src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Rectangle;
  27 import java.awt.Toolkit;
  28 import java.awt.datatransfer.Clipboard;
  29 import java.awt.datatransfer.DataFlavor;
  30 import java.awt.datatransfer.StringSelection;
  31 import java.awt.datatransfer.Transferable;
  32 import java.awt.dnd.DnDConstants;
  33 import java.awt.dnd.DropTargetDragEvent;
  34 import java.awt.dnd.DropTargetDropEvent;
  35 import java.awt.dnd.DropTargetEvent;
  36 import java.awt.dnd.DropTargetListener;
  37 import java.awt.event.ActionEvent;
  38 import java.awt.event.ActionListener;
  39 import java.awt.event.FocusAdapter;
  40 import java.awt.event.FocusEvent;
  41 import java.awt.event.ItemEvent;
  42 import java.awt.event.ItemListener;
  43 import java.awt.event.KeyAdapter;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.print.PageFormat;
  47 import java.awt.print.PrinterJob;
  48 import java.beans.PropertyChangeEvent;
  49 import java.io.File;
  50 import java.io.FileWriter;
  51 import java.io.IOException;
  52 import java.io.PrintWriter;
  53 import java.net.URL;
  54 import java.util.ArrayList;
  55 import java.util.Arrays;
  56 import java.util.Deque;
  57 import java.util.Enumeration;
  58 import java.util.Hashtable;
  59 import java.util.List;
  60 import java.util.Locale;
  61 import java.util.Vector;
  62 import java.util.concurrent.Callable;
  63
  64 import javax.swing.ButtonGroup;
  65 import javax.swing.JCheckBoxMenuItem;
  66 import javax.swing.JComponent;
  67 import javax.swing.JEditorPane;
  68 import javax.swing.JInternalFrame;
  69 import javax.swing.JLabel;
  70 import javax.swing.JLayeredPane;
  71 import javax.swing.JMenu;
  72 import javax.swing.JMenuItem;
  73 import javax.swing.JPanel;
  74 import javax.swing.JScrollPane;
  75 import javax.swing.SwingUtilities;
  76
  77 import ext.vamsas.ServiceHandle;
  78 import jalview.analysis.AlignmentSorter;
  79 import jalview.analysis.AlignmentUtils;
  80 import jalview.analysis.CrossRef;
  81 import jalview.analysis.Dna;
  82 import jalview.analysis.GeneticCodeI;
  83 import jalview.analysis.ParseProperties;
  84 import jalview.analysis.SequenceIdMatcher;
  85 import jalview.api.AlignExportSettingsI;
  86 import jalview.api.AlignViewControllerGuiI;
  87 import jalview.api.AlignViewControllerI;
  88 import jalview.api.AlignViewportI;
  89 import jalview.api.AlignmentViewPanel;
  90 import jalview.api.FeatureSettingsControllerI;
  91 import jalview.api.FeatureSettingsModelI;
  92 import jalview.api.SplitContainerI;
  93 import jalview.api.ViewStyleI;
  94 import jalview.api.analysis.SimilarityParamsI;
  95 import jalview.bin.Cache;
  96 import jalview.bin.Console;
  97 import jalview.bin.Jalview;
  98 import jalview.commands.CommandI;
  99 import jalview.commands.EditCommand;
 100 import jalview.commands.EditCommand.Action;
 101 import jalview.commands.OrderCommand;
 102 import jalview.commands.RemoveGapColCommand;
 103 import jalview.commands.RemoveGapsCommand;
 104 import jalview.commands.SlideSequencesCommand;
 105 import jalview.commands.TrimRegionCommand;
 106 import jalview.datamodel.AlignExportSettingsAdapter;
 107 import jalview.datamodel.AlignedCodonFrame;
 108 import jalview.datamodel.Alignment;
 109 import jalview.datamodel.AlignmentAnnotation;
 110 import jalview.datamodel.AlignmentExportData;
 111 import jalview.datamodel.AlignmentI;
 112 import jalview.datamodel.AlignmentOrder;
 113 import jalview.datamodel.AlignmentView;
 114 import jalview.datamodel.ColumnSelection;
 115 import jalview.datamodel.HiddenColumns;
 116 import jalview.datamodel.PDBEntry;
 117 import jalview.datamodel.SeqCigar;
 118 import jalview.datamodel.Sequence;
 119 import jalview.datamodel.SequenceGroup;
 120 import jalview.datamodel.SequenceI;
 121 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 122 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 123 import jalview.io.AlignmentProperties;
 124 import jalview.io.AnnotationFile;
 125 import jalview.io.BackupFiles;
 126 import jalview.io.BioJsHTMLOutput;
 127 import jalview.io.DataSourceType;
 128 import jalview.io.FileFormat;
 129 import jalview.io.FileFormatI;
 130 import jalview.io.FileFormats;
 131 import jalview.io.FileLoader;
 132 import jalview.io.FileParse;
 133 import jalview.io.FormatAdapter;
 134 import jalview.io.HtmlSvgOutput;
 135 import jalview.io.IdentifyFile;
 136 import jalview.io.JPredFile;
 137 import jalview.io.JalviewFileChooser;
 138 import jalview.io.JalviewFileView;
 139 import jalview.io.JnetAnnotationMaker;
 140 import jalview.io.NewickFile;
 141 import jalview.io.ScoreMatrixFile;
 142 import jalview.io.TCoffeeScoreFile;
 143 import jalview.io.vcf.VCFLoader;
 144 import jalview.jbgui.GAlignFrame;
 145 import jalview.project.Jalview2XML;
 146 import jalview.schemes.ColourSchemeI;
 147 import jalview.schemes.ColourSchemes;
 148 import jalview.schemes.ResidueColourScheme;
 149 import jalview.schemes.TCoffeeColourScheme;
 150 import jalview.util.HttpUtils;
 151 import jalview.util.ImageMaker.TYPE;
 152 import jalview.util.MessageManager;
 153 import jalview.util.Platform;
 154 import jalview.viewmodel.AlignmentViewport;
 155 import jalview.viewmodel.ViewportRanges;
 156 import jalview.ws.DBRefFetcher;
 157 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 158 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 159 import jalview.ws.jws1.Discoverer;
 160 import jalview.ws.jws2.Jws2Discoverer;
 161 import jalview.ws.jws2.jabaws2.Jws2Instance;
 162 import jalview.ws.seqfetcher.DbSourceProxy;
 163
 164 /**
 165  * DOCUMENT ME!
 166  *
 167  * @author $author$
 168  * @version $Revision$
 169  */
 170 @SuppressWarnings("serial")
 171 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 172         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 173 {
 174
 175   public static final int DEFAULT_WIDTH = 700;
 176
 177   public static final int DEFAULT_HEIGHT = 500;
 178
 179   /*
 180    * The currently displayed panel (selected tabbed view if more than one)
 181    */
 182   public AlignmentPanel alignPanel;
 183
 184   AlignViewport viewport;
 185
 186   public AlignViewControllerI avc;
 187
 188   List<AlignmentPanel> alignPanels = new ArrayList<>();
 189
 190   /**
 191    * Last format used to load or save alignments in this window
 192    */
 193   FileFormatI currentFileFormat = null;
 194
 195   /**
 196    * Current filename for this alignment
 197    */
 198   String fileName = null;
 199
 200   File fileObject;
 201
 202   /**
 203    * Creates a new AlignFrame object with specific width and height.
 204    *
 205    * @param al
 206    * @param width
 207    * @param height
 208    */
 209   public AlignFrame(AlignmentI al, int width, int height)
 210   {
 211     this(al, null, width, height);
 212   }
 213
 214   /**
 215    * Creates a new AlignFrame object with specific width, height and
 216    * sequenceSetId
 217    *
 218    * @param al
 219    * @param width
 220    * @param height
 221    * @param sequenceSetId
 222    */
 223   public AlignFrame(AlignmentI al, int width, int height,
 224           String sequenceSetId)
 225   {
 226     this(al, null, width, height, sequenceSetId);
 227   }
 228
 229   /**
 230    * Creates a new AlignFrame object with specific width, height and
 231    * sequenceSetId
 232    *
 233    * @param al
 234    * @param width
 235    * @param height
 236    * @param sequenceSetId
 237    * @param viewId
 238    */
 239   public AlignFrame(AlignmentI al, int width, int height,
 240           String sequenceSetId, String viewId)
 241   {
 242     this(al, null, width, height, sequenceSetId, viewId);
 243   }
 244
 245   /**
 246    * new alignment window with hidden columns
 247    *
 248    * @param al
 249    *          AlignmentI
 250    * @param hiddenColumns
 251    *          ColumnSelection or null
 252    * @param width
 253    *          Width of alignment frame
 254    * @param height
 255    *          height of frame.
 256    */
 257   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 258           int height)
 259   {
 260     this(al, hiddenColumns, width, height, null);
 261   }
 262
 263   /**
 264    * Create alignment frame for al with hiddenColumns, a specific width and
 265    * height, and specific sequenceId
 266    *
 267    * @param al
 268    * @param hiddenColumns
 269    * @param width
 270    * @param height
 271    * @param sequenceSetId
 272    *          (may be null)
 273    */
 274   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 275           int height, String sequenceSetId)
 276   {
 277     this(al, hiddenColumns, width, height, sequenceSetId, null);
 278   }
 279
 280   /**
 281    * Create alignment frame for al with hiddenColumns, a specific width and
 282    * height, and specific sequenceId
 283    *
 284    * @param al
 285    * @param hiddenColumns
 286    * @param width
 287    * @param height
 288    * @param sequenceSetId
 289    *          (may be null)
 290    * @param viewId
 291    *          (may be null)
 292    */
 293   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 294           int height, String sequenceSetId, String viewId)
 295   {
 296     setSize(width, height);
 297
 298     if (al.getDataset() == null)
 299     {
 300       al.setDataset(null);
 301     }
 302
 303     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 304
 305     alignPanel = new AlignmentPanel(this, viewport);
 306
 307     addAlignmentPanel(alignPanel, true);
 308     init();
 309   }
 310
 311   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 312           HiddenColumns hiddenColumns, int width, int height)
 313   {
 314     setSize(width, height);
 315
 316     if (al.getDataset() == null)
 317     {
 318       al.setDataset(null);
 319     }
 320
 321     viewport = new AlignViewport(al, hiddenColumns);
 322
 323     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 324     {
 325       viewport.hideSequence(hiddenSeqs);
 326     }
 327     alignPanel = new AlignmentPanel(this, viewport);
 328     addAlignmentPanel(alignPanel, true);
 329     init();
 330   }
 331
 332   /**
 333    * Make a new AlignFrame from existing alignmentPanels
 334    *
 335    * @param ap
 336    *          AlignmentPanel
 337    * @param av
 338    *          AlignViewport
 339    */
 340   public AlignFrame(AlignmentPanel ap)
 341   {
 342     viewport = ap.av;
 343     alignPanel = ap;
 344     addAlignmentPanel(ap, false);
 345     init();
 346   }
 347
 348   /**
 349    * initalise the alignframe from the underlying viewport data and the
 350    * configurations
 351    */
 352   void init()
 353   {
 354     setFrameIcon(null);
 355
 356     // setBackground(Color.white); // BH 2019
 357
 358     if (!Jalview.isHeadlessMode())
 359     {
 360       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 361     }
 362
 363     avc = new jalview.controller.AlignViewController(this, viewport,
 364             alignPanel);
 365     if (viewport.getAlignmentConservationAnnotation() == null)
 366     {
 367       // BLOSUM62Colour.setEnabled(false);
 368       conservationMenuItem.setEnabled(false);
 369       modifyConservation.setEnabled(false);
 370       // PIDColour.setEnabled(false);
 371       // abovePIDThreshold.setEnabled(false);
 372       // modifyPID.setEnabled(false);
 373     }
 374
 375     String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 376
 377     if (sortby.equals("Id"))
 378     {
 379       sortIDMenuItem_actionPerformed(null);
 380     }
 381     else if (sortby.equals("Pairwise Identity"))
 382     {
 383       sortPairwiseMenuItem_actionPerformed(null);
 384     }
 385
 386     this.alignPanel.av
 387             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 388
 389     setMenusFromViewport(viewport);
 390     buildSortByAnnotationScoresMenu();
 391     calculateTree.addActionListener(new ActionListener()
 392     {
 393
 394       @Override
 395       public void actionPerformed(ActionEvent e)
 396       {
 397         openTreePcaDialog();
 398       }
 399     });
 400     buildColourMenu();
 401
 402     if (Desktop.desktop != null)
 403     {
 404       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 405       if (!Platform.isJS())
 406       {
 407         addServiceListeners();
 408       }
 409       setGUINucleotide();
 410     }
 411
 412     if (viewport.getWrapAlignment())
 413     {
 414       wrapMenuItem_actionPerformed(null);
 415     }
 416
 417     if (Cache.getDefault("SHOW_OVERVIEW", false))
 418     {
 419       this.overviewMenuItem_actionPerformed(null);
 420     }
 421
 422     addKeyListener();
 423
 424     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 425     final List<AlignmentPanel> origview = new ArrayList<>();
 426     final String menuLabel = MessageManager
 427             .getString("label.copy_format_from");
 428     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 429             new ViewSetProvider()
 430             {
 431
 432               @Override
 433               public AlignmentPanel[] getAllAlignmentPanels()
 434               {
 435                 origview.clear();
 436                 origview.add(alignPanel);
 437                 // make an array of all alignment panels except for this one
 438                 List<AlignmentPanel> aps = new ArrayList<>(
 439                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 440                 aps.remove(AlignFrame.this.alignPanel);
 441                 return aps.toArray(new AlignmentPanel[aps.size()]);
 442               }
 443             }, selviews, new ItemListener()
 444             {
 445
 446               @Override
 447               public void itemStateChanged(ItemEvent e)
 448               {
 449                 if (origview.size() > 0)
 450                 {
 451                   final AlignmentPanel ap = origview.get(0);
 452
 453                   /*
 454                    * Copy the ViewStyle of the selected panel to 'this one'.
 455                    * Don't change value of 'scaleProteinAsCdna' unless copying
 456                    * from a SplitFrame.
 457                    */
 458                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 459                           .getViewStyle();
 460                   boolean fromSplitFrame = selviews.get(0)
 461                           .getAlignViewport().getCodingComplement() != null;
 462                   if (!fromSplitFrame)
 463                   {
 464                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 465                             .getViewStyle().isScaleProteinAsCdna());
 466                   }
 467                   ap.getAlignViewport().setViewStyle(vs);
 468
 469                   /*
 470                    * Also rescale ViewStyle of SplitFrame complement if there is
 471                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 472                    * the whole ViewStyle (allow cDNA protein to have different
 473                    * fonts)
 474                    */
 475                   AlignViewportI complement = ap.getAlignViewport()
 476                           .getCodingComplement();
 477                   if (complement != null && vs.isScaleProteinAsCdna())
 478                   {
 479                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 480                     ((SplitFrame) af.getSplitViewContainer())
 481                             .adjustLayout();
 482                     af.setMenusForViewport();
 483                   }
 484
 485                   ap.updateLayout();
 486                   ap.setSelected(true);
 487                   ap.alignFrame.setMenusForViewport();
 488
 489                 }
 490               }
 491             });
 492     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
 493             .indexOf("devel") > -1
 494             || Cache.getDefault("VERSION", "DEVELOPMENT")
 495                     .toLowerCase(Locale.ROOT).indexOf("test") > -1)
 496     {
 497       formatMenu.add(vsel);
 498     }
 499     addFocusListener(new FocusAdapter()
 500     {
 501       @Override
 502       public void focusGained(FocusEvent e)
 503       {
 504         Jalview.setCurrentAlignFrame(AlignFrame.this);
 505       }
 506     });
 507
 508   }
 509
 510   /**
 511    * Change the filename and format for the alignment, and enable the 'reload'
 512    * button functionality.
 513    *
 514    * @param file
 515    *          valid filename
 516    * @param format
 517    *          format of file
 518    */
 519   public void setFileName(String file, FileFormatI format)
 520   {
 521     fileName = file;
 522     setFileFormat(format);
 523     reload.setEnabled(true);
 524   }
 525
 526   /**
 527    * JavaScript will have this, maybe others. More dependable than a file name
 528    * and maintains a reference to the actual bytes loaded.
 529    *
 530    * @param file
 531    */
 532   public void setFileObject(File file)
 533   {
 534     this.fileObject = file;
 535   }
 536
 537   /**
 538    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 539    * events
 540    */
 541   void addKeyListener()
 542   {
 543     addKeyListener(new KeyAdapter()
 544     {
 545       @Override
 546       public void keyPressed(KeyEvent evt)
 547       {
 548         if (viewport.cursorMode
 549                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 550                         && evt.getKeyCode() <= KeyEvent.VK_9)
 551                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 552                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 553                 && Character.isDigit(evt.getKeyChar()))
 554         {
 555           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 556         }
 557
 558         switch (evt.getKeyCode())
 559         {
 560
 561         case 27: // escape key
 562           deselectAllSequenceMenuItem_actionPerformed(null);
 563
 564           break;
 565
 566         case KeyEvent.VK_DOWN:
 567           if (evt.isAltDown() || !viewport.cursorMode)
 568           {
 569             moveSelectedSequences(false);
 570           }
 571           if (viewport.cursorMode)
 572           {
 573             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 574           }
 575           break;
 576
 577         case KeyEvent.VK_UP:
 578           if (evt.isAltDown() || !viewport.cursorMode)
 579           {
 580             moveSelectedSequences(true);
 581           }
 582           if (viewport.cursorMode)
 583           {
 584             alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
 585           }
 586
 587           break;
 588
 589         case KeyEvent.VK_LEFT:
 590           if (evt.isAltDown() || !viewport.cursorMode)
 591           {
 592             slideSequences(false,
 593                     alignPanel.getSeqPanel().getKeyboardNo1());
 594           }
 595           else
 596           {
 597             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 598           }
 599
 600           break;
 601
 602         case KeyEvent.VK_RIGHT:
 603           if (evt.isAltDown() || !viewport.cursorMode)
 604           {
 605             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 606           }
 607           else
 608           {
 609             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 610           }
 611           break;
 612
 613         case KeyEvent.VK_SPACE:
 614           if (viewport.cursorMode)
 615           {
 616             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 617                     || evt.isShiftDown() || evt.isAltDown());
 618           }
 619           break;
 620
 621         // case KeyEvent.VK_A:
 622         // if (viewport.cursorMode)
 623         // {
 624         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 625         // //System.out.println("A");
 626         // }
 627         // break;
 628         /*
 629          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 630          * System.out.println("closing bracket"); } break;
 631          */
 632         case KeyEvent.VK_DELETE:
 633         case KeyEvent.VK_BACK_SPACE:
 634           if (!viewport.cursorMode)
 635           {
 636             cut_actionPerformed();
 637           }
 638           else
 639           {
 640             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 641                     || evt.isShiftDown() || evt.isAltDown());
 642           }
 643
 644           break;
 645
 646         case KeyEvent.VK_S:
 647           if (viewport.cursorMode)
 648           {
 649             alignPanel.getSeqPanel().setCursorRow();
 650           }
 651           break;
 652         case KeyEvent.VK_C:
 653           if (viewport.cursorMode && !evt.isControlDown())
 654           {
 655             alignPanel.getSeqPanel().setCursorColumn();
 656           }
 657           break;
 658         case KeyEvent.VK_P:
 659           if (viewport.cursorMode)
 660           {
 661             alignPanel.getSeqPanel().setCursorPosition();
 662           }
 663           break;
 664
 665         case KeyEvent.VK_ENTER:
 666         case KeyEvent.VK_COMMA:
 667           if (viewport.cursorMode)
 668           {
 669             alignPanel.getSeqPanel().setCursorRowAndColumn();
 670           }
 671           break;
 672
 673         case KeyEvent.VK_Q:
 674           if (viewport.cursorMode)
 675           {
 676             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 677           }
 678           break;
 679         case KeyEvent.VK_M:
 680           if (viewport.cursorMode)
 681           {
 682             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 683           }
 684           break;
 685
 686         case KeyEvent.VK_F2:
 687           viewport.cursorMode = !viewport.cursorMode;
 688           setStatus(MessageManager
 689                   .formatMessage("label.keyboard_editing_mode", new String[]
 690                   { (viewport.cursorMode ? "on" : "off") }));
 691           if (viewport.cursorMode)
 692           {
 693             ViewportRanges ranges = viewport.getRanges();
 694             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 695                     .getStartRes();
 696             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 697                     .getStartSeq();
 698           }
 699           alignPanel.getSeqPanel().seqCanvas.repaint();
 700           break;
 701
 702         case KeyEvent.VK_F1:
 703           try
 704           {
 705             Help.showHelpWindow();
 706           } catch (Exception ex)
 707           {
 708             ex.printStackTrace();
 709           }
 710           break;
 711         case KeyEvent.VK_H:
 712         {
 713           boolean toggleSeqs = !evt.isControlDown();
 714           boolean toggleCols = !evt.isShiftDown();
 715           toggleHiddenRegions(toggleSeqs, toggleCols);
 716           break;
 717         }
 718         case KeyEvent.VK_B:
 719         {
 720           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 721           boolean modifyExisting = true; // always modify, don't clear
 722                                          // evt.isShiftDown();
 723           boolean invertHighlighted = evt.isAltDown();
 724           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 725                   toggleSel);
 726           break;
 727         }
 728         case KeyEvent.VK_PAGE_UP:
 729           viewport.getRanges().pageUp();
 730           break;
 731         case KeyEvent.VK_PAGE_DOWN:
 732           viewport.getRanges().pageDown();
 733           break;
 734         }
 735       }
 736
 737       @Override
 738       public void keyReleased(KeyEvent evt)
 739       {
 740         switch (evt.getKeyCode())
 741         {
 742         case KeyEvent.VK_LEFT:
 743           if (evt.isAltDown() || !viewport.cursorMode)
 744           {
 745             viewport.firePropertyChange("alignment", null,
 746                     viewport.getAlignment().getSequences());
 747           }
 748           break;
 749
 750         case KeyEvent.VK_RIGHT:
 751           if (evt.isAltDown() || !viewport.cursorMode)
 752           {
 753             viewport.firePropertyChange("alignment", null,
 754                     viewport.getAlignment().getSequences());
 755           }
 756           break;
 757         }
 758       }
 759     });
 760   }
 761
 762   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 763   {
 764     ap.alignFrame = this;
 765     avc = new jalview.controller.AlignViewController(this, viewport,
 766             alignPanel);
 767
 768     alignPanels.add(ap);
 769
 770     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 771
 772     int aSize = alignPanels.size();
 773
 774     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 775
 776     if (aSize == 1 && ap.av.getViewName() == null)
 777     {
 778       this.getContentPane().add(ap, BorderLayout.CENTER);
 779     }
 780     else
 781     {
 782       if (aSize == 2)
 783       {
 784         setInitialTabVisible();
 785       }
 786
 787       expandViews.setEnabled(true);
 788       gatherViews.setEnabled(true);
 789       tabbedPane.addTab(ap.av.getViewName(), ap);
 790
 791       ap.setVisible(false);
 792     }
 793
 794     if (newPanel)
 795     {
 796       if (ap.av.isPadGaps())
 797       {
 798         ap.av.getAlignment().padGaps();
 799       }
 800       ap.av.updateConservation(ap);
 801       ap.av.updateConsensus(ap);
 802       ap.av.updateStrucConsensus(ap);
 803     }
 804   }
 805
 806   public void setInitialTabVisible()
 807   {
 808     expandViews.setEnabled(true);
 809     gatherViews.setEnabled(true);
 810     tabbedPane.setVisible(true);
 811     AlignmentPanel first = alignPanels.get(0);
 812     tabbedPane.addTab(first.av.getViewName(), first);
 813     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 814   }
 815
 816   public AlignViewport getViewport()
 817   {
 818     return viewport;
 819   }
 820
 821   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 822   private void addServiceListeners()
 823   {
 824     final java.beans.PropertyChangeListener thisListener;
 825     Desktop.instance.addJalviewPropertyChangeListener("services",
 826             thisListener = new java.beans.PropertyChangeListener()
 827             {
 828               @Override
 829               public void propertyChange(PropertyChangeEvent evt)
 830               {
 831                 // // System.out.println("Discoverer property change.");
 832                 // if (evt.getPropertyName().equals("services"))
 833                 {
 834                   SwingUtilities.invokeLater(new Runnable()
 835                   {
 836
 837                     @Override
 838                     public void run()
 839                     {
 840                       System.err.println(
 841                               "Rebuild WS Menu for service change");
 842                       BuildWebServiceMenu();
 843                     }
 844
 845                   });
 846                 }
 847               }
 848             });
 849     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 850     {
 851       @Override
 852       public void internalFrameClosed(
 853               javax.swing.event.InternalFrameEvent evt)
 854       {
 855         // System.out.println("deregistering discoverer listener");
 856         Desktop.instance.removeJalviewPropertyChangeListener("services",
 857                 thisListener);
 858         closeMenuItem_actionPerformed(true);
 859       }
 860     });
 861     // Finally, build the menu once to get current service state
 862     new Thread(new Runnable()
 863     {
 864       @Override
 865       public void run()
 866       {
 867         BuildWebServiceMenu();
 868       }
 869     }).start();
 870   }
 871
 872   /**
 873    * Configure menu items that vary according to whether the alignment is
 874    * nucleotide or protein
 875    */
 876   public void setGUINucleotide()
 877   {
 878     AlignmentI al = getViewport().getAlignment();
 879     boolean nucleotide = al.isNucleotide();
 880
 881     loadVcf.setVisible(nucleotide);
 882     showTranslation.setVisible(nucleotide);
 883     showReverse.setVisible(nucleotide);
 884     showReverseComplement.setVisible(nucleotide);
 885     conservationMenuItem.setEnabled(!nucleotide);
 886     modifyConservation
 887             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 888     showGroupConservation.setEnabled(!nucleotide);
 889
 890     showComplementMenuItem
 891             .setText(nucleotide ? MessageManager.getString("label.protein")
 892                     : MessageManager.getString("label.nucleotide"));
 893   }
 894
 895   /**
 896    * set up menus for the current viewport. This may be called after any
 897    * operation that affects the data in the current view (selection changed,
 898    * etc) to update the menus to reflect the new state.
 899    */
 900   @Override
 901   public void setMenusForViewport()
 902   {
 903     setMenusFromViewport(viewport);
 904   }
 905
 906   /**
 907    * Need to call this method when tabs are selected for multiple views, or when
 908    * loading from Jalview2XML.java
 909    *
 910    * @param av
 911    *          AlignViewport
 912    */
 913   public void setMenusFromViewport(AlignViewport av)
 914   {
 915     padGapsMenuitem.setSelected(av.isPadGaps());
 916     colourTextMenuItem.setSelected(av.isShowColourText());
 917     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 918     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 919     conservationMenuItem.setSelected(av.getConservationSelected());
 920     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 921     seqLimits.setSelected(av.getShowJVSuffix());
 922     idRightAlign.setSelected(av.isRightAlignIds());
 923     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 924     renderGapsMenuItem.setSelected(av.isRenderGaps());
 925     wrapMenuItem.setSelected(av.getWrapAlignment());
 926     scaleAbove.setVisible(av.getWrapAlignment());
 927     scaleLeft.setVisible(av.getWrapAlignment());
 928     scaleRight.setVisible(av.getWrapAlignment());
 929     annotationPanelMenuItem.setState(av.isShowAnnotation());
 930     /*
 931      * Show/hide annotations only enabled if annotation panel is shown
 932      */
 933     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 934     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 935     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 936     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 937     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 938     viewTextMenuItem.setSelected(av.getShowText());
 939     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 940     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 941     showGroupConservation.setSelected(av.isShowGroupConservation());
 942     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 943     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 944     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 945
 946     ColourMenuHelper.setColourSelected(colourMenu,
 947             av.getGlobalColourScheme());
 948
 949     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 950     hiddenMarkers.setState(av.getShowHiddenMarkers());
 951     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 952     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 953     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 954     autoCalculate.setSelected(av.autoCalculateConsensus);
 955     sortByTree.setSelected(av.sortByTree);
 956     listenToViewSelections.setSelected(av.followSelection);
 957
 958     showProducts.setEnabled(canShowProducts());
 959     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 960
 961     updateEditMenuBar();
 962   }
 963
 964   /**
 965    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 966    *
 967    * @param b
 968    */
 969   public void setGroovyEnabled(boolean b)
 970   {
 971     runGroovy.setEnabled(b);
 972   }
 973
 974   private IProgressIndicator progressBar;
 975
 976   /*
 977    * (non-Javadoc)
 978    *
 979    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 980    */
 981   @Override
 982   public void setProgressBar(String message, long id)
 983   {
 984     if (!Platform.isHeadless())
 985       progressBar.setProgressBar(message, id);
 986   }
 987
 988   @Override
 989   public void registerHandler(final long id,
 990           final IProgressIndicatorHandler handler)
 991   {
 992     progressBar.registerHandler(id, handler);
 993   }
 994
 995   /**
 996    *
 997    * @return true if any progress bars are still active
 998    */
 999   @Override
1000   public boolean operationInProgress()
1001   {
1002     return progressBar.operationInProgress();
1003   }
1004
1005   /**
1006    * Sets the text of the status bar. Note that setting a null or empty value
1007    * will cause the status bar to be hidden, with possibly undesirable flicker
1008    * of the screen layout.
1009    */
1010   @Override
1011   public void setStatus(String text)
1012   {
1013     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1014   }
1015
1016   /*
1017    * Added so Castor Mapping file can obtain Jalview Version
1018    */
1019   public String getVersion()
1020   {
1021     return Cache.getProperty("VERSION");
1022   }
1023
1024   public FeatureRenderer getFeatureRenderer()
1025   {
1026     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1027   }
1028
1029   @Override
1030   public void fetchSequence_actionPerformed()
1031   {
1032     new SequenceFetcher(this);
1033   }
1034
1035   @Override
1036   public void addFromFile_actionPerformed(ActionEvent e)
1037   {
1038     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1039   }
1040
1041   @Override
1042   public void reload_actionPerformed(ActionEvent e)
1043   {
1044     if (fileName != null)
1045     {
1046       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1047       // originating file's format
1048       // TODO: work out how to recover feature settings for correct view(s) when
1049       // file is reloaded.
1050       if (FileFormat.Jalview.equals(currentFileFormat))
1051       {
1052         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1053         for (int i = 0; i < frames.length; i++)
1054         {
1055           if (frames[i] instanceof AlignFrame && frames[i] != this
1056                   && ((AlignFrame) frames[i]).fileName != null
1057                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1058           {
1059             try
1060             {
1061               frames[i].setSelected(true);
1062               Desktop.instance.closeAssociatedWindows();
1063             } catch (java.beans.PropertyVetoException ex)
1064             {
1065             }
1066           }
1067
1068         }
1069         Desktop.instance.closeAssociatedWindows();
1070
1071         FileLoader loader = new FileLoader();
1072         DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1073                 ? DataSourceType.URL
1074                 : DataSourceType.FILE;
1075         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1076       }
1077       else
1078       {
1079         Rectangle bounds = this.getBounds();
1080
1081         FileLoader loader = new FileLoader();
1082
1083         AlignFrame newframe = null;
1084
1085         if (fileObject == null)
1086         {
1087
1088           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1089                   fileName) ? DataSourceType.URL : DataSourceType.FILE;
1090           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1091                   currentFileFormat);
1092         }
1093         else
1094         {
1095           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1096                   DataSourceType.FILE, currentFileFormat);
1097         }
1098
1099         newframe.setBounds(bounds);
1100         if (featureSettings != null && featureSettings.isShowing())
1101         {
1102           final Rectangle fspos = featureSettings.frame.getBounds();
1103           // TODO: need a 'show feature settings' function that takes bounds -
1104           // need to refactor Desktop.addFrame
1105           newframe.featureSettings_actionPerformed(null);
1106           final FeatureSettings nfs = newframe.featureSettings;
1107           SwingUtilities.invokeLater(new Runnable()
1108           {
1109             @Override
1110             public void run()
1111             {
1112               nfs.frame.setBounds(fspos);
1113             }
1114           });
1115           this.featureSettings.close();
1116           this.featureSettings = null;
1117         }
1118         this.closeMenuItem_actionPerformed(true);
1119       }
1120     }
1121   }
1122
1123   @Override
1124   public void addFromText_actionPerformed(ActionEvent e)
1125   {
1126     Desktop.instance
1127             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1128   }
1129
1130   @Override
1131   public void addFromURL_actionPerformed(ActionEvent e)
1132   {
1133     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1134   }
1135
1136   @Override
1137   public void save_actionPerformed(ActionEvent e)
1138   {
1139     if (fileName == null || (currentFileFormat == null)
1140             || HttpUtils.startsWithHttpOrHttps(fileName))
1141     {
1142       saveAs_actionPerformed();
1143     }
1144     else
1145     {
1146       saveAlignment(fileName, currentFileFormat);
1147     }
1148   }
1149
1150   /**
1151    * Saves the alignment to a file with a name chosen by the user, if necessary
1152    * warning if a file would be overwritten
1153    */
1154   @Override
1155   public void saveAs_actionPerformed()
1156   {
1157     String format = currentFileFormat == null ? null
1158             : currentFileFormat.getName();
1159     JalviewFileChooser chooser = JalviewFileChooser
1160             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1161
1162     chooser.setFileView(new JalviewFileView());
1163     chooser.setDialogTitle(
1164             MessageManager.getString("label.save_alignment_to_file"));
1165     chooser.setToolTipText(MessageManager.getString("action.save"));
1166
1167     int value = chooser.showSaveDialog(this);
1168
1169     if (value != JalviewFileChooser.APPROVE_OPTION)
1170     {
1171       return;
1172     }
1173     currentFileFormat = chooser.getSelectedFormat();
1174     // todo is this (2005) test now obsolete - value is never null?
1175     while (currentFileFormat == null)
1176     {
1177       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1178               MessageManager
1179                       .getString("label.select_file_format_before_saving"),
1180               MessageManager.getString("label.file_format_not_specified"),
1181               JvOptionPane.WARNING_MESSAGE);
1182       currentFileFormat = chooser.getSelectedFormat();
1183       value = chooser.showSaveDialog(this);
1184       if (value != JalviewFileChooser.APPROVE_OPTION)
1185       {
1186         return;
1187       }
1188     }
1189
1190     fileName = chooser.getSelectedFile().getPath();
1191
1192     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1193     Cache.setProperty("LAST_DIRECTORY", fileName);
1194     saveAlignment(fileName, currentFileFormat);
1195   }
1196
1197   boolean lastSaveSuccessful = false;
1198
1199   FileFormatI lastFormatSaved;
1200
1201   String lastFilenameSaved;
1202
1203   /**
1204    * Raise a dialog or status message for the last call to saveAlignment.
1205    *
1206    * @return true if last call to saveAlignment(file, format) was successful.
1207    */
1208   public boolean isSaveAlignmentSuccessful()
1209   {
1210
1211     if (!lastSaveSuccessful)
1212     {
1213       if (!Platform.isHeadless())
1214       {
1215         JvOptionPane.showInternalMessageDialog(this, MessageManager
1216                 .formatMessage("label.couldnt_save_file", new Object[]
1217                 { lastFilenameSaved }),
1218                 MessageManager.getString("label.error_saving_file"),
1219                 JvOptionPane.WARNING_MESSAGE);
1220       }
1221       else
1222       {
1223         Console.error(MessageManager
1224                 .formatMessage("label.couldnt_save_file", new Object[]
1225                 { lastFilenameSaved }));
1226       }
1227     }
1228     else
1229     {
1230
1231       setStatus(MessageManager.formatMessage(
1232               "label.successfully_saved_to_file_in_format", new Object[]
1233               { lastFilenameSaved, lastFormatSaved }));
1234
1235     }
1236     return lastSaveSuccessful;
1237   }
1238
1239   /**
1240    * Saves the alignment to the specified file path, in the specified format,
1241    * which may be an alignment format, or Jalview project format. If the
1242    * alignment has hidden regions, or the format is one capable of including
1243    * non-sequence data (features, annotations, groups), then the user may be
1244    * prompted to specify what to include in the output.
1245    *
1246    * @param file
1247    * @param format
1248    */
1249   public void saveAlignment(String file, FileFormatI format)
1250   {
1251     lastSaveSuccessful = true;
1252     lastFilenameSaved = file;
1253     lastFormatSaved = format;
1254
1255     if (FileFormat.Jalview.equals(format))
1256     {
1257       String shortName = title;
1258       if (shortName.indexOf(File.separatorChar) > -1)
1259       {
1260         shortName = shortName
1261                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1262       }
1263       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1264               shortName);
1265
1266       Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1267       if (lastSaveSuccessful)
1268       {
1269         this.getViewport().setSavedUpToDate(true);
1270       }
1271
1272       statusBar.setText(MessageManager.formatMessage(
1273               "label.successfully_saved_to_file_in_format", new Object[]
1274               { file, format }));
1275
1276       return;
1277     }
1278
1279     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1280     Callable<Void> cancelAction = () -> {
1281       lastSaveSuccessful = false;
1282       return null;
1283     };
1284     Callable<Void> outputAction = () -> {
1285       // todo defer this to inside formatSequences (or later)
1286       AlignmentExportData exportData = viewport.getAlignExportData(options);
1287       String output = new FormatAdapter(alignPanel, options)
1288               .formatSequences(format, exportData.getAlignment(),
1289                       exportData.getOmitHidden(),
1290                       exportData.getStartEndPostions(),
1291                       viewport.getAlignment().getHiddenColumns());
1292       if (output == null)
1293       {
1294         lastSaveSuccessful = false;
1295       }
1296       else
1297       {
1298         // create backupfiles object and get new temp filename destination
1299         boolean doBackup = BackupFiles.getEnabled();
1300         BackupFiles backupfiles = null;
1301         if (doBackup)
1302         {
1303           Console.trace("ALIGNFRAME making backupfiles object for " + file);
1304           backupfiles = new BackupFiles(file);
1305         }
1306         try
1307         {
1308           String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1309                   : file;
1310           Console.trace("ALIGNFRAME setting PrintWriter");
1311           PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1312
1313           if (backupfiles != null)
1314           {
1315             Console.trace("ALIGNFRAME about to write to temp file "
1316                     + backupfiles.getTempFilePath());
1317           }
1318
1319           out.print(output);
1320           Console.trace("ALIGNFRAME about to close file");
1321           out.close();
1322           Console.trace("ALIGNFRAME closed file");
1323           AlignFrame.this.setTitle(file);
1324           statusBar.setText(MessageManager.formatMessage(
1325                   "label.successfully_saved_to_file_in_format", new Object[]
1326                   { fileName, format.getName() }));
1327           lastSaveSuccessful = true;
1328         } catch (IOException e)
1329         {
1330           lastSaveSuccessful = false;
1331           Console.error(
1332                   "ALIGNFRAME Something happened writing the temp file");
1333           Console.error(e.getMessage());
1334           Console.debug(Cache.getStackTraceString(e));
1335         } catch (Exception ex)
1336         {
1337           lastSaveSuccessful = false;
1338           Console.error(
1339                   "ALIGNFRAME Something unexpected happened writing the temp file");
1340           Console.error(ex.getMessage());
1341           Console.debug(Cache.getStackTraceString(ex));
1342         }
1343
1344         if (doBackup)
1345         {
1346           backupfiles.setWriteSuccess(lastSaveSuccessful);
1347           Console.debug("ALIGNFRAME writing temp file was "
1348                   + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1349           // do the backup file roll and rename the temp file to actual file
1350           Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1351           lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1352           Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1353                   + (lastSaveSuccessful ? "" : "un") + "successfully");
1354         }
1355
1356         Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1357         if (lastSaveSuccessful)
1358         {
1359           AlignFrame.this.getViewport().setSavedUpToDate(true);
1360         }
1361       }
1362       return null;
1363     };
1364
1365     /*
1366      * show dialog with export options if applicable; else just do it
1367      */
1368     if (AlignExportOptions.isNeeded(viewport, format))
1369     {
1370       AlignExportOptions choices = new AlignExportOptions(
1371               alignPanel.getAlignViewport(), format, options);
1372       choices.setResponseAction(0, outputAction);
1373       choices.setResponseAction(1, cancelAction);
1374       choices.showDialog();
1375     }
1376     else
1377     {
1378       try
1379       {
1380         outputAction.call();
1381       } catch (Exception e)
1382       {
1383         // TODO Auto-generated catch block
1384         e.printStackTrace();
1385       }
1386     }
1387   }
1388
1389   /**
1390    * Outputs the alignment to textbox in the requested format, if necessary
1391    * first prompting the user for whether to include hidden regions or
1392    * non-sequence data
1393    *
1394    * @param fileFormatName
1395    */
1396   @Override
1397   protected void outputText_actionPerformed(String fileFormatName)
1398   {
1399     FileFormatI fileFormat = FileFormats.getInstance()
1400             .forName(fileFormatName);
1401     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1402     Callable<Void> outputAction = () -> {
1403       // todo defer this to inside formatSequences (or later)
1404       AlignmentExportData exportData = viewport.getAlignExportData(options);
1405       CutAndPasteTransfer cap = new CutAndPasteTransfer();
1406       cap.setForInput(null);
1407       try
1408       {
1409         FileFormatI format = fileFormat;
1410         cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
1411                 format, exportData.getAlignment(),
1412                 exportData.getOmitHidden(),
1413                 exportData.getStartEndPostions(),
1414                 viewport.getAlignment().getHiddenColumns()));
1415         Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1416                 "label.alignment_output_command", new Object[]
1417                 { fileFormat.getName() }), 600, 500);
1418       } catch (OutOfMemoryError oom)
1419       {
1420         new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1421                 oom);
1422         cap.dispose();
1423       }
1424       return null;
1425     };
1426
1427     /*
1428      * show dialog with export options if applicable; else just do it
1429      */
1430     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1431     {
1432       AlignExportOptions choices = new AlignExportOptions(
1433               alignPanel.getAlignViewport(), fileFormat, options);
1434       choices.setResponseAction(0, outputAction);
1435       choices.showDialog();
1436     }
1437     else
1438     {
1439       try
1440       {
1441         outputAction.call();
1442       } catch (Exception e)
1443       {
1444         e.printStackTrace();
1445       }
1446     }
1447   }
1448
1449   /**
1450    * DOCUMENT ME!
1451    *
1452    * @param e
1453    *          DOCUMENT ME!
1454    */
1455   @Override
1456   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1457   {
1458     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1459     htmlSVG.exportHTML(null);
1460   }
1461
1462   @Override
1463   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1464   {
1465     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1466     bjs.exportHTML(null);
1467   }
1468
1469   public void createImageMap(File file, String image)
1470   {
1471     alignPanel.makePNGImageMap(file, image);
1472   }
1473
1474   /**
1475    * Creates a PNG image of the alignment and writes it to the given file. If
1476    * the file is null, the user is prompted to choose a file.
1477    *
1478    * @param f
1479    */
1480   @Override
1481   public void createPNG(File f)
1482   {
1483     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1484   }
1485
1486   /**
1487    * Creates an EPS image of the alignment and writes it to the given file. If
1488    * the file is null, the user is prompted to choose a file.
1489    *
1490    * @param f
1491    */
1492   @Override
1493   public void createEPS(File f)
1494   {
1495     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1496   }
1497
1498   /**
1499    * Creates an SVG image of the alignment and writes it to the given file. If
1500    * the file is null, the user is prompted to choose a file.
1501    *
1502    * @param f
1503    */
1504   @Override
1505   public void createSVG(File f)
1506   {
1507     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1508   }
1509
1510   @Override
1511   public void pageSetup_actionPerformed(ActionEvent e)
1512   {
1513     PrinterJob printJob = PrinterJob.getPrinterJob();
1514     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1515   }
1516
1517   /**
1518    * DOCUMENT ME!
1519    *
1520    * @param e
1521    *          DOCUMENT ME!
1522    */
1523   @Override
1524   public void printMenuItem_actionPerformed(ActionEvent e)
1525   {
1526     // Putting in a thread avoids Swing painting problems
1527     PrintThread thread = new PrintThread(alignPanel);
1528     thread.start();
1529   }
1530
1531   @Override
1532   public void exportFeatures_actionPerformed(ActionEvent e)
1533   {
1534     new AnnotationExporter(alignPanel).exportFeatures();
1535   }
1536
1537   @Override
1538   public void exportAnnotations_actionPerformed(ActionEvent e)
1539   {
1540     new AnnotationExporter(alignPanel).exportAnnotations();
1541   }
1542
1543   @Override
1544   public void associatedData_actionPerformed(ActionEvent e)
1545   {
1546     final JalviewFileChooser chooser = new JalviewFileChooser(
1547             Cache.getProperty("LAST_DIRECTORY"));
1548     chooser.setFileView(new JalviewFileView());
1549     String tooltip = MessageManager
1550             .getString("label.load_jalview_annotations");
1551     chooser.setDialogTitle(tooltip);
1552     chooser.setToolTipText(tooltip);
1553     chooser.setResponseHandler(0, () -> {
1554       String choice = chooser.getSelectedFile().getPath();
1555       Cache.setProperty("LAST_DIRECTORY", choice);
1556       loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1557       return null;
1558     });
1559
1560     chooser.showOpenDialog(this);
1561   }
1562
1563   /**
1564    * Close the current view or all views in the alignment frame. If the frame
1565    * only contains one view then the alignment will be removed from memory.
1566    *
1567    * @param closeAllTabs
1568    */
1569   @Override
1570   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1571   {
1572     if (alignPanels != null && alignPanels.size() < 2)
1573     {
1574       closeAllTabs = true;
1575     }
1576
1577     try
1578     {
1579       if (alignPanels != null)
1580       {
1581         if (closeAllTabs)
1582         {
1583           if (this.isClosed())
1584           {
1585             // really close all the windows - otherwise wait till
1586             // setClosed(true) is called
1587             for (int i = 0; i < alignPanels.size(); i++)
1588             {
1589               AlignmentPanel ap = alignPanels.get(i);
1590               ap.closePanel();
1591             }
1592           }
1593         }
1594         else
1595         {
1596           closeView(alignPanel);
1597         }
1598       }
1599       if (closeAllTabs)
1600       {
1601         if (featureSettings != null && featureSettings.isOpen())
1602         {
1603           featureSettings.close();
1604           featureSettings = null;
1605         }
1606         /*
1607          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1608          * be called recursively, with the frame now in 'closed' state
1609          */
1610         this.setClosed(true);
1611       }
1612     } catch (Exception ex)
1613     {
1614       ex.printStackTrace();
1615     }
1616   }
1617
1618   /**
1619    * Close the specified panel and close up tabs appropriately.
1620    *
1621    * @param panelToClose
1622    */
1623   public void closeView(AlignmentPanel panelToClose)
1624   {
1625     int index = tabbedPane.getSelectedIndex();
1626     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1627     alignPanels.remove(panelToClose);
1628     panelToClose.closePanel();
1629     panelToClose = null;
1630
1631     tabbedPane.removeTabAt(closedindex);
1632     tabbedPane.validate();
1633
1634     if (index > closedindex || index == tabbedPane.getTabCount())
1635     {
1636       // modify currently selected tab index if necessary.
1637       index--;
1638     }
1639
1640     this.tabSelectionChanged(index);
1641   }
1642
1643   /**
1644    * DOCUMENT ME!
1645    */
1646   void updateEditMenuBar()
1647   {
1648
1649     if (viewport.getHistoryList().size() > 0)
1650     {
1651       undoMenuItem.setEnabled(true);
1652       CommandI command = viewport.getHistoryList().peek();
1653       undoMenuItem.setText(MessageManager
1654               .formatMessage("label.undo_command", new Object[]
1655               { command.getDescription() }));
1656     }
1657     else
1658     {
1659       undoMenuItem.setEnabled(false);
1660       undoMenuItem.setText(MessageManager.getString("action.undo"));
1661     }
1662
1663     if (viewport.getRedoList().size() > 0)
1664     {
1665       redoMenuItem.setEnabled(true);
1666
1667       CommandI command = viewport.getRedoList().peek();
1668       redoMenuItem.setText(MessageManager
1669               .formatMessage("label.redo_command", new Object[]
1670               { command.getDescription() }));
1671     }
1672     else
1673     {
1674       redoMenuItem.setEnabled(false);
1675       redoMenuItem.setText(MessageManager.getString("action.redo"));
1676     }
1677   }
1678
1679   @Override
1680   public void addHistoryItem(CommandI command)
1681   {
1682     if (command.getSize() > 0)
1683     {
1684       viewport.addToHistoryList(command);
1685       viewport.clearRedoList();
1686       updateEditMenuBar();
1687       viewport.updateHiddenColumns();
1688       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1689       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1690       // viewport.getColumnSelection()
1691       // .getHiddenColumns().size() > 0);
1692     }
1693   }
1694
1695   /**
1696    *
1697    * @return alignment objects for all views
1698    */
1699   AlignmentI[] getViewAlignments()
1700   {
1701     if (alignPanels != null)
1702     {
1703       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1704       int i = 0;
1705       for (AlignmentPanel ap : alignPanels)
1706       {
1707         als[i++] = ap.av.getAlignment();
1708       }
1709       return als;
1710     }
1711     if (viewport != null)
1712     {
1713       return new AlignmentI[] { viewport.getAlignment() };
1714     }
1715     return null;
1716   }
1717
1718   /**
1719    * DOCUMENT ME!
1720    *
1721    * @param e
1722    *          DOCUMENT ME!
1723    */
1724   @Override
1725   protected void undoMenuItem_actionPerformed(ActionEvent e)
1726   {
1727     if (viewport.getHistoryList().isEmpty())
1728     {
1729       return;
1730     }
1731     CommandI command = viewport.getHistoryList().pop();
1732     viewport.addToRedoList(command);
1733     command.undoCommand(getViewAlignments());
1734
1735     AlignmentViewport originalSource = getOriginatingSource(command);
1736     updateEditMenuBar();
1737
1738     if (originalSource != null)
1739     {
1740       if (originalSource != viewport)
1741       {
1742         Console.warn(
1743                 "Implementation worry: mismatch of viewport origin for undo");
1744       }
1745       originalSource.updateHiddenColumns();
1746       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1747       // null
1748       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1749       // viewport.getColumnSelection()
1750       // .getHiddenColumns().size() > 0);
1751       originalSource.firePropertyChange("alignment", null,
1752               originalSource.getAlignment().getSequences());
1753     }
1754   }
1755
1756   /**
1757    * DOCUMENT ME!
1758    *
1759    * @param e
1760    *          DOCUMENT ME!
1761    */
1762   @Override
1763   protected void redoMenuItem_actionPerformed(ActionEvent e)
1764   {
1765     if (viewport.getRedoList().size() < 1)
1766     {
1767       return;
1768     }
1769
1770     CommandI command = viewport.getRedoList().pop();
1771     viewport.addToHistoryList(command);
1772     command.doCommand(getViewAlignments());
1773
1774     AlignmentViewport originalSource = getOriginatingSource(command);
1775     updateEditMenuBar();
1776
1777     if (originalSource != null)
1778     {
1779
1780       if (originalSource != viewport)
1781       {
1782         Console.warn(
1783                 "Implementation worry: mismatch of viewport origin for redo");
1784       }
1785       originalSource.updateHiddenColumns();
1786       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1787       // null
1788       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1789       // viewport.getColumnSelection()
1790       // .getHiddenColumns().size() > 0);
1791       originalSource.firePropertyChange("alignment", null,
1792               originalSource.getAlignment().getSequences());
1793     }
1794   }
1795
1796   AlignmentViewport getOriginatingSource(CommandI command)
1797   {
1798     AlignmentViewport originalSource = null;
1799     // For sequence removal and addition, we need to fire
1800     // the property change event FROM the viewport where the
1801     // original alignment was altered
1802     AlignmentI al = null;
1803     if (command instanceof EditCommand)
1804     {
1805       EditCommand editCommand = (EditCommand) command;
1806       al = editCommand.getAlignment();
1807       List<Component> comps = PaintRefresher.components
1808               .get(viewport.getSequenceSetId());
1809
1810       for (Component comp : comps)
1811       {
1812         if (comp instanceof AlignmentPanel)
1813         {
1814           if (al == ((AlignmentPanel) comp).av.getAlignment())
1815           {
1816             originalSource = ((AlignmentPanel) comp).av;
1817             break;
1818           }
1819         }
1820       }
1821     }
1822
1823     if (originalSource == null)
1824     {
1825       // The original view is closed, we must validate
1826       // the current view against the closed view first
1827       if (al != null)
1828       {
1829         PaintRefresher.validateSequences(al, viewport.getAlignment());
1830       }
1831
1832       originalSource = viewport;
1833     }
1834
1835     return originalSource;
1836   }
1837
1838   /**
1839    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1840    * or the sequence under cursor in keyboard mode
1841    *
1842    * @param up
1843    *          or down (if !up)
1844    */
1845   public void moveSelectedSequences(boolean up)
1846   {
1847     SequenceGroup sg = viewport.getSelectionGroup();
1848
1849     if (sg == null)
1850     {
1851       if (viewport.cursorMode)
1852       {
1853         sg = new SequenceGroup();
1854         sg.addSequence(viewport.getAlignment().getSequenceAt(
1855                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1856       }
1857       else
1858       {
1859         return;
1860       }
1861     }
1862
1863     if (sg.getSize() < 1)
1864     {
1865       return;
1866     }
1867
1868     // TODO: JAL-3733 - add an event to the undo buffer for this !
1869
1870     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1871             viewport.getHiddenRepSequences(), up);
1872     alignPanel.paintAlignment(true, false);
1873   }
1874
1875   synchronized void slideSequences(boolean right, int size)
1876   {
1877     List<SequenceI> sg = new ArrayList<>();
1878     if (viewport.cursorMode)
1879     {
1880       sg.add(viewport.getAlignment()
1881               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1882     }
1883     else if (viewport.getSelectionGroup() != null
1884             && viewport.getSelectionGroup().getSize() != viewport
1885                     .getAlignment().getHeight())
1886     {
1887       sg = viewport.getSelectionGroup()
1888               .getSequences(viewport.getHiddenRepSequences());
1889     }
1890
1891     if (sg.size() < 1)
1892     {
1893       return;
1894     }
1895
1896     List<SequenceI> invertGroup = new ArrayList<>();
1897
1898     for (SequenceI seq : viewport.getAlignment().getSequences())
1899     {
1900       if (!sg.contains(seq))
1901       {
1902         invertGroup.add(seq);
1903       }
1904     }
1905
1906     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1907
1908     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1909     for (int i = 0; i < invertGroup.size(); i++)
1910     {
1911       seqs2[i] = invertGroup.get(i);
1912     }
1913
1914     SlideSequencesCommand ssc;
1915     if (right)
1916     {
1917       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1918               viewport.getGapCharacter());
1919     }
1920     else
1921     {
1922       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1923               viewport.getGapCharacter());
1924     }
1925
1926     int groupAdjustment = 0;
1927     if (ssc.getGapsInsertedBegin() && right)
1928     {
1929       if (viewport.cursorMode)
1930       {
1931         alignPanel.getSeqPanel().moveCursor(size, 0);
1932       }
1933       else
1934       {
1935         groupAdjustment = size;
1936       }
1937     }
1938     else if (!ssc.getGapsInsertedBegin() && !right)
1939     {
1940       if (viewport.cursorMode)
1941       {
1942         alignPanel.getSeqPanel().moveCursor(-size, 0);
1943       }
1944       else
1945       {
1946         groupAdjustment = -size;
1947       }
1948     }
1949
1950     if (groupAdjustment != 0)
1951     {
1952       viewport.getSelectionGroup().setStartRes(
1953               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1954       viewport.getSelectionGroup().setEndRes(
1955               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1956     }
1957
1958     /*
1959      * just extend the last slide command if compatible; but not if in
1960      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1961      */
1962     boolean appendHistoryItem = false;
1963     Deque<CommandI> historyList = viewport.getHistoryList();
1964     boolean inSplitFrame = getSplitViewContainer() != null;
1965     if (!inSplitFrame && historyList != null && historyList.size() > 0
1966             && historyList.peek() instanceof SlideSequencesCommand)
1967     {
1968       appendHistoryItem = ssc.appendSlideCommand(
1969               (SlideSequencesCommand) historyList.peek());
1970     }
1971
1972     if (!appendHistoryItem)
1973     {
1974       addHistoryItem(ssc);
1975     }
1976
1977     repaint();
1978   }
1979
1980   /**
1981    * DOCUMENT ME!
1982    *
1983    * @param e
1984    *          DOCUMENT ME!
1985    */
1986   @Override
1987   protected void copy_actionPerformed()
1988   {
1989     if (viewport.getSelectionGroup() == null)
1990     {
1991       return;
1992     }
1993     // TODO: preserve the ordering of displayed alignment annotation in any
1994     // internal paste (particularly sequence associated annotation)
1995     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1996     String[] omitHidden = null;
1997
1998     if (viewport.hasHiddenColumns())
1999     {
2000       omitHidden = viewport.getViewAsString(true);
2001     }
2002
2003     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2004             seqs, omitHidden, null);
2005
2006     StringSelection ss = new StringSelection(output);
2007
2008     try
2009     {
2010       jalview.gui.Desktop.internalCopy = true;
2011       // Its really worth setting the clipboard contents
2012       // to empty before setting the large StringSelection!!
2013       Toolkit.getDefaultToolkit().getSystemClipboard()
2014               .setContents(new StringSelection(""), null);
2015
2016       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2017               Desktop.instance);
2018     } catch (OutOfMemoryError er)
2019     {
2020       new OOMWarning("copying region", er);
2021       return;
2022     }
2023
2024     HiddenColumns hiddenColumns = null;
2025     if (viewport.hasHiddenColumns())
2026     {
2027       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2028       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2029
2030       // create new HiddenColumns object with copy of hidden regions
2031       // between startRes and endRes, offset by startRes
2032       hiddenColumns = new HiddenColumns(
2033               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2034               hiddenCutoff, hiddenOffset);
2035     }
2036
2037     Desktop.jalviewClipboard = new Object[] { seqs,
2038         viewport.getAlignment().getDataset(), hiddenColumns };
2039     setStatus(MessageManager.formatMessage(
2040             "label.copied_sequences_to_clipboard", new Object[]
2041             { Integer.valueOf(seqs.length).toString() }));
2042   }
2043
2044   /**
2045    * DOCUMENT ME!
2046    *
2047    * @param e
2048    *          DOCUMENT ME!
2049    */
2050   @Override
2051   protected void pasteNew_actionPerformed(ActionEvent e)
2052   {
2053     paste(true);
2054   }
2055
2056   /**
2057    * DOCUMENT ME!
2058    *
2059    * @param e
2060    *          DOCUMENT ME!
2061    */
2062   @Override
2063   protected void pasteThis_actionPerformed(ActionEvent e)
2064   {
2065     paste(false);
2066   }
2067
2068   /**
2069    * Paste contents of Jalview clipboard
2070    *
2071    * @param newAlignment
2072    *          true to paste to a new alignment, otherwise add to this.
2073    */
2074   void paste(boolean newAlignment)
2075   {
2076     boolean externalPaste = true;
2077     try
2078     {
2079       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2080       Transferable contents = c.getContents(this);
2081
2082       if (contents == null)
2083       {
2084         return;
2085       }
2086
2087       String str;
2088       FileFormatI format;
2089       try
2090       {
2091         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2092         if (str.length() < 1)
2093         {
2094           return;
2095         }
2096
2097         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2098
2099       } catch (OutOfMemoryError er)
2100       {
2101         new OOMWarning("Out of memory pasting sequences!!", er);
2102         return;
2103       }
2104
2105       SequenceI[] sequences;
2106       boolean annotationAdded = false;
2107       AlignmentI alignment = null;
2108
2109       if (Desktop.jalviewClipboard != null)
2110       {
2111         // The clipboard was filled from within Jalview, we must use the
2112         // sequences
2113         // And dataset from the copied alignment
2114         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2115         // be doubly sure that we create *new* sequence objects.
2116         sequences = new SequenceI[newseq.length];
2117         for (int i = 0; i < newseq.length; i++)
2118         {
2119           sequences[i] = new Sequence(newseq[i]);
2120         }
2121         alignment = new Alignment(sequences);
2122         externalPaste = false;
2123       }
2124       else
2125       {
2126         // parse the clipboard as an alignment.
2127         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2128                 format);
2129         sequences = alignment.getSequencesArray();
2130       }
2131
2132       int alwidth = 0;
2133       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2134       int fgroup = -1;
2135
2136       if (newAlignment)
2137       {
2138
2139         if (Desktop.jalviewClipboard != null)
2140         {
2141           // dataset is inherited
2142           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2143         }
2144         else
2145         {
2146           // new dataset is constructed
2147           alignment.setDataset(null);
2148         }
2149         alwidth = alignment.getWidth() + 1;
2150       }
2151       else
2152       {
2153         AlignmentI pastedal = alignment; // preserve pasted alignment object
2154         // Add pasted sequences and dataset into existing alignment.
2155         alignment = viewport.getAlignment();
2156         alwidth = alignment.getWidth() + 1;
2157         // decide if we need to import sequences from an existing dataset
2158         boolean importDs = Desktop.jalviewClipboard != null
2159                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2160         // importDs==true instructs us to copy over new dataset sequences from
2161         // an existing alignment
2162         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2163                                                                       // create
2164         // minimum dataset set
2165
2166         for (int i = 0; i < sequences.length; i++)
2167         {
2168           if (importDs)
2169           {
2170             newDs.addElement(null);
2171           }
2172           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2173           // paste
2174           if (importDs && ds != null)
2175           {
2176             if (!newDs.contains(ds))
2177             {
2178               newDs.setElementAt(ds, i);
2179               ds = new Sequence(ds);
2180               // update with new dataset sequence
2181               sequences[i].setDatasetSequence(ds);
2182             }
2183             else
2184             {
2185               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2186             }
2187           }
2188           else
2189           {
2190             // copy and derive new dataset sequence
2191             sequences[i] = sequences[i].deriveSequence();
2192             alignment.getDataset()
2193                     .addSequence(sequences[i].getDatasetSequence());
2194             // TODO: avoid creation of duplicate dataset sequences with a
2195             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2196           }
2197           alignment.addSequence(sequences[i]); // merges dataset
2198         }
2199         if (newDs != null)
2200         {
2201           newDs.clear(); // tidy up
2202         }
2203         if (alignment.getAlignmentAnnotation() != null)
2204         {
2205           for (AlignmentAnnotation alan : alignment
2206                   .getAlignmentAnnotation())
2207           {
2208             if (alan.graphGroup > fgroup)
2209             {
2210               fgroup = alan.graphGroup;
2211             }
2212           }
2213         }
2214         if (pastedal.getAlignmentAnnotation() != null)
2215         {
2216           // Add any annotation attached to alignment.
2217           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2218           for (int i = 0; i < alann.length; i++)
2219           {
2220             annotationAdded = true;
2221             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2222             {
2223               AlignmentAnnotation newann = new AlignmentAnnotation(
2224                       alann[i]);
2225               if (newann.graphGroup > -1)
2226               {
2227                 if (newGraphGroups.size() <= newann.graphGroup
2228                         || newGraphGroups.get(newann.graphGroup) == null)
2229                 {
2230                   for (int q = newGraphGroups
2231                           .size(); q <= newann.graphGroup; q++)
2232                   {
2233                     newGraphGroups.add(q, null);
2234                   }
2235                   newGraphGroups.set(newann.graphGroup,
2236                           Integer.valueOf(++fgroup));
2237                 }
2238                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2239                         .intValue();
2240               }
2241
2242               newann.padAnnotation(alwidth);
2243               alignment.addAnnotation(newann);
2244             }
2245           }
2246         }
2247       }
2248       if (!newAlignment)
2249       {
2250         // /////
2251         // ADD HISTORY ITEM
2252         //
2253         addHistoryItem(new EditCommand(
2254                 MessageManager.getString("label.add_sequences"),
2255                 Action.PASTE, sequences, 0, alignment.getWidth(),
2256                 alignment));
2257       }
2258       // Add any annotations attached to sequences
2259       for (int i = 0; i < sequences.length; i++)
2260       {
2261         if (sequences[i].getAnnotation() != null)
2262         {
2263           AlignmentAnnotation newann;
2264           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2265           {
2266             annotationAdded = true;
2267             newann = sequences[i].getAnnotation()[a];
2268             newann.adjustForAlignment();
2269             newann.padAnnotation(alwidth);
2270             if (newann.graphGroup > -1)
2271             {
2272               if (newann.graphGroup > -1)
2273               {
2274                 if (newGraphGroups.size() <= newann.graphGroup
2275                         || newGraphGroups.get(newann.graphGroup) == null)
2276                 {
2277                   for (int q = newGraphGroups
2278                           .size(); q <= newann.graphGroup; q++)
2279                   {
2280                     newGraphGroups.add(q, null);
2281                   }
2282                   newGraphGroups.set(newann.graphGroup,
2283                           Integer.valueOf(++fgroup));
2284                 }
2285                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2286                         .intValue();
2287               }
2288             }
2289             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2290             // was
2291             // duplicated
2292             // earlier
2293             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2294                     a);
2295           }
2296         }
2297       }
2298       if (!newAlignment)
2299       {
2300
2301         // propagate alignment changed.
2302         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2303         if (annotationAdded)
2304         {
2305           // Duplicate sequence annotation in all views.
2306           AlignmentI[] alview = this.getViewAlignments();
2307           for (int i = 0; i < sequences.length; i++)
2308           {
2309             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2310             if (sann == null)
2311             {
2312               continue;
2313             }
2314             for (int avnum = 0; avnum < alview.length; avnum++)
2315             {
2316               if (alview[avnum] != alignment)
2317               {
2318                 // duplicate in a view other than the one with input focus
2319                 int avwidth = alview[avnum].getWidth() + 1;
2320                 // this relies on sann being preserved after we
2321                 // modify the sequence's annotation array for each duplication
2322                 for (int a = 0; a < sann.length; a++)
2323                 {
2324                   AlignmentAnnotation newann = new AlignmentAnnotation(
2325                           sann[a]);
2326                   sequences[i].addAlignmentAnnotation(newann);
2327                   newann.padAnnotation(avwidth);
2328                   alview[avnum].addAnnotation(newann); // annotation was
2329                   // duplicated earlier
2330                   // TODO JAL-1145 graphGroups are not updated for sequence
2331                   // annotation added to several views. This may cause
2332                   // strangeness
2333                   alview[avnum].setAnnotationIndex(newann, a);
2334                 }
2335               }
2336             }
2337           }
2338           buildSortByAnnotationScoresMenu();
2339         }
2340         viewport.firePropertyChange("alignment", null,
2341                 alignment.getSequences());
2342         if (alignPanels != null)
2343         {
2344           for (AlignmentPanel ap : alignPanels)
2345           {
2346             ap.validateAnnotationDimensions(false);
2347           }
2348         }
2349         else
2350         {
2351           alignPanel.validateAnnotationDimensions(false);
2352         }
2353
2354       }
2355       else
2356       {
2357         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2358                 DEFAULT_HEIGHT);
2359         String newtitle = new String("Copied sequences");
2360
2361         if (Desktop.jalviewClipboard != null
2362                 && Desktop.jalviewClipboard[2] != null)
2363         {
2364           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2365           af.viewport.setHiddenColumns(hc);
2366         }
2367
2368         // >>>This is a fix for the moment, until a better solution is
2369         // found!!<<<
2370         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2371                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2372                         .getFeatureRenderer());
2373
2374         // TODO: maintain provenance of an alignment, rather than just make the
2375         // title a concatenation of operations.
2376         if (!externalPaste)
2377         {
2378           if (title.startsWith("Copied sequences"))
2379           {
2380             newtitle = title;
2381           }
2382           else
2383           {
2384             newtitle = newtitle.concat("- from " + title);
2385           }
2386         }
2387         else
2388         {
2389           newtitle = new String("Pasted sequences");
2390         }
2391
2392         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2393                 DEFAULT_HEIGHT);
2394
2395       }
2396
2397     } catch (Exception ex)
2398     {
2399       ex.printStackTrace();
2400       System.out.println("Exception whilst pasting: " + ex);
2401       // could be anything being pasted in here
2402     }
2403
2404   }
2405
2406   @Override
2407   protected void expand_newalign(ActionEvent e)
2408   {
2409     try
2410     {
2411       AlignmentI alignment = AlignmentUtils
2412               .expandContext(getViewport().getAlignment(), -1);
2413       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2414               DEFAULT_HEIGHT);
2415       String newtitle = new String("Flanking alignment");
2416
2417       if (Desktop.jalviewClipboard != null
2418               && Desktop.jalviewClipboard[2] != null)
2419       {
2420         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2421         af.viewport.setHiddenColumns(hc);
2422       }
2423
2424       // >>>This is a fix for the moment, until a better solution is
2425       // found!!<<<
2426       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2427               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2428                       .getFeatureRenderer());
2429
2430       // TODO: maintain provenance of an alignment, rather than just make the
2431       // title a concatenation of operations.
2432       {
2433         if (title.startsWith("Copied sequences"))
2434         {
2435           newtitle = title;
2436         }
2437         else
2438         {
2439           newtitle = newtitle.concat("- from " + title);
2440         }
2441       }
2442
2443       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2444
2445     } catch (Exception ex)
2446     {
2447       ex.printStackTrace();
2448       System.out.println("Exception whilst pasting: " + ex);
2449       // could be anything being pasted in here
2450     } catch (OutOfMemoryError oom)
2451     {
2452       new OOMWarning("Viewing flanking region of alignment", oom);
2453     }
2454   }
2455
2456   /**
2457    * Action Cut (delete and copy) the selected region
2458    */
2459   @Override
2460   protected void cut_actionPerformed()
2461   {
2462     copy_actionPerformed();
2463     delete_actionPerformed();
2464   }
2465
2466   /**
2467    * Performs menu option to Delete the currently selected region
2468    */
2469   @Override
2470   protected void delete_actionPerformed()
2471   {
2472
2473     SequenceGroup sg = viewport.getSelectionGroup();
2474     if (sg == null)
2475     {
2476       return;
2477     }
2478
2479     Callable okAction = () -> {
2480       SequenceI[] cut = sg.getSequences()
2481               .toArray(new SequenceI[sg.getSize()]);
2482
2483       addHistoryItem(new EditCommand(
2484               MessageManager.getString("label.cut_sequences"), Action.CUT,
2485               cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2486               viewport.getAlignment()));
2487
2488       viewport.setSelectionGroup(null);
2489       viewport.sendSelection();
2490       viewport.getAlignment().deleteGroup(sg);
2491
2492       viewport.firePropertyChange("alignment", null,
2493               viewport.getAlignment().getSequences());
2494       if (viewport.getAlignment().getHeight() < 1)
2495       {
2496         try
2497         {
2498           AlignFrame.this.setClosed(true);
2499         } catch (Exception ex)
2500         {
2501         }
2502       }
2503       return null;
2504     };
2505
2506     /*
2507      * If the cut affects all sequences, prompt for confirmation
2508      */
2509     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2510             .getHeight();
2511     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2512             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2513     if (wholeHeight && wholeWidth)
2514     {
2515       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2516       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2517       Object[] options = new Object[] {
2518           MessageManager.getString("action.ok"),
2519           MessageManager.getString("action.cancel") };
2520       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2521               MessageManager.getString("label.delete_all"),
2522               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2523               options, options[0]);
2524     }
2525     else
2526     {
2527       try
2528       {
2529         okAction.call();
2530       } catch (Exception e)
2531       {
2532         e.printStackTrace();
2533       }
2534     }
2535   }
2536
2537   /**
2538    * DOCUMENT ME!
2539    *
2540    * @param e
2541    *          DOCUMENT ME!
2542    */
2543   @Override
2544   protected void deleteGroups_actionPerformed(ActionEvent e)
2545   {
2546     if (avc.deleteGroups())
2547     {
2548       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2549       alignPanel.updateAnnotation();
2550       alignPanel.paintAlignment(true, true);
2551     }
2552   }
2553
2554   /**
2555    * DOCUMENT ME!
2556    *
2557    * @param e
2558    *          DOCUMENT ME!
2559    */
2560   @Override
2561   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2562   {
2563     SequenceGroup sg = new SequenceGroup(
2564             viewport.getAlignment().getSequences());
2565
2566     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2567     viewport.setSelectionGroup(sg);
2568     viewport.isSelectionGroupChanged(true);
2569     viewport.sendSelection();
2570     // JAL-2034 - should delegate to
2571     // alignPanel to decide if overview needs
2572     // updating.
2573     alignPanel.paintAlignment(false, false);
2574     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2575   }
2576
2577   /**
2578    * DOCUMENT ME!
2579    *
2580    * @param e
2581    *          DOCUMENT ME!
2582    */
2583   @Override
2584   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2585   {
2586     if (viewport.cursorMode)
2587     {
2588       alignPanel.getSeqPanel().keyboardNo1 = null;
2589       alignPanel.getSeqPanel().keyboardNo2 = null;
2590     }
2591     viewport.setSelectionGroup(null);
2592     viewport.getColumnSelection().clear();
2593     viewport.setSearchResults(null);
2594     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2595     // JAL-2034 - should delegate to
2596     // alignPanel to decide if overview needs
2597     // updating.
2598     alignPanel.paintAlignment(false, false);
2599     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2600     viewport.sendSelection();
2601   }
2602
2603   /**
2604    * DOCUMENT ME!
2605    *
2606    * @param e
2607    *          DOCUMENT ME!
2608    */
2609   @Override
2610   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2611   {
2612     SequenceGroup sg = viewport.getSelectionGroup();
2613
2614     if (sg == null)
2615     {
2616       selectAllSequenceMenuItem_actionPerformed(null);
2617
2618       return;
2619     }
2620
2621     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2622     {
2623       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2624     }
2625     // JAL-2034 - should delegate to
2626     // alignPanel to decide if overview needs
2627     // updating.
2628
2629     alignPanel.paintAlignment(true, false);
2630     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2631     viewport.sendSelection();
2632   }
2633
2634   @Override
2635   public void invertColSel_actionPerformed(ActionEvent e)
2636   {
2637     viewport.invertColumnSelection();
2638     alignPanel.paintAlignment(true, false);
2639     viewport.sendSelection();
2640   }
2641
2642   /**
2643    * DOCUMENT ME!
2644    *
2645    * @param e
2646    *          DOCUMENT ME!
2647    */
2648   @Override
2649   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2650   {
2651     trimAlignment(true);
2652   }
2653
2654   /**
2655    * DOCUMENT ME!
2656    *
2657    * @param e
2658    *          DOCUMENT ME!
2659    */
2660   @Override
2661   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2662   {
2663     trimAlignment(false);
2664   }
2665
2666   void trimAlignment(boolean trimLeft)
2667   {
2668     ColumnSelection colSel = viewport.getColumnSelection();
2669     int column;
2670
2671     if (!colSel.isEmpty())
2672     {
2673       if (trimLeft)
2674       {
2675         column = colSel.getMin();
2676       }
2677       else
2678       {
2679         column = colSel.getMax();
2680       }
2681
2682       SequenceI[] seqs;
2683       if (viewport.getSelectionGroup() != null)
2684       {
2685         seqs = viewport.getSelectionGroup()
2686                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2687       }
2688       else
2689       {
2690         seqs = viewport.getAlignment().getSequencesArray();
2691       }
2692
2693       TrimRegionCommand trimRegion;
2694       if (trimLeft)
2695       {
2696         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2697                 column, viewport.getAlignment());
2698         viewport.getRanges().setStartRes(0);
2699       }
2700       else
2701       {
2702         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2703                 column, viewport.getAlignment());
2704       }
2705
2706       setStatus(MessageManager.formatMessage("label.removed_columns",
2707               new String[]
2708               { Integer.valueOf(trimRegion.getSize()).toString() }));
2709
2710       addHistoryItem(trimRegion);
2711
2712       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2713       {
2714         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2715                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2716         {
2717           viewport.getAlignment().deleteGroup(sg);
2718         }
2719       }
2720
2721       viewport.firePropertyChange("alignment", null,
2722               viewport.getAlignment().getSequences());
2723     }
2724   }
2725
2726   /**
2727    * DOCUMENT ME!
2728    *
2729    * @param e
2730    *          DOCUMENT ME!
2731    */
2732   @Override
2733   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2734   {
2735     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2736
2737     SequenceI[] seqs;
2738     if (viewport.getSelectionGroup() != null)
2739     {
2740       seqs = viewport.getSelectionGroup()
2741               .getSequencesAsArray(viewport.getHiddenRepSequences());
2742       start = viewport.getSelectionGroup().getStartRes();
2743       end = viewport.getSelectionGroup().getEndRes();
2744     }
2745     else
2746     {
2747       seqs = viewport.getAlignment().getSequencesArray();
2748     }
2749
2750     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2751             "Remove Gapped Columns", seqs, start, end,
2752             viewport.getAlignment());
2753
2754     addHistoryItem(removeGapCols);
2755
2756     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2757             new Object[]
2758             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2759
2760     // This is to maintain viewport position on first residue
2761     // of first sequence
2762     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2763     ViewportRanges ranges = viewport.getRanges();
2764     int startRes = seq.findPosition(ranges.getStartRes());
2765     // ShiftList shifts;
2766     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2767     // edit.alColumnChanges=shifts.getInverse();
2768     // if (viewport.hasHiddenColumns)
2769     // viewport.getColumnSelection().compensateForEdits(shifts);
2770     ranges.setStartRes(seq.findIndex(startRes) - 1);
2771     viewport.firePropertyChange("alignment", null,
2772             viewport.getAlignment().getSequences());
2773
2774   }
2775
2776   /**
2777    * DOCUMENT ME!
2778    *
2779    * @param e
2780    *          DOCUMENT ME!
2781    */
2782   @Override
2783   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2784   {
2785     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2786
2787     SequenceI[] seqs;
2788     if (viewport.getSelectionGroup() != null)
2789     {
2790       seqs = viewport.getSelectionGroup()
2791               .getSequencesAsArray(viewport.getHiddenRepSequences());
2792       start = viewport.getSelectionGroup().getStartRes();
2793       end = viewport.getSelectionGroup().getEndRes();
2794     }
2795     else
2796     {
2797       seqs = viewport.getAlignment().getSequencesArray();
2798     }
2799
2800     // This is to maintain viewport position on first residue
2801     // of first sequence
2802     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2803     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2804
2805     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2806             viewport.getAlignment()));
2807
2808     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2809
2810     viewport.firePropertyChange("alignment", null,
2811             viewport.getAlignment().getSequences());
2812
2813   }
2814
2815   /**
2816    * DOCUMENT ME!
2817    *
2818    * @param e
2819    *          DOCUMENT ME!
2820    */
2821   @Override
2822   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2823   {
2824     viewport.setPadGaps(padGapsMenuitem.isSelected());
2825     viewport.firePropertyChange("alignment", null,
2826             viewport.getAlignment().getSequences());
2827   }
2828
2829   /**
2830    * Opens a Finder dialog
2831    *
2832    * @param e
2833    */
2834   @Override
2835   public void findMenuItem_actionPerformed(ActionEvent e)
2836   {
2837     new Finder(alignPanel, false, null);
2838   }
2839
2840   /**
2841    * Create a new view of the current alignment.
2842    */
2843   @Override
2844   public void newView_actionPerformed(ActionEvent e)
2845   {
2846     newView(null, true);
2847   }
2848
2849   /**
2850    * Creates and shows a new view of the current alignment.
2851    *
2852    * @param viewTitle
2853    *          title of newly created view; if null, one will be generated
2854    * @param copyAnnotation
2855    *          if true then duplicate all annnotation, groups and settings
2856    * @return new alignment panel, already displayed.
2857    */
2858   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2859   {
2860     /*
2861      * Create a new AlignmentPanel (with its own, new Viewport)
2862      */
2863     AlignmentPanel newap = new jalview.project.Jalview2XML()
2864             .copyAlignPanel(alignPanel);
2865     if (!copyAnnotation)
2866     {
2867       /*
2868        * remove all groups and annotation except for the automatic stuff
2869        */
2870       newap.av.getAlignment().deleteAllGroups();
2871       newap.av.getAlignment().deleteAllAnnotations(false);
2872     }
2873
2874     newap.av.setGatherViewsHere(false);
2875
2876     if (viewport.getViewName() == null)
2877     {
2878       viewport.setViewName(
2879               MessageManager.getString("label.view_name_original"));
2880     }
2881
2882     /*
2883      * Views share the same edits undo and redo stacks
2884      */
2885     newap.av.setHistoryList(viewport.getHistoryList());
2886     newap.av.setRedoList(viewport.getRedoList());
2887
2888     /*
2889      * copy any visualisation settings that are not saved in the project
2890      */
2891     newap.av.setColourAppliesToAllGroups(
2892             viewport.getColourAppliesToAllGroups());
2893
2894     /*
2895      * Views share the same mappings; need to deregister any new mappings
2896      * created by copyAlignPanel, and register the new reference to the shared
2897      * mappings
2898      */
2899     newap.av.replaceMappings(viewport.getAlignment());
2900
2901     /*
2902      * start up cDNA consensus (if applicable) now mappings are in place
2903      */
2904     if (newap.av.initComplementConsensus())
2905     {
2906       newap.refresh(true); // adjust layout of annotations
2907     }
2908
2909     newap.av.setViewName(getNewViewName(viewTitle));
2910
2911     addAlignmentPanel(newap, true);
2912     newap.alignmentChanged();
2913
2914     if (alignPanels.size() == 2)
2915     {
2916       viewport.setGatherViewsHere(true);
2917     }
2918     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2919
2920     return newap;
2921   }
2922
2923   /**
2924    * Make a new name for the view, ensuring it is unique within the current
2925    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2926    * these now use viewId. Unique view names are still desirable for usability.)
2927    *
2928    * @param viewTitle
2929    * @return
2930    */
2931   protected String getNewViewName(String viewTitle)
2932   {
2933     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2934     boolean addFirstIndex = false;
2935     if (viewTitle == null || viewTitle.trim().length() == 0)
2936     {
2937       viewTitle = MessageManager.getString("action.view");
2938       addFirstIndex = true;
2939     }
2940     else
2941     {
2942       index = 1;// we count from 1 if given a specific name
2943     }
2944     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2945
2946     List<Component> comps = PaintRefresher.components
2947             .get(viewport.getSequenceSetId());
2948
2949     List<String> existingNames = getExistingViewNames(comps);
2950
2951     while (existingNames.contains(newViewName))
2952     {
2953       newViewName = viewTitle + " " + (++index);
2954     }
2955     return newViewName;
2956   }
2957
2958   /**
2959    * Returns a list of distinct view names found in the given list of
2960    * components. View names are held on the viewport of an AlignmentPanel.
2961    *
2962    * @param comps
2963    * @return
2964    */
2965   protected List<String> getExistingViewNames(List<Component> comps)
2966   {
2967     List<String> existingNames = new ArrayList<>();
2968     for (Component comp : comps)
2969     {
2970       if (comp instanceof AlignmentPanel)
2971       {
2972         AlignmentPanel ap = (AlignmentPanel) comp;
2973         if (!existingNames.contains(ap.av.getViewName()))
2974         {
2975           existingNames.add(ap.av.getViewName());
2976         }
2977       }
2978     }
2979     return existingNames;
2980   }
2981
2982   /**
2983    * Explode tabbed views into separate windows.
2984    */
2985   @Override
2986   public void expandViews_actionPerformed(ActionEvent e)
2987   {
2988     Desktop.explodeViews(this);
2989   }
2990
2991   /**
2992    * Gather views in separate windows back into a tabbed presentation.
2993    */
2994   @Override
2995   public void gatherViews_actionPerformed(ActionEvent e)
2996   {
2997     Desktop.instance.gatherViews(this);
2998   }
2999
3000   /**
3001    * DOCUMENT ME!
3002    *
3003    * @param e
3004    *          DOCUMENT ME!
3005    */
3006   @Override
3007   public void font_actionPerformed(ActionEvent e)
3008   {
3009     new FontChooser(alignPanel);
3010   }
3011
3012   /**
3013    * DOCUMENT ME!
3014    *
3015    * @param e
3016    *          DOCUMENT ME!
3017    */
3018   @Override
3019   protected void seqLimit_actionPerformed(ActionEvent e)
3020   {
3021     viewport.setShowJVSuffix(seqLimits.isSelected());
3022
3023     alignPanel.getIdPanel().getIdCanvas()
3024             .setPreferredSize(alignPanel.calculateIdWidth());
3025     alignPanel.paintAlignment(true, false);
3026   }
3027
3028   @Override
3029   public void idRightAlign_actionPerformed(ActionEvent e)
3030   {
3031     viewport.setRightAlignIds(idRightAlign.isSelected());
3032     alignPanel.paintAlignment(false, false);
3033   }
3034
3035   @Override
3036   public void centreColumnLabels_actionPerformed(ActionEvent e)
3037   {
3038     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3039     alignPanel.paintAlignment(false, false);
3040   }
3041
3042   /*
3043    * (non-Javadoc)
3044    *
3045    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3046    */
3047   @Override
3048   protected void followHighlight_actionPerformed()
3049   {
3050     /*
3051      * Set the 'follow' flag on the Viewport (and scroll to position if now
3052      * true).
3053      */
3054     final boolean state = this.followHighlightMenuItem.getState();
3055     viewport.setFollowHighlight(state);
3056     if (state)
3057     {
3058       alignPanel.scrollToPosition(viewport.getSearchResults());
3059     }
3060   }
3061
3062   /**
3063    * DOCUMENT ME!
3064    *
3065    * @param e
3066    *          DOCUMENT ME!
3067    */
3068   @Override
3069   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3070   {
3071     viewport.setColourText(colourTextMenuItem.isSelected());
3072     alignPanel.paintAlignment(false, false);
3073   }
3074
3075   /**
3076    * DOCUMENT ME!
3077    *
3078    * @param e
3079    *          DOCUMENT ME!
3080    */
3081   @Override
3082   public void wrapMenuItem_actionPerformed(ActionEvent e)
3083   {
3084     scaleAbove.setVisible(wrapMenuItem.isSelected());
3085     scaleLeft.setVisible(wrapMenuItem.isSelected());
3086     scaleRight.setVisible(wrapMenuItem.isSelected());
3087     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3088     alignPanel.updateLayout();
3089   }
3090
3091   @Override
3092   public void showAllSeqs_actionPerformed(ActionEvent e)
3093   {
3094     viewport.showAllHiddenSeqs();
3095   }
3096
3097   @Override
3098   public void showAllColumns_actionPerformed(ActionEvent e)
3099   {
3100     viewport.showAllHiddenColumns();
3101     alignPanel.paintAlignment(true, true);
3102     viewport.sendSelection();
3103   }
3104
3105   @Override
3106   public void hideSelSequences_actionPerformed(ActionEvent e)
3107   {
3108     viewport.hideAllSelectedSeqs();
3109   }
3110
3111   /**
3112    * called by key handler and the hide all/show all menu items
3113    *
3114    * @param toggleSeqs
3115    * @param toggleCols
3116    */
3117   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3118   {
3119
3120     boolean hide = false;
3121     SequenceGroup sg = viewport.getSelectionGroup();
3122     if (!toggleSeqs && !toggleCols)
3123     {
3124       // Hide everything by the current selection - this is a hack - we do the
3125       // invert and then hide
3126       // first check that there will be visible columns after the invert.
3127       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3128               && sg.getStartRes() <= sg.getEndRes()))
3129       {
3130         // now invert the sequence set, if required - empty selection implies
3131         // that no hiding is required.
3132         if (sg != null)
3133         {
3134           invertSequenceMenuItem_actionPerformed(null);
3135           sg = viewport.getSelectionGroup();
3136           toggleSeqs = true;
3137
3138         }
3139         viewport.expandColSelection(sg, true);
3140         // finally invert the column selection and get the new sequence
3141         // selection.
3142         invertColSel_actionPerformed(null);
3143         toggleCols = true;
3144       }
3145     }
3146
3147     if (toggleSeqs)
3148     {
3149       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3150       {
3151         hideSelSequences_actionPerformed(null);
3152         hide = true;
3153       }
3154       else if (!(toggleCols && viewport.hasSelectedColumns()))
3155       {
3156         showAllSeqs_actionPerformed(null);
3157       }
3158     }
3159
3160     if (toggleCols)
3161     {
3162       if (viewport.hasSelectedColumns())
3163       {
3164         hideSelColumns_actionPerformed(null);
3165         if (!toggleSeqs)
3166         {
3167           viewport.setSelectionGroup(sg);
3168         }
3169       }
3170       else if (!hide)
3171       {
3172         showAllColumns_actionPerformed(null);
3173       }
3174     }
3175   }
3176
3177   /*
3178    * (non-Javadoc)
3179    *
3180    * @see
3181    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3182    * event.ActionEvent)
3183    */
3184   @Override
3185   public void hideAllButSelection_actionPerformed(ActionEvent e)
3186   {
3187     toggleHiddenRegions(false, false);
3188     viewport.sendSelection();
3189   }
3190
3191   /*
3192    * (non-Javadoc)
3193    *
3194    * @see
3195    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3196    * .ActionEvent)
3197    */
3198   @Override
3199   public void hideAllSelection_actionPerformed(ActionEvent e)
3200   {
3201     SequenceGroup sg = viewport.getSelectionGroup();
3202     viewport.expandColSelection(sg, false);
3203     viewport.hideAllSelectedSeqs();
3204     viewport.hideSelectedColumns();
3205     alignPanel.updateLayout();
3206     alignPanel.paintAlignment(true, true);
3207     viewport.sendSelection();
3208   }
3209
3210   /*
3211    * (non-Javadoc)
3212    *
3213    * @see
3214    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3215    * ActionEvent)
3216    */
3217   @Override
3218   public void showAllhidden_actionPerformed(ActionEvent e)
3219   {
3220     viewport.showAllHiddenColumns();
3221     viewport.showAllHiddenSeqs();
3222     alignPanel.paintAlignment(true, true);
3223     viewport.sendSelection();
3224   }
3225
3226   @Override
3227   public void hideSelColumns_actionPerformed(ActionEvent e)
3228   {
3229     viewport.hideSelectedColumns();
3230     alignPanel.updateLayout();
3231     alignPanel.paintAlignment(true, true);
3232     viewport.sendSelection();
3233   }
3234
3235   @Override
3236   public void hiddenMarkers_actionPerformed(ActionEvent e)
3237   {
3238     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3239     repaint();
3240   }
3241
3242   /**
3243    * DOCUMENT ME!
3244    *
3245    * @param e
3246    *          DOCUMENT ME!
3247    */
3248   @Override
3249   protected void scaleAbove_actionPerformed(ActionEvent e)
3250   {
3251     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3252     alignPanel.updateLayout();
3253     alignPanel.paintAlignment(true, false);
3254   }
3255
3256   /**
3257    * DOCUMENT ME!
3258    *
3259    * @param e
3260    *          DOCUMENT ME!
3261    */
3262   @Override
3263   protected void scaleLeft_actionPerformed(ActionEvent e)
3264   {
3265     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3266     alignPanel.updateLayout();
3267     alignPanel.paintAlignment(true, false);
3268   }
3269
3270   /**
3271    * DOCUMENT ME!
3272    *
3273    * @param e
3274    *          DOCUMENT ME!
3275    */
3276   @Override
3277   protected void scaleRight_actionPerformed(ActionEvent e)
3278   {
3279     viewport.setScaleRightWrapped(scaleRight.isSelected());
3280     alignPanel.updateLayout();
3281     alignPanel.paintAlignment(true, false);
3282   }
3283
3284   /**
3285    * DOCUMENT ME!
3286    *
3287    * @param e
3288    *          DOCUMENT ME!
3289    */
3290   @Override
3291   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3292   {
3293     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3294     alignPanel.paintAlignment(false, false);
3295   }
3296
3297   /**
3298    * DOCUMENT ME!
3299    *
3300    * @param e
3301    *          DOCUMENT ME!
3302    */
3303   @Override
3304   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3305   {
3306     viewport.setShowText(viewTextMenuItem.isSelected());
3307     alignPanel.paintAlignment(false, false);
3308   }
3309
3310   /**
3311    * DOCUMENT ME!
3312    *
3313    * @param e
3314    *          DOCUMENT ME!
3315    */
3316   @Override
3317   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3318   {
3319     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3320     alignPanel.paintAlignment(false, false);
3321   }
3322
3323   public FeatureSettings featureSettings;
3324
3325   @Override
3326   public FeatureSettingsControllerI getFeatureSettingsUI()
3327   {
3328     return featureSettings;
3329   }
3330
3331   @Override
3332   public void featureSettings_actionPerformed(ActionEvent e)
3333   {
3334     showFeatureSettingsUI();
3335   }
3336
3337   @Override
3338   public FeatureSettingsControllerI showFeatureSettingsUI()
3339   {
3340     if (featureSettings != null)
3341     {
3342       featureSettings.closeOldSettings();
3343       featureSettings = null;
3344     }
3345     if (!showSeqFeatures.isSelected())
3346     {
3347       // make sure features are actually displayed
3348       showSeqFeatures.setSelected(true);
3349       showSeqFeatures_actionPerformed(null);
3350     }
3351     featureSettings = new FeatureSettings(this);
3352     return featureSettings;
3353   }
3354
3355   /**
3356    * Set or clear 'Show Sequence Features'
3357    *
3358    * @param evt
3359    *          DOCUMENT ME!
3360    */
3361   @Override
3362   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3363   {
3364     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3365     alignPanel.paintAlignment(true, true);
3366   }
3367
3368   /**
3369    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3370    * the annotations panel as a whole.
3371    *
3372    * The options to show/hide all annotations should be enabled when the panel
3373    * is shown, and disabled when the panel is hidden.
3374    *
3375    * @param e
3376    */
3377   @Override
3378   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3379   {
3380     final boolean setVisible = annotationPanelMenuItem.isSelected();
3381     viewport.setShowAnnotation(setVisible);
3382     this.showAllSeqAnnotations.setEnabled(setVisible);
3383     this.hideAllSeqAnnotations.setEnabled(setVisible);
3384     this.showAllAlAnnotations.setEnabled(setVisible);
3385     this.hideAllAlAnnotations.setEnabled(setVisible);
3386     alignPanel.updateLayout();
3387   }
3388
3389   @Override
3390   public void alignmentProperties()
3391   {
3392     JComponent pane;
3393     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3394
3395             .formatAsHtml();
3396     String content = MessageManager.formatMessage("label.html_content",
3397             new Object[]
3398             { contents.toString() });
3399     contents = null;
3400
3401     if (Platform.isJS())
3402     {
3403       JLabel textLabel = new JLabel();
3404       textLabel.setText(content);
3405       textLabel.setBackground(Color.WHITE);
3406
3407       pane = new JPanel(new BorderLayout());
3408       ((JPanel) pane).setOpaque(true);
3409       pane.setBackground(Color.WHITE);
3410       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3411     }
3412     else
3413     /**
3414      * Java only
3415      *
3416      * @j2sIgnore
3417      */
3418     {
3419       JEditorPane editPane = new JEditorPane("text/html", "");
3420       editPane.setEditable(false);
3421       editPane.setText(content);
3422       pane = editPane;
3423     }
3424
3425     JInternalFrame frame = new JInternalFrame();
3426
3427     frame.getContentPane().add(new JScrollPane(pane));
3428
3429     Desktop.addInternalFrame(frame, MessageManager
3430             .formatMessage("label.alignment_properties", new Object[]
3431             { getTitle() }), 500, 400);
3432   }
3433
3434   /**
3435    * Opens an Overview panel for the alignment, unless one is open already
3436    *
3437    * @param e
3438    */
3439   @Override
3440   public void overviewMenuItem_actionPerformed(ActionEvent e)
3441   {
3442     boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
3443                 false);
3444     openOverviewPanel(showHiddenRegions);
3445   }
3446
3447   public OverviewPanel openOverviewPanel(boolean showHidden)
3448   {
3449     if (alignPanel.overviewPanel != null)
3450     {
3451       return alignPanel.overviewPanel;
3452     }
3453     JInternalFrame frame = new JInternalFrame();
3454     final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
3455     frame.setContentPane(overview);
3456     Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
3457             true, true);
3458     frame.setFrameIcon(null);
3459     frame.pack();
3460     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3461     final AlignmentPanel thePanel = this.alignPanel;
3462     frame.addInternalFrameListener(
3463             new javax.swing.event.InternalFrameAdapter()
3464             {
3465               @Override
3466               public void internalFrameClosed(
3467                       javax.swing.event.InternalFrameEvent evt)
3468               {
3469                 overview.dispose();
3470                 thePanel.setOverviewPanel(null);
3471               }
3472             });
3473     if (getKeyListeners().length > 0)
3474     {
3475       frame.addKeyListener(getKeyListeners()[0]);
3476     }
3477
3478     alignPanel.setOverviewPanel(overview);
3479     alignPanel.setOverviewTitle(this);
3480
3481     return overview;
3482   }
3483
3484   @Override
3485   public void textColour_actionPerformed()
3486   {
3487     new TextColourChooser().chooseColour(alignPanel, null);
3488   }
3489
3490   /*
3491    * public void covariationColour_actionPerformed() {
3492    * changeColour(new
3493    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3494    * ()[0])); }
3495    */
3496   @Override
3497   public void annotationColour_actionPerformed()
3498   {
3499     new AnnotationColourChooser(viewport, alignPanel);
3500   }
3501
3502   @Override
3503   public void annotationColumn_actionPerformed(ActionEvent e)
3504   {
3505     new AnnotationColumnChooser(viewport, alignPanel);
3506   }
3507
3508   /**
3509    * Action on the user checking or unchecking the option to apply the selected
3510    * colour scheme to all groups. If unchecked, groups may have their own
3511    * independent colour schemes.
3512    *
3513    * @param selected
3514    */
3515   @Override
3516   public void applyToAllGroups_actionPerformed(boolean selected)
3517   {
3518     viewport.setColourAppliesToAllGroups(selected);
3519   }
3520
3521   /**
3522    * Action on user selecting a colour from the colour menu
3523    *
3524    * @param name
3525    *          the name (not the menu item label!) of the colour scheme
3526    */
3527   @Override
3528   public void changeColour_actionPerformed(String name)
3529   {
3530     /*
3531      * 'User Defined' opens a panel to configure or load a
3532      * user-defined colour scheme
3533      */
3534     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3535     {
3536       new UserDefinedColours(alignPanel);
3537       return;
3538     }
3539
3540     /*
3541      * otherwise set the chosen colour scheme (or null for 'None')
3542      */
3543     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3544             viewport, viewport.getAlignment(),
3545             viewport.getHiddenRepSequences());
3546     changeColour(cs);
3547   }
3548
3549   /**
3550    * Actions on setting or changing the alignment colour scheme
3551    *
3552    * @param cs
3553    */
3554   @Override
3555   public void changeColour(ColourSchemeI cs)
3556   {
3557     // TODO: pull up to controller method
3558     ColourMenuHelper.setColourSelected(colourMenu, cs);
3559
3560     viewport.setGlobalColourScheme(cs);
3561
3562     alignPanel.paintAlignment(true, true);
3563   }
3564
3565   /**
3566    * Show the PID threshold slider panel
3567    */
3568   @Override
3569   protected void modifyPID_actionPerformed()
3570   {
3571     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3572             alignPanel.getViewName());
3573     SliderPanel.showPIDSlider();
3574   }
3575
3576   /**
3577    * Show the Conservation slider panel
3578    */
3579   @Override
3580   protected void modifyConservation_actionPerformed()
3581   {
3582     SliderPanel.setConservationSlider(alignPanel,
3583             viewport.getResidueShading(), alignPanel.getViewName());
3584     SliderPanel.showConservationSlider();
3585   }
3586
3587   /**
3588    * Action on selecting or deselecting (Colour) By Conservation
3589    */
3590   @Override
3591   public void conservationMenuItem_actionPerformed(boolean selected)
3592   {
3593     modifyConservation.setEnabled(selected);
3594     viewport.setConservationSelected(selected);
3595     viewport.getResidueShading().setConservationApplied(selected);
3596
3597     changeColour(viewport.getGlobalColourScheme());
3598     if (selected)
3599     {
3600       modifyConservation_actionPerformed();
3601     }
3602     else
3603     {
3604       SliderPanel.hideConservationSlider();
3605     }
3606   }
3607
3608   /**
3609    * Action on selecting or deselecting (Colour) Above PID Threshold
3610    */
3611   @Override
3612   public void abovePIDThreshold_actionPerformed(boolean selected)
3613   {
3614     modifyPID.setEnabled(selected);
3615     viewport.setAbovePIDThreshold(selected);
3616     if (!selected)
3617     {
3618       viewport.getResidueShading().setThreshold(0,
3619               viewport.isIgnoreGapsConsensus());
3620     }
3621
3622     changeColour(viewport.getGlobalColourScheme());
3623     if (selected)
3624     {
3625       modifyPID_actionPerformed();
3626     }
3627     else
3628     {
3629       SliderPanel.hidePIDSlider();
3630     }
3631   }
3632
3633   /**
3634    * DOCUMENT ME!
3635    *
3636    * @param e
3637    *          DOCUMENT ME!
3638    */
3639   @Override
3640   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3641   {
3642     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3643     AlignmentSorter.sortByPID(viewport.getAlignment(),
3644             viewport.getAlignment().getSequenceAt(0));
3645     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3646             viewport.getAlignment()));
3647     alignPanel.paintAlignment(true, false);
3648   }
3649
3650   /**
3651    * DOCUMENT ME!
3652    *
3653    * @param e
3654    *          DOCUMENT ME!
3655    */
3656   @Override
3657   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3658   {
3659     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3660     AlignmentSorter.sortByID(viewport.getAlignment());
3661     addHistoryItem(
3662             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3663     alignPanel.paintAlignment(true, false);
3664   }
3665
3666   /**
3667    * DOCUMENT ME!
3668    *
3669    * @param e
3670    *          DOCUMENT ME!
3671    */
3672   @Override
3673   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3674   {
3675     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3676     AlignmentSorter.sortByLength(viewport.getAlignment());
3677     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3678             viewport.getAlignment()));
3679     alignPanel.paintAlignment(true, false);
3680   }
3681
3682   /**
3683    * DOCUMENT ME!
3684    *
3685    * @param e
3686    *          DOCUMENT ME!
3687    */
3688   @Override
3689   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3690   {
3691     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3692     AlignmentSorter.sortByGroup(viewport.getAlignment());
3693     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3694             viewport.getAlignment()));
3695
3696     alignPanel.paintAlignment(true, false);
3697   }
3698
3699   /**
3700    * DOCUMENT ME!
3701    *
3702    * @param e
3703    *          DOCUMENT ME!
3704    */
3705   @Override
3706   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3707   {
3708     new RedundancyPanel(alignPanel, this);
3709   }
3710
3711   /**
3712    * DOCUMENT ME!
3713    *
3714    * @param e
3715    *          DOCUMENT ME!
3716    */
3717   @Override
3718   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3719   {
3720     if ((viewport.getSelectionGroup() == null)
3721             || (viewport.getSelectionGroup().getSize() < 2))
3722     {
3723       JvOptionPane.showInternalMessageDialog(this,
3724               MessageManager.getString(
3725                       "label.you_must_select_least_two_sequences"),
3726               MessageManager.getString("label.invalid_selection"),
3727               JvOptionPane.WARNING_MESSAGE);
3728     }
3729     else
3730     {
3731       JInternalFrame frame = new JInternalFrame();
3732       frame.setContentPane(new PairwiseAlignPanel(viewport));
3733       Desktop.addInternalFrame(frame,
3734               MessageManager.getString("action.pairwise_alignment"), 600,
3735               500);
3736     }
3737   }
3738
3739   @Override
3740   public void autoCalculate_actionPerformed(ActionEvent e)
3741   {
3742     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3743     if (viewport.autoCalculateConsensus)
3744     {
3745       viewport.firePropertyChange("alignment", null,
3746               viewport.getAlignment().getSequences());
3747     }
3748   }
3749
3750   @Override
3751   public void sortByTreeOption_actionPerformed(ActionEvent e)
3752   {
3753     viewport.sortByTree = sortByTree.isSelected();
3754   }
3755
3756   @Override
3757   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3758   {
3759     viewport.followSelection = listenToViewSelections.isSelected();
3760   }
3761
3762   /**
3763    * Constructs a tree panel and adds it to the desktop
3764    *
3765    * @param type
3766    *          tree type (NJ or AV)
3767    * @param modelName
3768    *          name of score model used to compute the tree
3769    * @param options
3770    *          parameters for the distance or similarity calculation
3771    */
3772   void newTreePanel(String type, String modelName,
3773           SimilarityParamsI options)
3774   {
3775     String frameTitle = "";
3776     TreePanel tp;
3777
3778     boolean onSelection = false;
3779     if (viewport.getSelectionGroup() != null
3780             && viewport.getSelectionGroup().getSize() > 0)
3781     {
3782       SequenceGroup sg = viewport.getSelectionGroup();
3783
3784       /* Decide if the selection is a column region */
3785       for (SequenceI _s : sg.getSequences())
3786       {
3787         if (_s.getLength() < sg.getEndRes())
3788         {
3789           JvOptionPane.showMessageDialog(Desktop.desktop,
3790                   MessageManager.getString(
3791                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3792                   MessageManager.getString(
3793                           "label.sequences_selection_not_aligned"),
3794                   JvOptionPane.WARNING_MESSAGE);
3795
3796           return;
3797         }
3798       }
3799       onSelection = true;
3800     }
3801     else
3802     {
3803       if (viewport.getAlignment().getHeight() < 2)
3804       {
3805         return;
3806       }
3807     }
3808
3809     tp = new TreePanel(alignPanel, type, modelName, options);
3810     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3811
3812     frameTitle += " from ";
3813
3814     if (viewport.getViewName() != null)
3815     {
3816       frameTitle += viewport.getViewName() + " of ";
3817     }
3818
3819     frameTitle += this.title;
3820
3821     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3822   }
3823
3824   /**
3825    * DOCUMENT ME!
3826    *
3827    * @param title
3828    *          DOCUMENT ME!
3829    * @param order
3830    *          DOCUMENT ME!
3831    */
3832   public void addSortByOrderMenuItem(String title,
3833           final AlignmentOrder order)
3834   {
3835     final JMenuItem item = new JMenuItem(MessageManager
3836             .formatMessage("action.by_title_param", new Object[]
3837             { title }));
3838     sort.add(item);
3839     item.addActionListener(new java.awt.event.ActionListener()
3840     {
3841       @Override
3842       public void actionPerformed(ActionEvent e)
3843       {
3844         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3845
3846         // TODO: JBPNote - have to map order entries to curent SequenceI
3847         // pointers
3848         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3849
3850         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3851                 viewport.getAlignment()));
3852
3853         alignPanel.paintAlignment(true, false);
3854       }
3855     });
3856   }
3857
3858   /**
3859    * Add a new sort by annotation score menu item
3860    *
3861    * @param sort
3862    *          the menu to add the option to
3863    * @param scoreLabel
3864    *          the label used to retrieve scores for each sequence on the
3865    *          alignment
3866    */
3867   public void addSortByAnnotScoreMenuItem(JMenu sort,
3868           final String scoreLabel)
3869   {
3870     final JMenuItem item = new JMenuItem(scoreLabel);
3871     sort.add(item);
3872     item.addActionListener(new java.awt.event.ActionListener()
3873     {
3874       @Override
3875       public void actionPerformed(ActionEvent e)
3876       {
3877         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3878         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3879                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3880         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3881                 viewport.getAlignment()));
3882         alignPanel.paintAlignment(true, false);
3883       }
3884     });
3885   }
3886
3887   /**
3888    * last hash for alignment's annotation array - used to minimise cost of
3889    * rebuild.
3890    */
3891   protected int _annotationScoreVectorHash;
3892
3893   /**
3894    * search the alignment and rebuild the sort by annotation score submenu the
3895    * last alignment annotation vector hash is stored to minimize cost of
3896    * rebuilding in subsequence calls.
3897    *
3898    */
3899   @Override
3900   public void buildSortByAnnotationScoresMenu()
3901   {
3902     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3903     {
3904       return;
3905     }
3906
3907     if (viewport.getAlignment().getAlignmentAnnotation()
3908             .hashCode() != _annotationScoreVectorHash)
3909     {
3910       sortByAnnotScore.removeAll();
3911       // almost certainly a quicker way to do this - but we keep it simple
3912       Hashtable<String, String> scoreSorts = new Hashtable<>();
3913       AlignmentAnnotation aann[];
3914       for (SequenceI sqa : viewport.getAlignment().getSequences())
3915       {
3916         aann = sqa.getAnnotation();
3917         for (int i = 0; aann != null && i < aann.length; i++)
3918         {
3919           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3920           {
3921             scoreSorts.put(aann[i].label, aann[i].label);
3922           }
3923         }
3924       }
3925       Enumeration<String> labels = scoreSorts.keys();
3926       while (labels.hasMoreElements())
3927       {
3928         addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
3929       }
3930       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3931       scoreSorts.clear();
3932
3933       _annotationScoreVectorHash = viewport.getAlignment()
3934               .getAlignmentAnnotation().hashCode();
3935     }
3936   }
3937
3938   /**
3939    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3940    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3941    * call. Listeners are added to remove the menu item when the treePanel is
3942    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3943    * modified.
3944    */
3945   @Override
3946   public void buildTreeSortMenu()
3947   {
3948     sortByTreeMenu.removeAll();
3949
3950     List<Component> comps = PaintRefresher.components
3951             .get(viewport.getSequenceSetId());
3952     List<TreePanel> treePanels = new ArrayList<>();
3953     for (Component comp : comps)
3954     {
3955       if (comp instanceof TreePanel)
3956       {
3957         treePanels.add((TreePanel) comp);
3958       }
3959     }
3960
3961     if (treePanels.size() < 1)
3962     {
3963       sortByTreeMenu.setVisible(false);
3964       return;
3965     }
3966
3967     sortByTreeMenu.setVisible(true);
3968
3969     for (final TreePanel tp : treePanels)
3970     {
3971       final JMenuItem item = new JMenuItem(tp.getTitle());
3972       item.addActionListener(new java.awt.event.ActionListener()
3973       {
3974         @Override
3975         public void actionPerformed(ActionEvent e)
3976         {
3977           tp.sortByTree_actionPerformed();
3978           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3979
3980         }
3981       });
3982
3983       sortByTreeMenu.add(item);
3984     }
3985   }
3986
3987   public boolean sortBy(AlignmentOrder alorder, String undoname)
3988   {
3989     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3990     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3991     if (undoname != null)
3992     {
3993       addHistoryItem(new OrderCommand(undoname, oldOrder,
3994               viewport.getAlignment()));
3995     }
3996     alignPanel.paintAlignment(true, false);
3997     return true;
3998   }
3999
4000   /**
4001    * Work out whether the whole set of sequences or just the selected set will
4002    * be submitted for multiple alignment.
4003    *
4004    */
4005   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4006   {
4007     // Now, check we have enough sequences
4008     AlignmentView msa = null;
4009
4010     if ((viewport.getSelectionGroup() != null)
4011             && (viewport.getSelectionGroup().getSize() > 1))
4012     {
4013       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4014       // some common interface!
4015       /*
4016        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4017        * SequenceI[sz = seqs.getSize(false)];
4018        *
4019        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4020        * seqs.getSequenceAt(i); }
4021        */
4022       msa = viewport.getAlignmentView(true);
4023     }
4024     else if (viewport.getSelectionGroup() != null
4025             && viewport.getSelectionGroup().getSize() == 1)
4026     {
4027       int option = JvOptionPane.showConfirmDialog(this,
4028               MessageManager.getString("warn.oneseq_msainput_selection"),
4029               MessageManager.getString("label.invalid_selection"),
4030               JvOptionPane.OK_CANCEL_OPTION);
4031       if (option == JvOptionPane.OK_OPTION)
4032       {
4033         msa = viewport.getAlignmentView(false);
4034       }
4035     }
4036     else
4037     {
4038       msa = viewport.getAlignmentView(false);
4039     }
4040     return msa;
4041   }
4042
4043   /**
4044    * Decides what is submitted to a secondary structure prediction service: the
4045    * first sequence in the alignment, or in the current selection, or, if the
4046    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4047    * region or the whole alignment. (where the first sequence in the set is the
4048    * one that the prediction will be for).
4049    */
4050   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4051   {
4052     AlignmentView seqs = null;
4053
4054     if ((viewport.getSelectionGroup() != null)
4055             && (viewport.getSelectionGroup().getSize() > 0))
4056     {
4057       seqs = viewport.getAlignmentView(true);
4058     }
4059     else
4060     {
4061       seqs = viewport.getAlignmentView(false);
4062     }
4063     // limit sequences - JBPNote in future - could spawn multiple prediction
4064     // jobs
4065     // TODO: viewport.getAlignment().isAligned is a global state - the local
4066     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4067     if (!viewport.getAlignment().isAligned(false))
4068     {
4069       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4070       // TODO: if seqs.getSequences().length>1 then should really have warned
4071       // user!
4072
4073     }
4074     return seqs;
4075   }
4076
4077   /**
4078    * DOCUMENT ME!
4079    *
4080    * @param e
4081    *          DOCUMENT ME!
4082    */
4083   @Override
4084   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4085   {
4086     // Pick the tree file
4087     JalviewFileChooser chooser = new JalviewFileChooser(
4088             Cache.getProperty("LAST_DIRECTORY"));
4089     chooser.setFileView(new JalviewFileView());
4090     chooser.setDialogTitle(
4091             MessageManager.getString("label.select_newick_like_tree_file"));
4092     chooser.setToolTipText(
4093             MessageManager.getString("label.load_tree_file"));
4094
4095     chooser.setResponseHandler(0, () -> {
4096       String filePath = chooser.getSelectedFile().getPath();
4097       Cache.setProperty("LAST_DIRECTORY", filePath);
4098       NewickFile fin = null;
4099       try
4100       {
4101         fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4102                 DataSourceType.FILE));
4103         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4104       } catch (Exception ex)
4105       {
4106         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4107                 MessageManager.getString("label.problem_reading_tree_file"),
4108                 JvOptionPane.WARNING_MESSAGE);
4109         ex.printStackTrace();
4110       }
4111       if (fin != null && fin.hasWarningMessage())
4112       {
4113         JvOptionPane.showMessageDialog(Desktop.desktop,
4114                 fin.getWarningMessage(),
4115                 MessageManager
4116                         .getString("label.possible_problem_with_tree_file"),
4117                 JvOptionPane.WARNING_MESSAGE);
4118       }
4119       return null;
4120     });
4121     chooser.showOpenDialog(this);
4122   }
4123
4124   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4125   {
4126     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4127   }
4128
4129   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4130           int h, int x, int y)
4131   {
4132     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4133   }
4134
4135
4136   /**
4137    * Add a treeviewer for the tree extracted from a Newick file object to the
4138    * current alignment view
4139    *
4140    * @param nf
4141    *          the tree
4142    * @param title
4143    *          tree viewer title
4144    * @param input
4145    *          Associated alignment input data (or null)
4146    * @param w
4147    *          width
4148    * @param h
4149    *          height
4150    * @param x
4151    *          position
4152    * @param y
4153    *          position
4154    * @return TreePanel handle
4155    */
4156   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4157           AlignmentView input, int w, int h, int x, int y)
4158   {
4159     TreePanel tp = null;
4160
4161     try
4162     {
4163       nf.parse();
4164
4165       if (nf.getTree() != null)
4166       {
4167         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4168
4169         tp.setSize(w, h);
4170
4171         if (x > 0 && y > 0)
4172         {
4173           tp.setLocation(x, y);
4174         }
4175
4176         Desktop.addInternalFrame(tp, treeTitle, w, h);
4177       }
4178     } catch (Exception ex)
4179     {
4180       ex.printStackTrace();
4181     }
4182
4183     return tp;
4184   }
4185
4186
4187   public void showContactMapTree(AlignmentAnnotation aa,
4188           PAEContactMatrix cm)
4189   {
4190     int x = 4, y = 5;
4191     int w = 400, h = 500;
4192
4193     try
4194     {
4195       NewickFile fin = new NewickFile(
4196               new FileParse(cm.getNewick(), DataSourceType.PASTE));
4197       String title = "PAE Matrix Tree for "
4198               + cm.getReferenceSeq().getDisplayId(false);
4199
4200       showColumnWiseTree(fin, aa, title, w,h, x,y);
4201     } catch (Throwable xx)
4202     {
4203       Console.error("Unexpected exception showing tree for contact matrix",
4204               xx);
4205     }
4206   }
4207   public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle,
4208            int w, int h, int x, int y)
4209   {
4210       try
4211       {
4212         nf.parse();
4213         if (nf.getTree() == null)
4214         {
4215           return null;
4216         }
4217         TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
4218
4219         tp.setSize(w, h);
4220
4221         if (x > 0 && y > 0)
4222         {
4223           tp.setLocation(x, y);
4224         }
4225
4226         Desktop.addInternalFrame(tp, title, w, h);
4227         return tp;
4228       } catch (Throwable xx)
4229       {
4230         Console.error("Unexpected exception showing tree for contact matrix",
4231                 xx);
4232       }
4233       return null;
4234   }
4235
4236   private boolean buildingMenu = false;
4237
4238   /**
4239    * Generates menu items and listener event actions for web service clients
4240    *
4241    */
4242   public void BuildWebServiceMenu()
4243   {
4244     while (buildingMenu)
4245     {
4246       try
4247       {
4248         System.err.println("Waiting for building menu to finish.");
4249         Thread.sleep(10);
4250       } catch (Exception e)
4251       {
4252       }
4253     }
4254     final AlignFrame me = this;
4255     buildingMenu = true;
4256     new Thread(new Runnable()
4257     {
4258       @Override
4259       public void run()
4260       {
4261         final List<JMenuItem> legacyItems = new ArrayList<>();
4262         try
4263         {
4264           // System.err.println("Building ws menu again "
4265           // + Thread.currentThread());
4266           // TODO: add support for context dependent disabling of services based
4267           // on
4268           // alignment and current selection
4269           // TODO: add additional serviceHandle parameter to specify abstract
4270           // handler
4271           // class independently of AbstractName
4272           // TODO: add in rediscovery GUI function to restart discoverer
4273           // TODO: group services by location as well as function and/or
4274           // introduce
4275           // object broker mechanism.
4276           final Vector<JMenu> wsmenu = new Vector<>();
4277           final IProgressIndicator af = me;
4278
4279           /*
4280            * do not i18n these strings - they are hard-coded in class
4281            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4282            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4283            */
4284           final JMenu msawsmenu = new JMenu("Alignment");
4285           final JMenu secstrmenu = new JMenu(
4286                   "Secondary Structure Prediction");
4287           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4288           final JMenu analymenu = new JMenu("Analysis");
4289           final JMenu dismenu = new JMenu("Protein Disorder");
4290           // JAL-940 - only show secondary structure prediction services from
4291           // the legacy server
4292           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4293               // &&
4294           Discoverer.services != null && (Discoverer.services.size() > 0))
4295           {
4296             // TODO: refactor to allow list of AbstractName/Handler bindings to
4297             // be
4298             // stored or retrieved from elsewhere
4299             // No MSAWS used any more:
4300             // Vector msaws = null; // (Vector)
4301             // Discoverer.services.get("MsaWS");
4302             Vector<ServiceHandle> secstrpr = Discoverer.services
4303                     .get("SecStrPred");
4304             if (secstrpr != null)
4305             {
4306               // Add any secondary structure prediction services
4307               for (int i = 0, j = secstrpr.size(); i < j; i++)
4308               {
4309                 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4310                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4311                         .getServiceClient(sh);
4312                 int p = secstrmenu.getItemCount();
4313                 impl.attachWSMenuEntry(secstrmenu, me);
4314                 int q = secstrmenu.getItemCount();
4315                 for (int litm = p; litm < q; litm++)
4316                 {
4317                   legacyItems.add(secstrmenu.getItem(litm));
4318                 }
4319               }
4320             }
4321           }
4322
4323           // Add all submenus in the order they should appear on the web
4324           // services menu
4325           wsmenu.add(msawsmenu);
4326           wsmenu.add(secstrmenu);
4327           wsmenu.add(dismenu);
4328           wsmenu.add(analymenu);
4329           // No search services yet
4330           // wsmenu.add(seqsrchmenu);
4331
4332           javax.swing.SwingUtilities.invokeLater(new Runnable()
4333           {
4334             @Override
4335             public void run()
4336             {
4337               try
4338               {
4339                 webService.removeAll();
4340                 // first, add discovered services onto the webservices menu
4341                 if (wsmenu.size() > 0)
4342                 {
4343                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4344                   {
4345                     webService.add(wsmenu.get(i));
4346                   }
4347                 }
4348                 else
4349                 {
4350                   webService.add(me.webServiceNoServices);
4351                 }
4352                 // TODO: move into separate menu builder class.
4353                 {
4354                   // logic for 2.11.1.4 is
4355                   // always look to see if there is a discover. if there isn't
4356                   // we can't show any Jws2 services
4357                   // if there are services available, show them - regardless of
4358                   // the 'show JWS2 preference'
4359                   // if the discoverer is running then say so
4360                   // otherwise offer to trigger discovery if 'show JWS2' is not
4361                   // enabled
4362                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4363                   if (jws2servs != null)
4364                   {
4365                     if (jws2servs.hasServices())
4366                     {
4367                       jws2servs.attachWSMenuEntry(webService, me);
4368                       for (Jws2Instance sv : jws2servs.getServices())
4369                       {
4370                         if (sv.description.toLowerCase(Locale.ROOT)
4371                                 .contains("jpred"))
4372                         {
4373                           for (JMenuItem jmi : legacyItems)
4374                           {
4375                             jmi.setVisible(false);
4376                           }
4377                         }
4378                       }
4379                     }
4380
4381                     if (jws2servs.isRunning())
4382                     {
4383                       JMenuItem tm = new JMenuItem(
4384                               "Still discovering JABA Services");
4385                       tm.setEnabled(false);
4386                       webService.add(tm);
4387                     }
4388                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4389                     {
4390                       JMenuItem enableJws2 = new JMenuItem(
4391                               "Discover Web Services");
4392                       enableJws2.setToolTipText(
4393                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4394                       enableJws2.setEnabled(true);
4395                       enableJws2.addActionListener(new ActionListener()
4396                       {
4397
4398                         @Override
4399                         public void actionPerformed(ActionEvent e)
4400                         {
4401                           // start service discoverer, but ignore preference
4402                           Desktop.instance.startServiceDiscovery(false,
4403                                   true);
4404                         }
4405                       });
4406                       webService.add(enableJws2);
4407                     }
4408                   }
4409                 }
4410                 build_urlServiceMenu(me.webService);
4411                 build_fetchdbmenu(webService);
4412                 for (JMenu item : wsmenu)
4413                 {
4414                   if (item.getItemCount() == 0)
4415                   {
4416                     item.setEnabled(false);
4417                   }
4418                   else
4419                   {
4420                     item.setEnabled(true);
4421                   }
4422                 }
4423               } catch (Exception e)
4424               {
4425                 Console.debug(
4426                         "Exception during web service menu building process.",
4427                         e);
4428               }
4429             }
4430           });
4431         } catch (Exception e)
4432         {
4433         }
4434         buildingMenu = false;
4435       }
4436     }).start();
4437
4438   }
4439
4440   /**
4441    * construct any groupURL type service menu entries.
4442    *
4443    * @param webService
4444    */
4445   protected void build_urlServiceMenu(JMenu webService)
4446   {
4447     // TODO: remove this code when 2.7 is released
4448     // DEBUG - alignmentView
4449     /*
4450      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4451      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4452      *
4453      * @Override public void actionPerformed(ActionEvent e) {
4454      * jalview.datamodel.AlignmentView
4455      * .testSelectionViews(af.viewport.getAlignment(),
4456      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4457      *
4458      * }); webService.add(testAlView);
4459      */
4460     // TODO: refactor to RestClient discoverer and merge menu entries for
4461     // rest-style services with other types of analysis/calculation service
4462     // SHmmr test client - still being implemented.
4463     // DEBUG - alignmentView
4464
4465     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4466             .getRestClients())
4467     {
4468       client.attachWSMenuEntry(
4469               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4470               this);
4471     }
4472   }
4473
4474   /**
4475    * Searches the alignment sequences for xRefs and builds the Show
4476    * Cross-References menu (formerly called Show Products), with database
4477    * sources for which cross-references are found (protein sources for a
4478    * nucleotide alignment and vice versa)
4479    *
4480    * @return true if Show Cross-references menu should be enabled
4481    */
4482   public boolean canShowProducts()
4483   {
4484     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4485     AlignmentI dataset = viewport.getAlignment().getDataset();
4486
4487     showProducts.removeAll();
4488     final boolean dna = viewport.getAlignment().isNucleotide();
4489
4490     if (seqs == null || seqs.length == 0)
4491     {
4492       // nothing to see here.
4493       return false;
4494     }
4495
4496     boolean showp = false;
4497     try
4498     {
4499       List<String> ptypes = new CrossRef(seqs, dataset)
4500               .findXrefSourcesForSequences(dna);
4501
4502       for (final String source : ptypes)
4503       {
4504         showp = true;
4505         final AlignFrame af = this;
4506         JMenuItem xtype = new JMenuItem(source);
4507         xtype.addActionListener(new ActionListener()
4508         {
4509           @Override
4510           public void actionPerformed(ActionEvent e)
4511           {
4512             showProductsFor(af.viewport.getSequenceSelection(), dna,
4513                     source);
4514           }
4515         });
4516         showProducts.add(xtype);
4517       }
4518       showProducts.setVisible(showp);
4519       showProducts.setEnabled(showp);
4520     } catch (Exception e)
4521     {
4522       Console.warn(
4523               "canShowProducts threw an exception - please report to help@jalview.org",
4524               e);
4525       return false;
4526     }
4527     return showp;
4528   }
4529
4530   /**
4531    * Finds and displays cross-references for the selected sequences (protein
4532    * products for nucleotide sequences, dna coding sequences for peptides).
4533    *
4534    * @param sel
4535    *          the sequences to show cross-references for
4536    * @param dna
4537    *          true if from a nucleotide alignment (so showing proteins)
4538    * @param source
4539    *          the database to show cross-references for
4540    */
4541   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4542           final String source)
4543   {
4544     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4545             .start();
4546   }
4547
4548   /**
4549    * Construct and display a new frame containing the translation of this
4550    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4551    */
4552   @Override
4553   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4554   {
4555     AlignmentI al = null;
4556     try
4557     {
4558       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4559
4560       al = dna.translateCdna(codeTable);
4561     } catch (Exception ex)
4562     {
4563       Console.error("Exception during translation. Please report this !",
4564               ex);
4565       final String msg = MessageManager.getString(
4566               "label.error_when_translating_sequences_submit_bug_report");
4567       final String errorTitle = MessageManager
4568               .getString("label.implementation_error")
4569               + MessageManager.getString("label.translation_failed");
4570       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4571               JvOptionPane.ERROR_MESSAGE);
4572       return;
4573     }
4574     if (al == null || al.getHeight() == 0)
4575     {
4576       final String msg = MessageManager.getString(
4577               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4578       final String errorTitle = MessageManager
4579               .getString("label.translation_failed");
4580       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4581               JvOptionPane.WARNING_MESSAGE);
4582     }
4583     else
4584     {
4585       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4586       af.setFileFormat(this.currentFileFormat);
4587       final String newTitle = MessageManager
4588               .formatMessage("label.translation_of_params", new Object[]
4589               { this.getTitle(), codeTable.getId() });
4590       af.setTitle(newTitle);
4591       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4592       {
4593         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4594         viewport.openSplitFrame(af, new Alignment(seqs));
4595       }
4596       else
4597       {
4598         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4599                 DEFAULT_HEIGHT);
4600       }
4601     }
4602   }
4603
4604   /**
4605    * Set the file format
4606    *
4607    * @param format
4608    */
4609   public void setFileFormat(FileFormatI format)
4610   {
4611     this.currentFileFormat = format;
4612   }
4613
4614   /**
4615    * Try to load a features file onto the alignment.
4616    *
4617    * @param file
4618    *          contents or path to retrieve file or a File object
4619    * @param sourceType
4620    *          access mode of file (see jalview.io.AlignFile)
4621    * @return true if features file was parsed correctly.
4622    */
4623   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4624   {
4625     // BH 2018
4626     return avc.parseFeaturesFile(file, sourceType,
4627             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4628
4629   }
4630
4631   @Override
4632   public void refreshFeatureUI(boolean enableIfNecessary)
4633   {
4634     // note - currently this is only still here rather than in the controller
4635     // because of the featureSettings hard reference that is yet to be
4636     // abstracted
4637     if (enableIfNecessary)
4638     {
4639       viewport.setShowSequenceFeatures(true);
4640       showSeqFeatures.setSelected(true);
4641     }
4642
4643   }
4644
4645   @Override
4646   public void dragEnter(DropTargetDragEvent evt)
4647   {
4648   }
4649
4650   @Override
4651   public void dragExit(DropTargetEvent evt)
4652   {
4653   }
4654
4655   @Override
4656   public void dragOver(DropTargetDragEvent evt)
4657   {
4658   }
4659
4660   @Override
4661   public void dropActionChanged(DropTargetDragEvent evt)
4662   {
4663   }
4664
4665   @Override
4666   public void drop(DropTargetDropEvent evt)
4667   {
4668     // JAL-1552 - acceptDrop required before getTransferable call for
4669     // Java's Transferable for native dnd
4670     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4671     Transferable t = evt.getTransferable();
4672
4673     final AlignFrame thisaf = this;
4674     final List<Object> files = new ArrayList<>();
4675     List<DataSourceType> protocols = new ArrayList<>();
4676
4677     try
4678     {
4679       Desktop.transferFromDropTarget(files, protocols, evt, t);
4680     } catch (Exception e)
4681     {
4682       e.printStackTrace();
4683     }
4684     if (files != null)
4685     {
4686       new Thread(new Runnable()
4687       {
4688         @Override
4689         public void run()
4690         {
4691           try
4692           {
4693             // check to see if any of these files have names matching sequences
4694             // in
4695             // the alignment
4696             SequenceIdMatcher idm = new SequenceIdMatcher(
4697                     viewport.getAlignment().getSequencesArray());
4698             /**
4699              * Object[] { String,SequenceI}
4700              */
4701             ArrayList<Object[]> filesmatched = new ArrayList<>();
4702             ArrayList<Object> filesnotmatched = new ArrayList<>();
4703             for (int i = 0; i < files.size(); i++)
4704             {
4705               // BH 2018
4706               Object file = files.get(i);
4707               String fileName = file.toString();
4708               String pdbfn = "";
4709               DataSourceType protocol = (file instanceof File
4710                       ? DataSourceType.FILE
4711                       : FormatAdapter.checkProtocol(fileName));
4712               if (protocol == DataSourceType.FILE)
4713               {
4714                 File fl;
4715                 if (file instanceof File)
4716                 {
4717                   fl = (File) file;
4718                   Platform.cacheFileData(fl);
4719                 }
4720                 else
4721                 {
4722                   fl = new File(fileName);
4723                 }
4724                 pdbfn = fl.getName();
4725               }
4726               else if (protocol == DataSourceType.URL)
4727               {
4728                 URL url = new URL(fileName);
4729                 pdbfn = url.getFile();
4730               }
4731               if (pdbfn.length() > 0)
4732               {
4733                 // attempt to find a match in the alignment
4734                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4735                 int l = 0, c = pdbfn.indexOf(".");
4736                 while (mtch == null && c != -1)
4737                 {
4738                   do
4739                   {
4740                     l = c;
4741                   } while ((c = pdbfn.indexOf(".", l)) > l);
4742                   if (l > -1)
4743                   {
4744                     pdbfn = pdbfn.substring(0, l);
4745                   }
4746                   mtch = idm.findAllIdMatches(pdbfn);
4747                 }
4748                 if (mtch != null)
4749                 {
4750                   FileFormatI type;
4751                   try
4752                   {
4753                     type = new IdentifyFile().identify(file, protocol);
4754                   } catch (Exception ex)
4755                   {
4756                     type = null;
4757                   }
4758                   if (type != null && type.isStructureFile())
4759                   {
4760                     filesmatched.add(new Object[] { file, protocol, mtch });
4761                     continue;
4762                   }
4763                 }
4764                 // File wasn't named like one of the sequences or wasn't a PDB
4765                 // file.
4766                 filesnotmatched.add(file);
4767               }
4768             }
4769             int assocfiles = 0;
4770             if (filesmatched.size() > 0)
4771             {
4772               boolean autoAssociate = Cache
4773                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4774               if (!autoAssociate)
4775               {
4776                 String msg = MessageManager.formatMessage(
4777                         "label.automatically_associate_structure_files_with_sequences_same_name",
4778                         new Object[]
4779                         { Integer.valueOf(filesmatched.size())
4780                                 .toString() });
4781                 String ttl = MessageManager.getString(
4782                         "label.automatically_associate_structure_files_by_name");
4783                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4784                         ttl, JvOptionPane.YES_NO_OPTION);
4785                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4786               }
4787               if (autoAssociate)
4788               {
4789                 for (Object[] fm : filesmatched)
4790                 {
4791                   // try and associate
4792                   // TODO: may want to set a standard ID naming formalism for
4793                   // associating PDB files which have no IDs.
4794                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4795                   {
4796                     PDBEntry pe = new AssociatePdbFileWithSeq()
4797                             .associatePdbWithSeq(fm[0].toString(),
4798                                     (DataSourceType) fm[1], toassoc, false,
4799                                     Desktop.instance);
4800                     if (pe != null)
4801                     {
4802                       System.err.println("Associated file : "
4803                               + (fm[0].toString()) + " with "
4804                               + toassoc.getDisplayId(true));
4805                       assocfiles++;
4806                     }
4807                   }
4808                   // TODO: do we need to update overview ? only if features are
4809                   // shown I guess
4810                   alignPanel.paintAlignment(true, false);
4811                 }
4812               }
4813               else
4814               {
4815                 /*
4816                  * add declined structures as sequences
4817                  */
4818                 for (Object[] o : filesmatched)
4819                 {
4820                   filesnotmatched.add(o[0]);
4821                 }
4822               }
4823             }
4824             if (filesnotmatched.size() > 0)
4825             {
4826               if (assocfiles > 0 && (Cache.getDefault(
4827                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4828                       || JvOptionPane.showConfirmDialog(thisaf,
4829                               "<html>" + MessageManager.formatMessage(
4830                                       "label.ignore_unmatched_dropped_files_info",
4831                                       new Object[]
4832                                       { Integer.valueOf(
4833                                               filesnotmatched.size())
4834                                               .toString() })
4835                                       + "</html>",
4836                               MessageManager.getString(
4837                                       "label.ignore_unmatched_dropped_files"),
4838                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4839               {
4840                 return;
4841               }
4842               for (Object fn : filesnotmatched)
4843               {
4844                 loadJalviewDataFile(fn, null, null, null);
4845               }
4846
4847             }
4848           } catch (Exception ex)
4849           {
4850             ex.printStackTrace();
4851           }
4852         }
4853       }).start();
4854     }
4855   }
4856
4857   /**
4858    * Attempt to load a "dropped" file or URL string, by testing in turn for
4859    * <ul>
4860    * <li>an Annotation file</li>
4861    * <li>a JNet file</li>
4862    * <li>a features file</li>
4863    * <li>else try to interpret as an alignment file</li>
4864    * </ul>
4865    *
4866    * @param file
4867    *          either a filename or a URL string.
4868    */
4869   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4870           FileFormatI format, SequenceI assocSeq)
4871   {
4872     // BH 2018 was String file
4873     try
4874     {
4875       if (sourceType == null)
4876       {
4877         sourceType = FormatAdapter.checkProtocol(file);
4878       }
4879       // if the file isn't identified, or not positively identified as some
4880       // other filetype (PFAM is default unidentified alignment file type) then
4881       // try to parse as annotation.
4882       boolean isAnnotation = (format == null
4883               || FileFormat.Pfam.equals(format))
4884                       ? new AnnotationFile().annotateAlignmentView(viewport,
4885                               file, sourceType)
4886                       : false;
4887
4888       if (!isAnnotation)
4889       {
4890         // first see if its a T-COFFEE score file
4891         TCoffeeScoreFile tcf = null;
4892         try
4893         {
4894           tcf = new TCoffeeScoreFile(file, sourceType);
4895           if (tcf.isValid())
4896           {
4897             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4898             {
4899               buildColourMenu();
4900               changeColour(
4901                       new TCoffeeColourScheme(viewport.getAlignment()));
4902               isAnnotation = true;
4903               setStatus(MessageManager.getString(
4904                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4905             }
4906             else
4907             {
4908               // some problem - if no warning its probable that the ID matching
4909               // process didn't work
4910               JvOptionPane.showMessageDialog(Desktop.desktop,
4911                       tcf.getWarningMessage() == null
4912                               ? MessageManager.getString(
4913                                       "label.check_file_matches_sequence_ids_alignment")
4914                               : tcf.getWarningMessage(),
4915                       MessageManager.getString(
4916                               "label.problem_reading_tcoffee_score_file"),
4917                       JvOptionPane.WARNING_MESSAGE);
4918             }
4919           }
4920           else
4921           {
4922             tcf = null;
4923           }
4924         } catch (Exception x)
4925         {
4926           Console.debug(
4927                   "Exception when processing data source as T-COFFEE score file",
4928                   x);
4929           tcf = null;
4930         }
4931         if (tcf == null)
4932         {
4933           // try to see if its a JNet 'concise' style annotation file *before*
4934           // we
4935           // try to parse it as a features file
4936           if (format == null)
4937           {
4938             format = new IdentifyFile().identify(file, sourceType);
4939           }
4940           if (FileFormat.ScoreMatrix == format)
4941           {
4942             ScoreMatrixFile sm = new ScoreMatrixFile(
4943                     new FileParse(file, sourceType));
4944             sm.parse();
4945             // todo: i18n this message
4946             setStatus(MessageManager.formatMessage(
4947                     "label.successfully_loaded_matrix",
4948                     sm.getMatrixName()));
4949           }
4950           else if (FileFormat.Jnet.equals(format))
4951           {
4952             JPredFile predictions = new JPredFile(file, sourceType);
4953             new JnetAnnotationMaker();
4954             JnetAnnotationMaker.add_annotation(predictions,
4955                     viewport.getAlignment(), 0, false);
4956             viewport.getAlignment().setupJPredAlignment();
4957             isAnnotation = true;
4958           }
4959           // else if (IdentifyFile.FeaturesFile.equals(format))
4960           else if (FileFormat.Features.equals(format))
4961           {
4962             if (parseFeaturesFile(file, sourceType))
4963             {
4964               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4965               if (splitFrame != null)
4966               {
4967                 splitFrame.repaint();
4968               }
4969               else
4970               {
4971                 alignPanel.paintAlignment(true, true);
4972               }
4973             }
4974           }
4975           else
4976           {
4977             new FileLoader().LoadFile(viewport, file, sourceType, format);
4978           }
4979         }
4980       }
4981       if (isAnnotation)
4982       {
4983
4984         alignPanel.adjustAnnotationHeight();
4985         viewport.updateSequenceIdColours();
4986         buildSortByAnnotationScoresMenu();
4987         alignPanel.paintAlignment(true, true);
4988       }
4989     } catch (Exception ex)
4990     {
4991       ex.printStackTrace();
4992     } catch (OutOfMemoryError oom)
4993     {
4994       try
4995       {
4996         System.gc();
4997       } catch (Exception x)
4998       {
4999       }
5000       new OOMWarning(
5001               "loading data "
5002                       + (sourceType != null
5003                               ? (sourceType == DataSourceType.PASTE
5004                                       ? "from clipboard."
5005                                       : "using " + sourceType + " from "
5006                                               + file)
5007                               : ".")
5008                       + (format != null
5009                               ? "(parsing as '" + format + "' file)"
5010                               : ""),
5011               oom, Desktop.desktop);
5012     }
5013   }
5014
5015   /**
5016    * Method invoked by the ChangeListener on the tabbed pane, in other words
5017    * when a different tabbed pane is selected by the user or programmatically.
5018    */
5019   @Override
5020   public void tabSelectionChanged(int index)
5021   {
5022     if (index > -1)
5023     {
5024       /*
5025        * update current Overview window title (if there is one)
5026        * to add view name "Original" if necessary
5027        */
5028       alignPanel.setOverviewTitle(this);
5029
5030       /*
5031        * switch panels and set Overview title (if there is one
5032        * because it was opened automatically)
5033        */
5034       alignPanel = alignPanels.get(index);
5035       alignPanel.setOverviewTitle(this);
5036
5037       viewport = alignPanel.av;
5038       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5039       setMenusFromViewport(viewport);
5040       if (featureSettings != null && featureSettings.isOpen()
5041               && featureSettings.fr.getViewport() != viewport)
5042       {
5043         if (viewport.isShowSequenceFeatures())
5044         {
5045           // refresh the featureSettings to reflect UI change
5046           showFeatureSettingsUI();
5047         }
5048         else
5049         {
5050           // close feature settings for this view.
5051           featureSettings.close();
5052         }
5053       }
5054
5055     }
5056
5057     /*
5058      * 'focus' any colour slider that is open to the selected viewport
5059      */
5060     if (viewport.getConservationSelected())
5061     {
5062       SliderPanel.setConservationSlider(alignPanel,
5063               viewport.getResidueShading(), alignPanel.getViewName());
5064     }
5065     else
5066     {
5067       SliderPanel.hideConservationSlider();
5068     }
5069     if (viewport.getAbovePIDThreshold())
5070     {
5071       SliderPanel.setPIDSliderSource(alignPanel,
5072               viewport.getResidueShading(), alignPanel.getViewName());
5073     }
5074     else
5075     {
5076       SliderPanel.hidePIDSlider();
5077     }
5078
5079     /*
5080      * If there is a frame linked to this one in a SplitPane, switch it to the
5081      * same view tab index. No infinite recursion of calls should happen, since
5082      * tabSelectionChanged() should not get invoked on setting the selected
5083      * index to an unchanged value. Guard against setting an invalid index
5084      * before the new view peer tab has been created.
5085      */
5086     final AlignViewportI peer = viewport.getCodingComplement();
5087     if (peer != null)
5088     {
5089       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5090               .getAlignPanel().alignFrame;
5091       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5092       {
5093         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5094       }
5095     }
5096   }
5097
5098   /**
5099    * On right mouse click on view tab, prompt for and set new view name.
5100    */
5101   @Override
5102   public void tabbedPane_mousePressed(MouseEvent e)
5103   {
5104     if (e.isPopupTrigger())
5105     {
5106       String msg = MessageManager.getString("label.enter_view_name");
5107       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5108       String reply = JvOptionPane.showInputDialog(msg, ttl);
5109
5110       if (reply != null)
5111       {
5112         viewport.setViewName(reply);
5113         // TODO warn if reply is in getExistingViewNames()?
5114         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5115       }
5116     }
5117   }
5118
5119   public AlignViewport getCurrentView()
5120   {
5121     return viewport;
5122   }
5123
5124   /**
5125    * Open the dialog for regex description parsing.
5126    */
5127   @Override
5128   protected void extractScores_actionPerformed(ActionEvent e)
5129   {
5130     ParseProperties pp = new jalview.analysis.ParseProperties(
5131             viewport.getAlignment());
5132     // TODO: verify regex and introduce GUI dialog for version 2.5
5133     // if (pp.getScoresFromDescription("col", "score column ",
5134     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5135     // true)>0)
5136     if (pp.getScoresFromDescription("description column",
5137             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5138     {
5139       buildSortByAnnotationScoresMenu();
5140     }
5141   }
5142
5143   /*
5144    * (non-Javadoc)
5145    *
5146    * @see
5147    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5148    * )
5149    */
5150   @Override
5151   protected void showDbRefs_actionPerformed(ActionEvent e)
5152   {
5153     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5154   }
5155
5156   /*
5157    * (non-Javadoc)
5158    *
5159    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5160    * ActionEvent)
5161    */
5162   @Override
5163   protected void showNpFeats_actionPerformed(ActionEvent e)
5164   {
5165     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5166   }
5167
5168   /**
5169    * find the viewport amongst the tabs in this alignment frame and close that
5170    * tab
5171    *
5172    * @param av
5173    */
5174   public boolean closeView(AlignViewportI av)
5175   {
5176     if (viewport == av)
5177     {
5178       this.closeMenuItem_actionPerformed(false);
5179       return true;
5180     }
5181     Component[] comp = tabbedPane.getComponents();
5182     for (int i = 0; comp != null && i < comp.length; i++)
5183     {
5184       if (comp[i] instanceof AlignmentPanel)
5185       {
5186         if (((AlignmentPanel) comp[i]).av == av)
5187         {
5188           // close the view.
5189           closeView((AlignmentPanel) comp[i]);
5190           return true;
5191         }
5192       }
5193     }
5194     return false;
5195   }
5196
5197   protected void build_fetchdbmenu(JMenu webService)
5198   {
5199     // Temporary hack - DBRef Fetcher always top level ws entry.
5200     // TODO We probably want to store a sequence database checklist in
5201     // preferences and have checkboxes.. rather than individual sources selected
5202     // here
5203     final JMenu rfetch = new JMenu(
5204             MessageManager.getString("action.fetch_db_references"));
5205     rfetch.setToolTipText(MessageManager.getString(
5206             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5207     webService.add(rfetch);
5208
5209     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5210             MessageManager.getString("option.trim_retrieved_seqs"));
5211     trimrs.setToolTipText(
5212             MessageManager.getString("label.trim_retrieved_sequences"));
5213     trimrs.setSelected(
5214             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5215     trimrs.addActionListener(new ActionListener()
5216     {
5217       @Override
5218       public void actionPerformed(ActionEvent e)
5219       {
5220         trimrs.setSelected(trimrs.isSelected());
5221         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5222                 Boolean.valueOf(trimrs.isSelected()).toString());
5223       }
5224     });
5225     rfetch.add(trimrs);
5226     JMenuItem fetchr = new JMenuItem(
5227             MessageManager.getString("label.standard_databases"));
5228     fetchr.setToolTipText(
5229             MessageManager.getString("label.fetch_embl_uniprot"));
5230     fetchr.addActionListener(new ActionListener()
5231     {
5232
5233       @Override
5234       public void actionPerformed(ActionEvent e)
5235       {
5236         new Thread(new Runnable()
5237         {
5238           @Override
5239           public void run()
5240           {
5241             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5242                     .getAlignment().isNucleotide();
5243             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5244                     alignPanel.av.getSequenceSelection(),
5245                     alignPanel.alignFrame, null,
5246                     alignPanel.alignFrame.featureSettings, isNucleotide);
5247             dbRefFetcher.addListener(new FetchFinishedListenerI()
5248             {
5249               @Override
5250               public void finished()
5251               {
5252
5253                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5254                         .getFeatureSettingsModels())
5255                 {
5256
5257                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5258                 }
5259                 AlignFrame.this.setMenusForViewport();
5260               }
5261             });
5262             dbRefFetcher.fetchDBRefs(false);
5263           }
5264         }).start();
5265
5266       }
5267
5268     });
5269     rfetch.add(fetchr);
5270     new Thread(new Runnable()
5271     {
5272       @Override
5273       public void run()
5274       {
5275         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5276                 .getSequenceFetcherSingleton();
5277         javax.swing.SwingUtilities.invokeLater(new Runnable()
5278         {
5279           @Override
5280           public void run()
5281           {
5282             String[] dbclasses = sf.getNonAlignmentSources();
5283             List<DbSourceProxy> otherdb;
5284             JMenu dfetch = new JMenu();
5285             JMenu ifetch = new JMenu();
5286             JMenuItem fetchr = null;
5287             int comp = 0, icomp = 0, mcomp = 15;
5288             String mname = null;
5289             int dbi = 0;
5290             for (String dbclass : dbclasses)
5291             {
5292               otherdb = sf.getSourceProxy(dbclass);
5293               // add a single entry for this class, or submenu allowing 'fetch
5294               // all' or pick one
5295               if (otherdb == null || otherdb.size() < 1)
5296               {
5297                 continue;
5298               }
5299               if (mname == null)
5300               {
5301                 mname = "From " + dbclass;
5302               }
5303               if (otherdb.size() == 1)
5304               {
5305                 final DbSourceProxy[] dassource = otherdb
5306                         .toArray(new DbSourceProxy[0]);
5307                 DbSourceProxy src = otherdb.get(0);
5308                 fetchr = new JMenuItem(src.getDbSource());
5309                 fetchr.addActionListener(new ActionListener()
5310                 {
5311
5312                   @Override
5313                   public void actionPerformed(ActionEvent e)
5314                   {
5315                     new Thread(new Runnable()
5316                     {
5317
5318                       @Override
5319                       public void run()
5320                       {
5321                         boolean isNucleotide = alignPanel.alignFrame
5322                                 .getViewport().getAlignment()
5323                                 .isNucleotide();
5324                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5325                                 alignPanel.av.getSequenceSelection(),
5326                                 alignPanel.alignFrame, dassource,
5327                                 alignPanel.alignFrame.featureSettings,
5328                                 isNucleotide);
5329                         dbRefFetcher
5330                                 .addListener(new FetchFinishedListenerI()
5331                                 {
5332                                   @Override
5333                                   public void finished()
5334                                   {
5335                                     FeatureSettingsModelI srcSettings = dassource[0]
5336                                             .getFeatureColourScheme();
5337                                     alignPanel.av.mergeFeaturesStyle(
5338                                             srcSettings);
5339                                     AlignFrame.this.setMenusForViewport();
5340                                   }
5341                                 });
5342                         dbRefFetcher.fetchDBRefs(false);
5343                       }
5344                     }).start();
5345                   }
5346
5347                 });
5348                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5349                         MessageManager.formatMessage(
5350                                 "label.fetch_retrieve_from", new Object[]
5351                                 { src.getDbName() })));
5352                 dfetch.add(fetchr);
5353                 comp++;
5354               }
5355               else
5356               {
5357                 final DbSourceProxy[] dassource = otherdb
5358                         .toArray(new DbSourceProxy[0]);
5359                 // fetch all entry
5360                 DbSourceProxy src = otherdb.get(0);
5361                 fetchr = new JMenuItem(MessageManager
5362                         .formatMessage("label.fetch_all_param", new Object[]
5363                         { src.getDbSource() }));
5364                 fetchr.addActionListener(new ActionListener()
5365                 {
5366                   @Override
5367                   public void actionPerformed(ActionEvent e)
5368                   {
5369                     new Thread(new Runnable()
5370                     {
5371
5372                       @Override
5373                       public void run()
5374                       {
5375                         boolean isNucleotide = alignPanel.alignFrame
5376                                 .getViewport().getAlignment()
5377                                 .isNucleotide();
5378                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5379                                 alignPanel.av.getSequenceSelection(),
5380                                 alignPanel.alignFrame, dassource,
5381                                 alignPanel.alignFrame.featureSettings,
5382                                 isNucleotide);
5383                         dbRefFetcher
5384                                 .addListener(new FetchFinishedListenerI()
5385                                 {
5386                                   @Override
5387                                   public void finished()
5388                                   {
5389                                     AlignFrame.this.setMenusForViewport();
5390                                   }
5391                                 });
5392                         dbRefFetcher.fetchDBRefs(false);
5393                       }
5394                     }).start();
5395                   }
5396                 });
5397
5398                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5399                         MessageManager.formatMessage(
5400                                 "label.fetch_retrieve_from_all_sources",
5401                                 new Object[]
5402                                 { Integer.valueOf(otherdb.size())
5403                                         .toString(),
5404                                     src.getDbSource(), src.getDbName() })));
5405                 dfetch.add(fetchr);
5406                 comp++;
5407                 // and then build the rest of the individual menus
5408                 ifetch = new JMenu(MessageManager.formatMessage(
5409                         "label.source_from_db_source", new Object[]
5410                         { src.getDbSource() }));
5411                 icomp = 0;
5412                 String imname = null;
5413                 int i = 0;
5414                 for (DbSourceProxy sproxy : otherdb)
5415                 {
5416                   String dbname = sproxy.getDbName();
5417                   String sname = dbname.length() > 5
5418                           ? dbname.substring(0, 5) + "..."
5419                           : dbname;
5420                   String msname = dbname.length() > 10
5421                           ? dbname.substring(0, 10) + "..."
5422                           : dbname;
5423                   if (imname == null)
5424                   {
5425                     imname = MessageManager
5426                             .formatMessage("label.from_msname", new Object[]
5427                             { sname });
5428                   }
5429                   fetchr = new JMenuItem(msname);
5430                   final DbSourceProxy[] dassrc = { sproxy };
5431                   fetchr.addActionListener(new ActionListener()
5432                   {
5433
5434                     @Override
5435                     public void actionPerformed(ActionEvent e)
5436                     {
5437                       new Thread(new Runnable()
5438                       {
5439
5440                         @Override
5441                         public void run()
5442                         {
5443                           boolean isNucleotide = alignPanel.alignFrame
5444                                   .getViewport().getAlignment()
5445                                   .isNucleotide();
5446                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5447                                   alignPanel.av.getSequenceSelection(),
5448                                   alignPanel.alignFrame, dassrc,
5449                                   alignPanel.alignFrame.featureSettings,
5450                                   isNucleotide);
5451                           dbRefFetcher
5452                                   .addListener(new FetchFinishedListenerI()
5453                                   {
5454                                     @Override
5455                                     public void finished()
5456                                     {
5457                                       AlignFrame.this.setMenusForViewport();
5458                                     }
5459                                   });
5460                           dbRefFetcher.fetchDBRefs(false);
5461                         }
5462                       }).start();
5463                     }
5464
5465                   });
5466                   fetchr.setToolTipText(
5467                           "<html>" + MessageManager.formatMessage(
5468                                   "label.fetch_retrieve_from", new Object[]
5469                                   { dbname }));
5470                   ifetch.add(fetchr);
5471                   ++i;
5472                   if (++icomp >= mcomp || i == (otherdb.size()))
5473                   {
5474                     ifetch.setText(MessageManager.formatMessage(
5475                             "label.source_to_target", imname, sname));
5476                     dfetch.add(ifetch);
5477                     ifetch = new JMenu();
5478                     imname = null;
5479                     icomp = 0;
5480                     comp++;
5481                   }
5482                 }
5483               }
5484               ++dbi;
5485               if (comp >= mcomp || dbi >= (dbclasses.length))
5486               {
5487                 dfetch.setText(MessageManager.formatMessage(
5488                         "label.source_to_target", mname, dbclass));
5489                 rfetch.add(dfetch);
5490                 dfetch = new JMenu();
5491                 mname = null;
5492                 comp = 0;
5493               }
5494             }
5495           }
5496         });
5497       }
5498     }).start();
5499
5500   }
5501
5502   /**
5503    * Left justify the whole alignment.
5504    */
5505   @Override
5506   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5507   {
5508     AlignmentI al = viewport.getAlignment();
5509     al.justify(false);
5510     viewport.firePropertyChange("alignment", null, al);
5511   }
5512
5513   /**
5514    * Right justify the whole alignment.
5515    */
5516   @Override
5517   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5518   {
5519     AlignmentI al = viewport.getAlignment();
5520     al.justify(true);
5521     viewport.firePropertyChange("alignment", null, al);
5522   }
5523
5524   @Override
5525   public void setShowSeqFeatures(boolean b)
5526   {
5527     showSeqFeatures.setSelected(b);
5528     viewport.setShowSequenceFeatures(b);
5529   }
5530
5531   /*
5532    * (non-Javadoc)
5533    *
5534    * @see
5535    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5536    * awt.event.ActionEvent)
5537    */
5538   @Override
5539   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5540   {
5541     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5542     alignPanel.paintAlignment(false, false);
5543   }
5544
5545   /*
5546    * (non-Javadoc)
5547    *
5548    * @see
5549    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5550    * .ActionEvent)
5551    */
5552   @Override
5553   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5554   {
5555     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5556     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5557
5558   }
5559
5560   /*
5561    * (non-Javadoc)
5562    *
5563    * @see
5564    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5565    * .event.ActionEvent)
5566    */
5567   @Override
5568   protected void showGroupConservation_actionPerformed(ActionEvent e)
5569   {
5570     viewport.setShowGroupConservation(showGroupConservation.getState());
5571     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5572   }
5573
5574   /*
5575    * (non-Javadoc)
5576    *
5577    * @see
5578    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5579    * .event.ActionEvent)
5580    */
5581   @Override
5582   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5583   {
5584     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5585     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5586   }
5587
5588   /*
5589    * (non-Javadoc)
5590    *
5591    * @see
5592    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5593    * .event.ActionEvent)
5594    */
5595   @Override
5596   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5597   {
5598     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5599     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5600   }
5601
5602   @Override
5603   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5604   {
5605     showSequenceLogo.setState(true);
5606     viewport.setShowSequenceLogo(true);
5607     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5608     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5609   }
5610
5611   @Override
5612   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5613   {
5614     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5615   }
5616
5617   /*
5618    * (non-Javadoc)
5619    *
5620    * @see
5621    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5622    * .event.ActionEvent)
5623    */
5624   @Override
5625   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5626   {
5627     if (avc.makeGroupsFromSelection())
5628     {
5629       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5630       alignPanel.updateAnnotation();
5631       alignPanel.paintAlignment(true,
5632               viewport.needToUpdateStructureViews());
5633     }
5634   }
5635
5636   public void clearAlignmentSeqRep()
5637   {
5638     // TODO refactor alignmentseqrep to controller
5639     if (viewport.getAlignment().hasSeqrep())
5640     {
5641       viewport.getAlignment().setSeqrep(null);
5642       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5643       alignPanel.updateAnnotation();
5644       alignPanel.paintAlignment(true, true);
5645     }
5646   }
5647
5648   @Override
5649   protected void createGroup_actionPerformed(ActionEvent e)
5650   {
5651     if (avc.createGroup())
5652     {
5653       if (applyAutoAnnotationSettings.isSelected())
5654       {
5655         alignPanel.updateAnnotation(true, false);
5656       }
5657       alignPanel.alignmentChanged();
5658     }
5659   }
5660
5661   @Override
5662   protected void unGroup_actionPerformed(ActionEvent e)
5663   {
5664     if (avc.unGroup())
5665     {
5666       alignPanel.alignmentChanged();
5667     }
5668   }
5669
5670   /**
5671    * make the given alignmentPanel the currently selected tab
5672    *
5673    * @param alignmentPanel
5674    */
5675   public void setDisplayedView(AlignmentPanel alignmentPanel)
5676   {
5677     if (!viewport.getSequenceSetId()
5678             .equals(alignmentPanel.av.getSequenceSetId()))
5679     {
5680       throw new Error(MessageManager.getString(
5681               "error.implementation_error_cannot_show_view_alignment_frame"));
5682     }
5683     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5684             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5685     {
5686       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5687     }
5688   }
5689
5690   /**
5691    * Action on selection of menu options to Show or Hide annotations.
5692    *
5693    * @param visible
5694    * @param forSequences
5695    *          update sequence-related annotations
5696    * @param forAlignment
5697    *          update non-sequence-related annotations
5698    */
5699   @Override
5700   protected void setAnnotationsVisibility(boolean visible,
5701           boolean forSequences, boolean forAlignment)
5702   {
5703     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5704             .getAlignmentAnnotation();
5705     if (anns == null)
5706     {
5707       return;
5708     }
5709     for (AlignmentAnnotation aa : anns)
5710     {
5711       /*
5712        * don't display non-positional annotations on an alignment
5713        */
5714       if (aa.annotations == null)
5715       {
5716         continue;
5717       }
5718       boolean apply = (aa.sequenceRef == null && forAlignment)
5719               || (aa.sequenceRef != null && forSequences);
5720       if (apply)
5721       {
5722         aa.visible = visible;
5723       }
5724     }
5725     alignPanel.validateAnnotationDimensions(true);
5726     alignPanel.alignmentChanged();
5727   }
5728
5729   /**
5730    * Store selected annotation sort order for the view and repaint.
5731    */
5732   @Override
5733   protected void sortAnnotations_actionPerformed()
5734   {
5735     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5736     this.alignPanel.av
5737             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5738     alignPanel.paintAlignment(false, false);
5739   }
5740
5741   /**
5742    *
5743    * @return alignment panels in this alignment frame
5744    */
5745   public List<? extends AlignmentViewPanel> getAlignPanels()
5746   {
5747     // alignPanels is never null
5748     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5749     return alignPanels;
5750   }
5751
5752   /**
5753    * Open a new alignment window, with the cDNA associated with this (protein)
5754    * alignment, aligned as is the protein.
5755    */
5756   protected void viewAsCdna_actionPerformed()
5757   {
5758     // TODO no longer a menu action - refactor as required
5759     final AlignmentI alignment = getViewport().getAlignment();
5760     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5761     if (mappings == null)
5762     {
5763       return;
5764     }
5765     List<SequenceI> cdnaSeqs = new ArrayList<>();
5766     for (SequenceI aaSeq : alignment.getSequences())
5767     {
5768       for (AlignedCodonFrame acf : mappings)
5769       {
5770         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5771         if (dnaSeq != null)
5772         {
5773           /*
5774            * There is a cDNA mapping for this protein sequence - add to new
5775            * alignment. It will share the same dataset sequence as other mapped
5776            * cDNA (no new mappings need to be created).
5777            */
5778           final Sequence newSeq = new Sequence(dnaSeq);
5779           newSeq.setDatasetSequence(dnaSeq);
5780           cdnaSeqs.add(newSeq);
5781         }
5782       }
5783     }
5784     if (cdnaSeqs.size() == 0)
5785     {
5786       // show a warning dialog no mapped cDNA
5787       return;
5788     }
5789     AlignmentI cdna = new Alignment(
5790             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5791     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5792             AlignFrame.DEFAULT_HEIGHT);
5793     cdna.alignAs(alignment);
5794     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5795             + this.title;
5796     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5797             AlignFrame.DEFAULT_HEIGHT);
5798   }
5799
5800   /**
5801    * Set visibility of dna/protein complement view (available when shown in a
5802    * split frame).
5803    *
5804    * @param show
5805    */
5806   @Override
5807   protected void showComplement_actionPerformed(boolean show)
5808   {
5809     SplitContainerI sf = getSplitViewContainer();
5810     if (sf != null)
5811     {
5812       sf.setComplementVisible(this, show);
5813     }
5814   }
5815
5816   /**
5817    * Generate the reverse (optionally complemented) of the selected sequences,
5818    * and add them to the alignment
5819    */
5820   @Override
5821   protected void showReverse_actionPerformed(boolean complement)
5822   {
5823     AlignmentI al = null;
5824     try
5825     {
5826       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5827       al = dna.reverseCdna(complement);
5828       viewport.addAlignment(al, "");
5829       addHistoryItem(new EditCommand(
5830               MessageManager.getString("label.add_sequences"), Action.PASTE,
5831               al.getSequencesArray(), 0, al.getWidth(),
5832               viewport.getAlignment()));
5833     } catch (Exception ex)
5834     {
5835       System.err.println(ex.getMessage());
5836       return;
5837     }
5838   }
5839
5840   /**
5841    * Try to run a script in the Groovy console, having first ensured that this
5842    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5843    * be targeted at this alignment.
5844    */
5845   @Override
5846   protected void runGroovy_actionPerformed()
5847   {
5848     Jalview.setCurrentAlignFrame(this);
5849     groovy.ui.Console console = Desktop.getGroovyConsole();
5850     if (console != null)
5851     {
5852       try
5853       {
5854         console.runScript();
5855       } catch (Exception ex)
5856       {
5857         System.err.println((ex.toString()));
5858         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5859                 MessageManager.getString("label.couldnt_run_groovy_script"),
5860                 MessageManager.getString("label.groovy_support_failed"),
5861                 JvOptionPane.ERROR_MESSAGE);
5862       }
5863     }
5864     else
5865     {
5866       System.err.println("Can't run Groovy script as console not found");
5867     }
5868   }
5869
5870   /**
5871    * Hides columns containing (or not containing) a specified feature, provided
5872    * that would not leave all columns hidden
5873    *
5874    * @param featureType
5875    * @param columnsContaining
5876    * @return
5877    */
5878   public boolean hideFeatureColumns(String featureType,
5879           boolean columnsContaining)
5880   {
5881     boolean notForHiding = avc.markColumnsContainingFeatures(
5882             columnsContaining, false, false, featureType);
5883     if (notForHiding)
5884     {
5885       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5886               false, featureType))
5887       {
5888         getViewport().hideSelectedColumns();
5889         return true;
5890       }
5891     }
5892     return false;
5893   }
5894
5895   @Override
5896   protected void selectHighlightedColumns_actionPerformed(
5897           ActionEvent actionEvent)
5898   {
5899     // include key modifier check in case user selects from menu
5900     avc.markHighlightedColumns(
5901             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5902             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5903                     | ActionEvent.CTRL_MASK)) != 0);
5904   }
5905
5906   @Override
5907   protected void copyHighlightedColumns_actionPerformed(
5908           ActionEvent actionEvent)
5909   {
5910     avc.copyHighlightedRegionsToClipboard();
5911   }
5912
5913   /**
5914    * Rebuilds the Colour menu, including any user-defined colours which have
5915    * been loaded either on startup or during the session
5916    */
5917   public void buildColourMenu()
5918   {
5919     colourMenu.removeAll();
5920
5921     colourMenu.add(applyToAllGroups);
5922     colourMenu.add(textColour);
5923     colourMenu.addSeparator();
5924
5925     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5926             viewport.getAlignment(), false);
5927
5928     colourMenu.add(annotationColour);
5929     bg.add(annotationColour);
5930     colourMenu.addSeparator();
5931     colourMenu.add(conservationMenuItem);
5932     colourMenu.add(modifyConservation);
5933     colourMenu.add(abovePIDThreshold);
5934     colourMenu.add(modifyPID);
5935
5936     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5937     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5938   }
5939
5940   /**
5941    * Open a dialog (if not already open) that allows the user to select and
5942    * calculate PCA or Tree analysis
5943    */
5944   protected void openTreePcaDialog()
5945   {
5946     if (alignPanel.getCalculationDialog() == null)
5947     {
5948       new CalculationChooser(AlignFrame.this);
5949     }
5950   }
5951
5952   @Override
5953   protected void loadVcf_actionPerformed()
5954   {
5955     JalviewFileChooser chooser = new JalviewFileChooser(
5956             Cache.getProperty("LAST_DIRECTORY"));
5957     chooser.setFileView(new JalviewFileView());
5958     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5959     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5960     final AlignFrame us = this;
5961     chooser.setResponseHandler(0, () -> {
5962       String choice = chooser.getSelectedFile().getPath();
5963       Cache.setProperty("LAST_DIRECTORY", choice);
5964       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5965       new VCFLoader(choice).loadVCF(seqs, us);
5966       return null;
5967     });
5968     chooser.showOpenDialog(null);
5969
5970   }
5971
5972   private Rectangle lastFeatureSettingsBounds = null;
5973
5974   @Override
5975   public void setFeatureSettingsGeometry(Rectangle bounds)
5976   {
5977     lastFeatureSettingsBounds = bounds;
5978   }
5979
5980   @Override
5981   public Rectangle getFeatureSettingsGeometry()
5982   {
5983     return lastFeatureSettingsBounds;
5984   }
5985
5986 }
5987
5988 class PrintThread extends Thread
5989 {
5990   AlignmentPanel ap;
5991
5992   public PrintThread(AlignmentPanel ap)
5993   {
5994     this.ap = ap;
5995   }
5996
5997   static PageFormat pf;
5998
5999   @Override
6000   public void run()
6001   {
6002     PrinterJob printJob = PrinterJob.getPrinterJob();
6003
6004     if (pf != null)
6005     {
6006       printJob.setPrintable(ap, pf);
6007     }
6008     else
6009     {
6010       printJob.setPrintable(ap);
6011     }
6012
6013     if (printJob.printDialog())
6014     {
6015       try
6016       {
6017         printJob.print();
6018       } catch (Exception PrintException)
6019       {
6020         PrintException.printStackTrace();
6021       }
6022     }
6023   }
6024 }