override
4992           public void run()
4993           {
4994             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4995                     .getAlignment().isNucleotide();
4996             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4997                     alignPanel.av.getSequenceSelection(),
4998                     alignPanel.alignFrame, null,
4999                     alignPanel.alignFrame.featureSettings, isNucleotide);
5000             dbRefFetcher.addListener(new FetchFinishedListenerI()
5001             {
5002               @Override
5003               public void finished()
5004               {
5005                 AlignFrame.this.setMenusForViewport();
5006               }
5007             });
5008             dbRefFetcher.fetchDBRefs(false);
5009           }
5010         }).start();
5011
5012       }
5013
5014     });
5015     rfetch.add(fetchr);
5016     final AlignFrame me = this;
5017     new Thread(new Runnable()
5018     {
5019       @Override
5020       public void run()
5021       {
5022         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5023                 .getSequenceFetcherSingleton(me);
5024         javax.swing.SwingUtilities.invokeLater(new Runnable()
5025         {
5026           @Override
5027           public void run()
5028           {
5029             String[] dbclasses = sf.getOrderedSupportedSources();
5030             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5031             // jalview.util.QuickSort.sort(otherdb, otherdb);
5032             List<DbSourceProxy> otherdb;
5033             JMenu dfetch = new JMenu();
5034             JMenu ifetch = new JMenu();
5035             JMenuItem fetchr = null;
5036             int comp = 0, icomp = 0, mcomp = 15;
5037             String mname = null;
5038             int dbi = 0;
5039             for (String dbclass : dbclasses)
5040             {
5041               otherdb = sf.getSourceProxy(dbclass);
5042               // add a single entry for this class, or submenu allowing 'fetch
5043               // all' or pick one
5044               if (otherdb == null || otherdb.size() < 1)
5045               {
5046                 continue;
5047               }
5048               // List<DbSourceProxy> dbs=otherdb;
5049               // otherdb=new ArrayList<DbSourceProxy>();
5050               // for (DbSourceProxy db:dbs)
5051               // {
5052               // if (!db.isA(DBRefSource.ALIGNMENTDB)
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       alignPanel.alignmentChanged();
5404     }
5405   }
5406
5407   @Override
5408   protected void unGroup_actionPerformed(ActionEvent e)
5409   {
5410     if (avc.unGroup())
5411     {
5412       alignPanel.alignmentChanged();
5413     }
5414   }
5415
5416   /**
5417    * make the given alignmentPanel the currently selected tab
5418    *
5419    * @param alignmentPanel
5420    */
5421   public void setDisplayedView(AlignmentPanel alignmentPanel)
5422   {
5423     if (!viewport.getSequenceSetId()
5424             .equals(alignmentPanel.av.getSequenceSetId()))
5425     {
5426       throw new Error(MessageManager.getString(
5427               "error.implementation_error_cannot_show_view_alignment_frame"));
5428     }
5429     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5430             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5431     {
5432       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5433     }
5434   }
5435
5436   /**
5437    * Action on selection of menu options to Show or Hide annotations.
5438    *
5439    * @param visible
5440    * @param forSequences
5441    *          update sequence-related annotations
5442    * @param forAlignment
5443    *          update non-sequence-related annotations
5444    */
5445   @Override
5446   protected void setAnnotationsVisibility(boolean visible,
5447           boolean forSequences, boolean forAlignment)
5448   {
5449     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5450             .getAlignmentAnnotation();
5451     if (anns == null)
5452     {
5453       return;
5454     }
5455     for (AlignmentAnnotation aa : anns)
5456     {
5457       /*
5458        * don't display non-positional annotations on an alignment
5459        */
5460       if (aa.annotations == null)
5461       {
5462         continue;
5463       }
5464       boolean apply = (aa.sequenceRef == null && forAlignment)
5465               || (aa.sequenceRef != null && forSequences);
5466       if (apply)
5467       {
5468         aa.visible = visible;
5469       }
5470     }
5471     alignPanel.validateAnnotationDimensions(true);
5472     alignPanel.alignmentChanged();
5473   }
5474
5475   /**
5476    * Store selected annotation sort order for the view and repaint.
5477    */
5478   @Override
5479   protected void sortAnnotations_actionPerformed()
5480   {
5481     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5482     this.alignPanel.av
5483             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5484     alignPanel.paintAlignment(false, false);
5485   }
5486
5487   /**
5488    *
5489    * @return alignment panels in this alignment frame
5490    */
5491   public List<? extends AlignmentViewPanel> getAlignPanels()
5492   {
5493     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5494   }
5495
5496   /**
5497    * Open a new alignment window, with the cDNA associated with this (protein)
5498    * alignment, aligned as is the protein.
5499    */
5500   protected void viewAsCdna_actionPerformed()
5501   {
5502     // TODO no longer a menu action - refactor as required
5503     final AlignmentI alignment = getViewport().getAlignment();
5504     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5505     if (mappings == null)
5506     {
5507       return;
5508     }
5509     List<SequenceI> cdnaSeqs = new ArrayList<>();
5510     for (SequenceI aaSeq : alignment.getSequences())
5511     {
5512       for (AlignedCodonFrame acf : mappings)
5513       {
5514         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5515         if (dnaSeq != null)
5516         {
5517           /*
5518            * There is a cDNA mapping for this protein sequence - add to new
5519            * alignment. It will share the same dataset sequence as other mapped
5520            * cDNA (no new mappings need to be created).
5521            */
5522           final Sequence newSeq = new Sequence(dnaSeq);
5523           newSeq.setDatasetSequence(dnaSeq);
5524           cdnaSeqs.add(newSeq);
5525         }
5526       }
5527     }
5528     if (cdnaSeqs.size() == 0)
5529     {
5530       // show a warning dialog no mapped cDNA
5531       return;
5532     }
5533     AlignmentI cdna = new Alignment(
5534             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5535     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5536             AlignFrame.DEFAULT_HEIGHT);
5537     cdna.alignAs(alignment);
5538     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5539             + this.title;
5540     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5541             AlignFrame.DEFAULT_HEIGHT);
5542   }
5543
5544   /**
5545    * Set visibility of dna/protein complement view (available when shown in a
5546    * split frame).
5547    *
5548    * @param show
5549    */
5550   @Override
5551   protected void showComplement_actionPerformed(boolean show)
5552   {
5553     SplitContainerI sf = getSplitViewContainer();
5554     if (sf != null)
5555     {
5556       sf.setComplementVisible(this, show);
5557     }
5558   }
5559
5560   /**
5561    * Generate the reverse (optionally complemented) of the selected sequences,
5562    * and add them to the alignment
5563    */
5564   @Override
5565   protected void showReverse_actionPerformed(boolean complement)
5566   {
5567     AlignmentI al = null;
5568     try
5569     {
5570       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5571       al = dna.reverseCdna(complement);
5572       viewport.addAlignment(al, "");
5573       addHistoryItem(new EditCommand(
5574               MessageManager.getString("label.add_sequences"), Action.PASTE,
5575               al.getSequencesArray(), 0, al.getWidth(),
5576               viewport.getAlignment()));
5577     } catch (Exception ex)
5578     {
5579       System.err.println(ex.getMessage());
5580       return;
5581     }
5582   }
5583
5584   /**
5585    * Try to run a script in the Groovy console, having first ensured that this
5586    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5587    * be targeted at this alignment.
5588    */
5589   @Override
5590   protected void runGroovy_actionPerformed()
5591   {
5592     Jalview.setCurrentAlignFrame(this);
5593     groovy.ui.Console console = Desktop.getGroovyConsole();
5594     if (console != null)
5595     {
5596       try
5597       {
5598         console.runScript();
5599       } catch (Exception ex)
5600       {
5601         System.err.println((ex.toString()));
5602         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5603                 MessageManager.getString("label.couldnt_run_groovy_script"),
5604                 MessageManager.getString("label.groovy_support_failed"),
5605                 JvOptionPane.ERROR_MESSAGE);
5606       }
5607     }
5608     else
5609     {
5610       System.err.println("Can't run Groovy script as console not found");
5611     }
5612   }
5613
5614   /**
5615    * Hides columns containing (or not containing) a specified feature, provided
5616    * that would not leave all columns hidden
5617    *
5618    * @param featureType
5619    * @param columnsContaining
5620    * @return
5621    */
5622   public boolean hideFeatureColumns(String featureType,
5623           boolean columnsContaining)
5624   {
5625     boolean notForHiding = avc.markColumnsContainingFeatures(
5626             columnsContaining, false, false, featureType);
5627     if (notForHiding)
5628     {
5629       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5630               false, featureType))
5631       {
5632         getViewport().hideSelectedColumns();
5633         return true;
5634       }
5635     }
5636     return false;
5637   }
5638
5639   @Override
5640   protected void selectHighlightedColumns_actionPerformed(
5641           ActionEvent actionEvent)
5642   {
5643     // include key modifier check in case user selects from menu
5644     avc.markHighlightedColumns(
5645             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5646             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5647                     | ActionEvent.CTRL_MASK)) != 0);
5648   }
5649
5650   /**
5651    * Rebuilds the Colour menu, including any user-defined colours which have
5652    * been loaded either on startup or during the session
5653    */
5654   public void buildColourMenu()
5655   {
5656     colourMenu.removeAll();
5657
5658     colourMenu.add(applyToAllGroups);
5659     colourMenu.add(textColour);
5660     colourMenu.addSeparator();
5661
5662     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5663             false);
5664
5665     colourMenu.addSeparator();
5666     colourMenu.add(conservationMenuItem);
5667     colourMenu.add(modifyConservation);
5668     colourMenu.add(abovePIDThreshold);
5669     colourMenu.add(modifyPID);
5670     colourMenu.add(annotationColour);
5671
5672     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5673     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5674   }
5675
5676   /**
5677    * Open a dialog (if not already open) that allows the user to select and
5678    * calculate PCA or Tree analysis
5679    */
5680   protected void openTreePcaDialog()
5681   {
5682     if (alignPanel.getCalculationDialog() == null)
5683     {
5684       new CalculationChooser(AlignFrame.this);
5685     }
5686   }
5687
5688   @Override
5689   protected void loadVcf_actionPerformed()
5690   {
5691     JalviewFileChooser chooser = new JalviewFileChooser(
5692             Cache.getProperty("LAST_DIRECTORY"));
5693     chooser.setFileView(new JalviewFileView());
5694     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5695     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5696     final AlignFrame us = this;
5697     chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5698     {
5699       @Override
5700       public void run()
5701       {
5702
5703         {
5704           String choice = chooser.getSelectedFile().getPath();
5705           Cache.setProperty("LAST_DIRECTORY", choice);
5706           SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5707           new VCFLoader(choice).loadVCF(seqs, us);
5708         }
5709
5710       };
5711     }).openDialog(null);
5712
5713   }
5714
5715 }
5716
5717 class PrintThread extends Thread
5718 {
5719   AlignmentPanel ap;
5720
5721   public PrintThread(AlignmentPanel ap)
5722   {
5723     this.ap = ap;
5724   }
5725
5726   static PageFormat pf;
5727
5728   @Override
5729   public void run()
5730   {
5731     PrinterJob printJob = PrinterJob.getPrinterJob();
5732
5733     if (pf != null)
5734     {
5735       printJob.setPrintable(ap, pf);
5736     }
5737     else
5738     {
5739       printJob.setPrintable(ap);
5740     }
5741
5742     if (printJob.printDialog())
5743     {
5744       try
5745       {
5746         printJob.print();
5747       } catch (Exception PrintException)
5748       {
5749         PrintException.printStackTrace();
5750       }
5751     }
5752   }
5753 }