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
  63 import javax.swing.ButtonGroup;
  64 import javax.swing.JCheckBoxMenuItem;
  65 import javax.swing.JComponent;
  66 import javax.swing.JEditorPane;
  67 import javax.swing.JInternalFrame;
  68 import javax.swing.JLabel;
  69 import javax.swing.JLayeredPane;
  70 import javax.swing.JMenu;
  71 import javax.swing.JMenuItem;
  72 import javax.swing.JPanel;
  73 import javax.swing.JScrollPane;
  74 import javax.swing.SwingUtilities;
  75
  76 import ext.vamsas.ServiceHandle;
  77 import jalview.analysis.AlignmentSorter;
  78 import jalview.analysis.AlignmentUtils;
  79 import jalview.analysis.CrossRef;
  80 import jalview.analysis.Dna;
  81 import jalview.analysis.GeneticCodeI;
  82 import jalview.analysis.ParseProperties;
  83 import jalview.analysis.SequenceIdMatcher;
  84 import jalview.api.AlignExportSettingsI;
  85 import jalview.api.AlignViewControllerGuiI;
  86 import jalview.api.AlignViewControllerI;
  87 import jalview.api.AlignViewportI;
  88 import jalview.api.AlignmentViewPanel;
  89 import jalview.api.FeatureSettingsControllerI;
  90 import jalview.api.FeatureSettingsModelI;
  91 import jalview.api.SplitContainerI;
  92 import jalview.api.ViewStyleI;
  93 import jalview.api.analysis.SimilarityParamsI;
  94 import jalview.bin.Cache;
  95 import jalview.bin.Console;
  96 import jalview.bin.Jalview;
  97 import jalview.commands.CommandI;
  98 import jalview.commands.EditCommand;
  99 import jalview.commands.EditCommand.Action;
 100 import jalview.commands.OrderCommand;
 101 import jalview.commands.RemoveGapColCommand;
 102 import jalview.commands.RemoveGapsCommand;
 103 import jalview.commands.SlideSequencesCommand;
 104 import jalview.commands.TrimRegionCommand;
 105 import jalview.datamodel.AlignExportSettingsAdapter;
 106 import jalview.datamodel.AlignedCodonFrame;
 107 import jalview.datamodel.Alignment;
 108 import jalview.datamodel.AlignmentAnnotation;
 109 import jalview.datamodel.AlignmentExportData;
 110 import jalview.datamodel.AlignmentI;
 111 import jalview.datamodel.AlignmentOrder;
 112 import jalview.datamodel.AlignmentView;
 113 import jalview.datamodel.ColumnSelection;
 114 import jalview.datamodel.ContactMatrixI;
 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.exceptions.ImageOutputException;
 144 import jalview.io.vcf.VCFLoader;
 145 import jalview.jbgui.GAlignFrame;
 146 import jalview.project.Jalview2XML;
 147 import jalview.schemes.ColourSchemeI;
 148 import jalview.schemes.ColourSchemes;
 149 import jalview.schemes.ResidueColourScheme;
 150 import jalview.schemes.TCoffeeColourScheme;
 151 import jalview.util.HttpUtils;
 152 import jalview.util.ImageMaker.TYPE;
 153 import jalview.util.MessageManager;
 154 import jalview.util.Platform;
 155 import jalview.util.imagemaker.BitmapImageSizing;
 156 import jalview.viewmodel.AlignmentViewport;
 157 import jalview.viewmodel.ViewportRanges;
 158 import jalview.ws.DBRefFetcher;
 159 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 160 import jalview.ws.jws1.Discoverer;
 161 import jalview.ws.jws2.Jws2Discoverer;
 162 import jalview.ws.jws2.jabaws2.Jws2Instance;
 163 import jalview.ws.seqfetcher.DbSourceProxy;
 164
 165 /**
 166  * DOCUMENT ME!
 167  *
 168  * @author $author$
 169  * @version $Revision$
 170  */
 171 @SuppressWarnings("serial")
 172 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 173         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 174 {
 175
 176   public static final int DEFAULT_WIDTH = 700;
 177
 178   public static final int DEFAULT_HEIGHT = 500;
 179
 180   /*
 181    * The currently displayed panel (selected tabbed view if more than one)
 182    */
 183   public AlignmentPanel alignPanel;
 184
 185   AlignViewport viewport;
 186
 187   public AlignViewControllerI avc;
 188
 189   List<AlignmentPanel> alignPanels = new ArrayList<>();
 190
 191   /**
 192    * Last format used to load or save alignments in this window
 193    */
 194   FileFormatI currentFileFormat = null;
 195
 196   /**
 197    * Current filename for this alignment
 198    */
 199   String fileName = null;
 200
 201   File fileObject;
 202
 203   /**
 204    * Creates a new AlignFrame object with specific width and height.
 205    *
 206    * @param al
 207    * @param width
 208    * @param height
 209    */
 210   public AlignFrame(AlignmentI al, int width, int height)
 211   {
 212     this(al, null, width, height);
 213   }
 214
 215   /**
 216    * Creates a new AlignFrame object with specific width, height and
 217    * sequenceSetId
 218    *
 219    * @param al
 220    * @param width
 221    * @param height
 222    * @param sequenceSetId
 223    */
 224   public AlignFrame(AlignmentI al, int width, int height,
 225           String sequenceSetId)
 226   {
 227     this(al, null, width, height, sequenceSetId);
 228   }
 229
 230   /**
 231    * Creates a new AlignFrame object with specific width, height and
 232    * sequenceSetId
 233    *
 234    * @param al
 235    * @param width
 236    * @param height
 237    * @param sequenceSetId
 238    * @param viewId
 239    */
 240   public AlignFrame(AlignmentI al, int width, int height,
 241           String sequenceSetId, String viewId)
 242   {
 243     this(al, null, width, height, sequenceSetId, viewId);
 244   }
 245
 246   /**
 247    * new alignment window with hidden columns
 248    *
 249    * @param al
 250    *          AlignmentI
 251    * @param hiddenColumns
 252    *          ColumnSelection or null
 253    * @param width
 254    *          Width of alignment frame
 255    * @param height
 256    *          height of frame.
 257    */
 258   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 259           int height)
 260   {
 261     this(al, hiddenColumns, width, height, null);
 262   }
 263
 264   /**
 265    * Create alignment frame for al with hiddenColumns, a specific width and
 266    * height, and specific sequenceId
 267    *
 268    * @param al
 269    * @param hiddenColumns
 270    * @param width
 271    * @param height
 272    * @param sequenceSetId
 273    *          (may be null)
 274    */
 275   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 276           int height, String sequenceSetId)
 277   {
 278     this(al, hiddenColumns, width, height, sequenceSetId, null);
 279   }
 280
 281   /**
 282    * Create alignment frame for al with hiddenColumns, a specific width and
 283    * height, and specific sequenceId
 284    *
 285    * @param al
 286    * @param hiddenColumns
 287    * @param width
 288    * @param height
 289    * @param sequenceSetId
 290    *          (may be null)
 291    * @param viewId
 292    *          (may be null)
 293    */
 294   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 295           int height, String sequenceSetId, String viewId)
 296   {
 297     setSize(width, height);
 298
 299     if (al.getDataset() == null)
 300     {
 301       al.setDataset(null);
 302     }
 303
 304     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 305
 306     alignPanel = new AlignmentPanel(this, viewport);
 307
 308     addAlignmentPanel(alignPanel, true);
 309     init();
 310   }
 311
 312   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 313           HiddenColumns hiddenColumns, int width, int height)
 314   {
 315     setSize(width, height);
 316
 317     if (al.getDataset() == null)
 318     {
 319       al.setDataset(null);
 320     }
 321
 322     viewport = new AlignViewport(al, hiddenColumns);
 323
 324     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 325     {
 326       viewport.hideSequence(hiddenSeqs);
 327     }
 328     alignPanel = new AlignmentPanel(this, viewport);
 329     addAlignmentPanel(alignPanel, true);
 330     init();
 331   }
 332
 333   /**
 334    * Make a new AlignFrame from existing alignmentPanels
 335    *
 336    * @param ap
 337    *          AlignmentPanel
 338    * @param av
 339    *          AlignViewport
 340    */
 341   public AlignFrame(AlignmentPanel ap)
 342   {
 343     viewport = ap.av;
 344     alignPanel = ap;
 345     addAlignmentPanel(ap, false);
 346     init();
 347   }
 348
 349   /**
 350    * initalise the alignframe from the underlying viewport data and the
 351    * configurations
 352    */
 353   void init()
 354   {
 355     setFrameIcon(null);
 356
 357     // setBackground(Color.white); // BH 2019
 358
 359     if (!Jalview.isHeadlessMode())
 360     {
 361       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 362     }
 363
 364     avc = new jalview.controller.AlignViewController(this, viewport,
 365             alignPanel);
 366     if (viewport.getAlignmentConservationAnnotation() == null)
 367     {
 368       // BLOSUM62Colour.setEnabled(false);
 369       conservationMenuItem.setEnabled(false);
 370       modifyConservation.setEnabled(false);
 371       // PIDColour.setEnabled(false);
 372       // abovePIDThreshold.setEnabled(false);
 373       // modifyPID.setEnabled(false);
 374     }
 375
 376     String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 377
 378     if (sortby.equals("Id"))
 379     {
 380       sortIDMenuItem_actionPerformed(null);
 381     }
 382     else if (sortby.equals("Pairwise Identity"))
 383     {
 384       sortPairwiseMenuItem_actionPerformed(null);
 385     }
 386
 387     this.alignPanel.av
 388             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 389
 390     setMenusFromViewport(viewport);
 391     buildSortByAnnotationScoresMenu();
 392     calculateTree.addActionListener(new ActionListener()
 393     {
 394
 395       @Override
 396       public void actionPerformed(ActionEvent e)
 397       {
 398         openTreePcaDialog();
 399       }
 400     });
 401     buildColourMenu();
 402
 403     if (Desktop.desktop != null)
 404     {
 405       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 406       if (!Platform.isJS())
 407       {
 408         addServiceListeners();
 409       }
 410       setGUINucleotide();
 411     }
 412
 413     if (viewport.getWrapAlignment())
 414     {
 415       wrapMenuItem_actionPerformed(null);
 416     }
 417
 418     if (Cache.getDefault("SHOW_OVERVIEW", false))
 419     {
 420       this.overviewMenuItem_actionPerformed(null);
 421     }
 422
 423     addKeyListener();
 424
 425     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 426     final List<AlignmentPanel> origview = new ArrayList<>();
 427     final String menuLabel = MessageManager
 428             .getString("label.copy_format_from");
 429     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 430             new ViewSetProvider()
 431             {
 432
 433               @Override
 434               public AlignmentPanel[] getAllAlignmentPanels()
 435               {
 436                 origview.clear();
 437                 origview.add(alignPanel);
 438                 // make an array of all alignment panels except for this one
 439                 List<AlignmentPanel> aps = new ArrayList<>(
 440                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 441                 aps.remove(AlignFrame.this.alignPanel);
 442                 return aps.toArray(new AlignmentPanel[aps.size()]);
 443               }
 444             }, selviews, new ItemListener()
 445             {
 446
 447               @Override
 448               public void itemStateChanged(ItemEvent e)
 449               {
 450                 if (origview.size() > 0)
 451                 {
 452                   final AlignmentPanel ap = origview.get(0);
 453
 454                   /*
 455                    * Copy the ViewStyle of the selected panel to 'this one'.
 456                    * Don't change value of 'scaleProteinAsCdna' unless copying
 457                    * from a SplitFrame.
 458                    */
 459                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 460                           .getViewStyle();
 461                   boolean fromSplitFrame = selviews.get(0)
 462                           .getAlignViewport().getCodingComplement() != null;
 463                   if (!fromSplitFrame)
 464                   {
 465                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 466                             .getViewStyle().isScaleProteinAsCdna());
 467                   }
 468                   ap.getAlignViewport().setViewStyle(vs);
 469
 470                   /*
 471                    * Also rescale ViewStyle of SplitFrame complement if there is
 472                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 473                    * the whole ViewStyle (allow cDNA protein to have different
 474                    * fonts)
 475                    */
 476                   AlignViewportI complement = ap.getAlignViewport()
 477                           .getCodingComplement();
 478                   if (complement != null && vs.isScaleProteinAsCdna())
 479                   {
 480                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 481                     ((SplitFrame) af.getSplitViewContainer())
 482                             .adjustLayout();
 483                     af.setMenusForViewport();
 484                   }
 485
 486                   ap.updateLayout();
 487                   ap.setSelected(true);
 488                   ap.alignFrame.setMenusForViewport();
 489
 490                 }
 491               }
 492             });
 493     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
 494             .indexOf("devel") > -1
 495             || Cache.getDefault("VERSION", "DEVELOPMENT")
 496                     .toLowerCase(Locale.ROOT).indexOf("test") > -1)
 497     {
 498       formatMenu.add(vsel);
 499     }
 500     addFocusListener(new FocusAdapter()
 501     {
 502       @Override
 503       public void focusGained(FocusEvent e)
 504       {
 505         Jalview.setCurrentAlignFrame(AlignFrame.this);
 506       }
 507     });
 508
 509   }
 510
 511   /**
 512    * Change the filename and format for the alignment, and enable the 'reload'
 513    * button functionality.
 514    *
 515    * @param file
 516    *          valid filename
 517    * @param format
 518    *          format of file
 519    */
 520   public void setFileName(String file, FileFormatI format)
 521   {
 522     fileName = file;
 523     setFileFormat(format);
 524     reload.setEnabled(true);
 525   }
 526
 527   /**
 528    * JavaScript will have this, maybe others. More dependable than a file name
 529    * and maintains a reference to the actual bytes loaded.
 530    *
 531    * @param file
 532    */
 533   public void setFileObject(File file)
 534   {
 535     this.fileObject = file;
 536   }
 537
 538   /**
 539    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 540    * events
 541    */
 542   void addKeyListener()
 543   {
 544     addKeyListener(new KeyAdapter()
 545     {
 546       @Override
 547       public void keyPressed(KeyEvent evt)
 548       {
 549         if (viewport.cursorMode
 550                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 551                         && evt.getKeyCode() <= KeyEvent.VK_9)
 552                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 553                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 554                 && Character.isDigit(evt.getKeyChar()))
 555         {
 556           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 557         }
 558
 559         switch (evt.getKeyCode())
 560         {
 561
 562         case 27: // escape key
 563           deselectAllSequenceMenuItem_actionPerformed(null);
 564
 565           break;
 566
 567         case KeyEvent.VK_DOWN:
 568           if (evt.isAltDown() || !viewport.cursorMode)
 569           {
 570             moveSelectedSequences(false);
 571           }
 572           if (viewport.cursorMode)
 573           {
 574             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 575           }
 576           break;
 577
 578         case KeyEvent.VK_UP:
 579           if (evt.isAltDown() || !viewport.cursorMode)
 580           {
 581             moveSelectedSequences(true);
 582           }
 583           if (viewport.cursorMode)
 584           {
 585             alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
 586           }
 587
 588           break;
 589
 590         case KeyEvent.VK_LEFT:
 591           if (evt.isAltDown() || !viewport.cursorMode)
 592           {
 593             slideSequences(false,
 594                     alignPanel.getSeqPanel().getKeyboardNo1());
 595           }
 596           else
 597           {
 598             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 599           }
 600
 601           break;
 602
 603         case KeyEvent.VK_RIGHT:
 604           if (evt.isAltDown() || !viewport.cursorMode)
 605           {
 606             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 607           }
 608           else
 609           {
 610             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 611           }
 612           break;
 613
 614         case KeyEvent.VK_SPACE:
 615           if (viewport.cursorMode)
 616           {
 617             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 618                     || evt.isShiftDown() || evt.isAltDown());
 619           }
 620           break;
 621
 622         // case KeyEvent.VK_A:
 623         // if (viewport.cursorMode)
 624         // {
 625         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 626         // //System.out.println("A");
 627         // }
 628         // break;
 629         /*
 630          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 631          * System.out.println("closing bracket"); } break;
 632          */
 633         case KeyEvent.VK_DELETE:
 634         case KeyEvent.VK_BACK_SPACE:
 635           if (!viewport.cursorMode)
 636           {
 637             cut_actionPerformed();
 638           }
 639           else
 640           {
 641             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 642                     || evt.isShiftDown() || evt.isAltDown());
 643           }
 644
 645           break;
 646
 647         case KeyEvent.VK_S:
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().setCursorRow();
 651           }
 652           break;
 653         case KeyEvent.VK_C:
 654           if (viewport.cursorMode && !evt.isControlDown())
 655           {
 656             alignPanel.getSeqPanel().setCursorColumn();
 657           }
 658           break;
 659         case KeyEvent.VK_P:
 660           if (viewport.cursorMode)
 661           {
 662             alignPanel.getSeqPanel().setCursorPosition();
 663           }
 664           break;
 665
 666         case KeyEvent.VK_ENTER:
 667         case KeyEvent.VK_COMMA:
 668           if (viewport.cursorMode)
 669           {
 670             alignPanel.getSeqPanel().setCursorRowAndColumn();
 671           }
 672           break;
 673
 674         case KeyEvent.VK_Q:
 675           if (viewport.cursorMode)
 676           {
 677             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 678           }
 679           break;
 680         case KeyEvent.VK_M:
 681           if (viewport.cursorMode)
 682           {
 683             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 684           }
 685           break;
 686
 687         case KeyEvent.VK_F2:
 688           viewport.cursorMode = !viewport.cursorMode;
 689           setStatus(MessageManager
 690                   .formatMessage("label.keyboard_editing_mode", new String[]
 691                   { (viewport.cursorMode ? "on" : "off") }));
 692           if (viewport.cursorMode)
 693           {
 694             ViewportRanges ranges = viewport.getRanges();
 695             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 696                     .getStartRes();
 697             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 698                     .getStartSeq();
 699           }
 700           alignPanel.getSeqPanel().seqCanvas.repaint();
 701           break;
 702
 703         case KeyEvent.VK_F1:
 704           try
 705           {
 706             Help.showHelpWindow();
 707           } catch (Exception ex)
 708           {
 709             ex.printStackTrace();
 710           }
 711           break;
 712         case KeyEvent.VK_H:
 713         {
 714           boolean toggleSeqs = !evt.isControlDown();
 715           boolean toggleCols = !evt.isShiftDown();
 716           toggleHiddenRegions(toggleSeqs, toggleCols);
 717           break;
 718         }
 719         case KeyEvent.VK_B:
 720         {
 721           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 722           boolean modifyExisting = true; // always modify, don't clear
 723                                          // evt.isShiftDown();
 724           boolean invertHighlighted = evt.isAltDown();
 725           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 726                   toggleSel);
 727           break;
 728         }
 729         case KeyEvent.VK_PAGE_UP:
 730           viewport.getRanges().pageUp();
 731           break;
 732         case KeyEvent.VK_PAGE_DOWN:
 733           viewport.getRanges().pageDown();
 734           break;
 735         }
 736       }
 737
 738       @Override
 739       public void keyReleased(KeyEvent evt)
 740       {
 741         switch (evt.getKeyCode())
 742         {
 743         case KeyEvent.VK_LEFT:
 744           if (evt.isAltDown() || !viewport.cursorMode)
 745           {
 746             viewport.firePropertyChange("alignment", null,
 747                     viewport.getAlignment().getSequences());
 748           }
 749           break;
 750
 751         case KeyEvent.VK_RIGHT:
 752           if (evt.isAltDown() || !viewport.cursorMode)
 753           {
 754             viewport.firePropertyChange("alignment", null,
 755                     viewport.getAlignment().getSequences());
 756           }
 757           break;
 758         }
 759       }
 760     });
 761   }
 762
 763   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 764   {
 765     ap.alignFrame = this;
 766     avc = new jalview.controller.AlignViewController(this, viewport,
 767             alignPanel);
 768
 769     alignPanels.add(ap);
 770
 771     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 772
 773     int aSize = alignPanels.size();
 774
 775     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 776
 777     if (aSize == 1 && ap.av.getViewName() == null)
 778     {
 779       this.getContentPane().add(ap, BorderLayout.CENTER);
 780     }
 781     else
 782     {
 783       if (aSize == 2)
 784       {
 785         setInitialTabVisible();
 786       }
 787
 788       expandViews.setEnabled(true);
 789       gatherViews.setEnabled(true);
 790       tabbedPane.addTab(ap.av.getViewName(), ap);
 791
 792       ap.setVisible(false);
 793     }
 794
 795     if (newPanel)
 796     {
 797       if (ap.av.isPadGaps())
 798       {
 799         ap.av.getAlignment().padGaps();
 800       }
 801       ap.av.updateConservation(ap);
 802       ap.av.updateConsensus(ap);
 803       ap.av.updateStrucConsensus(ap);
 804     }
 805   }
 806
 807   public void setInitialTabVisible()
 808   {
 809     expandViews.setEnabled(true);
 810     gatherViews.setEnabled(true);
 811     tabbedPane.setVisible(true);
 812     AlignmentPanel first = alignPanels.get(0);
 813     tabbedPane.addTab(first.av.getViewName(), first);
 814     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 815   }
 816
 817   public AlignViewport getViewport()
 818   {
 819     return viewport;
 820   }
 821
 822   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 823   private void addServiceListeners()
 824   {
 825     final java.beans.PropertyChangeListener thisListener;
 826     Desktop.instance.addJalviewPropertyChangeListener("services",
 827             thisListener = new java.beans.PropertyChangeListener()
 828             {
 829               @Override
 830               public void propertyChange(PropertyChangeEvent evt)
 831               {
 832                 // // System.out.println("Discoverer property change.");
 833                 // if (evt.getPropertyName().equals("services"))
 834                 {
 835                   SwingUtilities.invokeLater(new Runnable()
 836                   {
 837
 838                     @Override
 839                     public void run()
 840                     {
 841                       System.err.println(
 842                               "Rebuild WS Menu for service change");
 843                       BuildWebServiceMenu();
 844                     }
 845
 846                   });
 847                 }
 848               }
 849             });
 850     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 851     {
 852       @Override
 853       public void internalFrameClosed(
 854               javax.swing.event.InternalFrameEvent evt)
 855       {
 856         // System.out.println("deregistering discoverer listener");
 857         Desktop.instance.removeJalviewPropertyChangeListener("services",
 858                 thisListener);
 859         closeMenuItem_actionPerformed(true);
 860       }
 861     });
 862     // Finally, build the menu once to get current service state
 863     new Thread(new Runnable()
 864     {
 865       @Override
 866       public void run()
 867       {
 868         BuildWebServiceMenu();
 869       }
 870     }).start();
 871   }
 872
 873   /**
 874    * Configure menu items that vary according to whether the alignment is
 875    * nucleotide or protein
 876    */
 877   public void setGUINucleotide()
 878   {
 879     AlignmentI al = getViewport().getAlignment();
 880     boolean nucleotide = al.isNucleotide();
 881
 882     loadVcf.setVisible(nucleotide);
 883     showTranslation.setVisible(nucleotide);
 884     showReverse.setVisible(nucleotide);
 885     showReverseComplement.setVisible(nucleotide);
 886     conservationMenuItem.setEnabled(!nucleotide);
 887     modifyConservation
 888             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 889     showGroupConservation.setEnabled(!nucleotide);
 890
 891     showComplementMenuItem
 892             .setText(nucleotide ? MessageManager.getString("label.protein")
 893                     : MessageManager.getString("label.nucleotide"));
 894   }
 895
 896   /**
 897    * set up menus for the current viewport. This may be called after any
 898    * operation that affects the data in the current view (selection changed,
 899    * etc) to update the menus to reflect the new state.
 900    */
 901   @Override
 902   public void setMenusForViewport()
 903   {
 904     setMenusFromViewport(viewport);
 905   }
 906
 907   /**
 908    * Need to call this method when tabs are selected for multiple views, or when
 909    * loading from Jalview2XML.java
 910    *
 911    * @param av
 912    *          AlignViewport
 913    */
 914   public void setMenusFromViewport(AlignViewport av)
 915   {
 916     padGapsMenuitem.setSelected(av.isPadGaps());
 917     colourTextMenuItem.setSelected(av.isShowColourText());
 918     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 919     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 920     conservationMenuItem.setSelected(av.getConservationSelected());
 921     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 922     seqLimits.setSelected(av.getShowJVSuffix());
 923     idRightAlign.setSelected(av.isRightAlignIds());
 924     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 925     renderGapsMenuItem.setSelected(av.isRenderGaps());
 926     wrapMenuItem.setSelected(av.getWrapAlignment());
 927     scaleAbove.setVisible(av.getWrapAlignment());
 928     scaleLeft.setVisible(av.getWrapAlignment());
 929     scaleRight.setVisible(av.getWrapAlignment());
 930     annotationPanelMenuItem.setState(av.isShowAnnotation());
 931     /*
 932      * Show/hide annotations only enabled if annotation panel is shown
 933      */
 934     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 935     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 936     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 937     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 938     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 939     viewTextMenuItem.setSelected(av.getShowText());
 940     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 941     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 942     showGroupConservation.setSelected(av.isShowGroupConservation());
 943     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 944     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 945     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 946
 947     ColourMenuHelper.setColourSelected(colourMenu,
 948             av.getGlobalColourScheme());
 949
 950     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 951     hiddenMarkers.setState(av.getShowHiddenMarkers());
 952     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 953     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 954     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 955     autoCalculate.setSelected(av.autoCalculateConsensus);
 956     sortByTree.setSelected(av.sortByTree);
 957     listenToViewSelections.setSelected(av.followSelection);
 958
 959     showProducts.setEnabled(canShowProducts());
 960     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 961
 962     updateEditMenuBar();
 963   }
 964
 965   /**
 966    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 967    *
 968    * @param b
 969    */
 970   public void setGroovyEnabled(boolean b)
 971   {
 972     runGroovy.setEnabled(b);
 973   }
 974
 975   private IProgressIndicator progressBar;
 976
 977   /*
 978    * (non-Javadoc)
 979    *
 980    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 981    */
 982   @Override
 983   public void setProgressBar(String message, long id)
 984   {
 985     if (!Platform.isHeadless() && progressBar != null)
 986       progressBar.setProgressBar(message, id);
 987   }
 988
 989   @Override
 990   public void registerHandler(final long id,
 991           final IProgressIndicatorHandler handler)
 992   {
 993     if (progressBar != null)
 994       progressBar.registerHandler(id, handler);
 995   }
 996
 997   /**
 998    *
 999    * @return true if any progress bars are still active
1000    */
1001   @Override
1002   public boolean operationInProgress()
1003   {
1004     return progressBar == null ? false : progressBar.operationInProgress();
1005   }
1006
1007   /**
1008    * Sets the text of the status bar. Note that setting a null or empty value
1009    * will cause the status bar to be hidden, with possibly undesirable flicker
1010    * of the screen layout.
1011    */
1012   @Override
1013   public void setStatus(String text)
1014   {
1015     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1016   }
1017
1018   /*
1019    * Added so Castor Mapping file can obtain Jalview Version
1020    */
1021   public String getVersion()
1022   {
1023     return Cache.getProperty("VERSION");
1024   }
1025
1026   public FeatureRenderer getFeatureRenderer()
1027   {
1028     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1029   }
1030
1031   @Override
1032   public void fetchSequence_actionPerformed()
1033   {
1034     new SequenceFetcher(this);
1035   }
1036
1037   @Override
1038   public void addFromFile_actionPerformed(ActionEvent e)
1039   {
1040     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1041   }
1042
1043   @Override
1044   public void reload_actionPerformed(ActionEvent e)
1045   {
1046     if (fileName != null)
1047     {
1048       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1049       // originating file's format
1050       // TODO: work out how to recover feature settings for correct view(s) when
1051       // file is reloaded.
1052       if (FileFormat.Jalview.equals(currentFileFormat))
1053       {
1054         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1055         for (int i = 0; i < frames.length; i++)
1056         {
1057           if (frames[i] instanceof AlignFrame && frames[i] != this
1058                   && ((AlignFrame) frames[i]).fileName != null
1059                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1060           {
1061             try
1062             {
1063               frames[i].setSelected(true);
1064               Desktop.instance.closeAssociatedWindows();
1065             } catch (java.beans.PropertyVetoException ex)
1066             {
1067             }
1068           }
1069
1070         }
1071         Desktop.instance.closeAssociatedWindows();
1072
1073         FileLoader loader = new FileLoader();
1074         DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1075                 ? DataSourceType.URL
1076                 : DataSourceType.FILE;
1077         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1078       }
1079       else
1080       {
1081         Rectangle bounds = this.getBounds();
1082
1083         FileLoader loader = new FileLoader();
1084
1085         AlignFrame newframe = null;
1086
1087         if (fileObject == null)
1088         {
1089
1090           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1091                   fileName) ? DataSourceType.URL : DataSourceType.FILE;
1092           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1093                   currentFileFormat);
1094         }
1095         else
1096         {
1097           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1098                   DataSourceType.FILE, currentFileFormat);
1099         }
1100
1101         newframe.setBounds(bounds);
1102         if (featureSettings != null && featureSettings.isShowing())
1103         {
1104           final Rectangle fspos = featureSettings.frame.getBounds();
1105           // TODO: need a 'show feature settings' function that takes bounds -
1106           // need to refactor Desktop.addFrame
1107           newframe.featureSettings_actionPerformed(null);
1108           final FeatureSettings nfs = newframe.featureSettings;
1109           SwingUtilities.invokeLater(new Runnable()
1110           {
1111             @Override
1112             public void run()
1113             {
1114               nfs.frame.setBounds(fspos);
1115             }
1116           });
1117           this.featureSettings.close();
1118           this.featureSettings = null;
1119         }
1120         this.closeMenuItem_actionPerformed(true);
1121       }
1122     }
1123   }
1124
1125   @Override
1126   public void addFromText_actionPerformed(ActionEvent e)
1127   {
1128     Desktop.instance
1129             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1130   }
1131
1132   @Override
1133   public void addFromURL_actionPerformed(ActionEvent e)
1134   {
1135     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1136   }
1137
1138   @Override
1139   public void save_actionPerformed(ActionEvent e)
1140   {
1141     if (fileName == null || (currentFileFormat == null)
1142             || HttpUtils.startsWithHttpOrHttps(fileName))
1143     {
1144       saveAs_actionPerformed();
1145     }
1146     else
1147     {
1148       saveAlignment(fileName, currentFileFormat);
1149     }
1150   }
1151
1152   /**
1153    * Saves the alignment to a file with a name chosen by the user, if necessary
1154    * warning if a file would be overwritten
1155    */
1156   @Override
1157   public void saveAs_actionPerformed()
1158   {
1159     String format = currentFileFormat == null ? null
1160             : currentFileFormat.getName();
1161     JalviewFileChooser chooser = JalviewFileChooser
1162             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1163
1164     chooser.setFileView(new JalviewFileView());
1165     chooser.setDialogTitle(
1166             MessageManager.getString("label.save_alignment_to_file"));
1167     chooser.setToolTipText(MessageManager.getString("action.save"));
1168
1169     int value = chooser.showSaveDialog(this);
1170
1171     if (value != JalviewFileChooser.APPROVE_OPTION)
1172     {
1173       return;
1174     }
1175     currentFileFormat = chooser.getSelectedFormat();
1176     // todo is this (2005) test now obsolete - value is never null?
1177     while (currentFileFormat == null)
1178     {
1179       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1180               MessageManager
1181                       .getString("label.select_file_format_before_saving"),
1182               MessageManager.getString("label.file_format_not_specified"),
1183               JvOptionPane.WARNING_MESSAGE);
1184       currentFileFormat = chooser.getSelectedFormat();
1185       value = chooser.showSaveDialog(this);
1186       if (value != JalviewFileChooser.APPROVE_OPTION)
1187       {
1188         return;
1189       }
1190     }
1191
1192     fileName = chooser.getSelectedFile().getPath();
1193
1194     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1195     Cache.setProperty("LAST_DIRECTORY", fileName);
1196     saveAlignment(fileName, currentFileFormat);
1197   }
1198
1199   boolean lastSaveSuccessful = false;
1200
1201   FileFormatI lastFormatSaved;
1202
1203   String lastFilenameSaved;
1204
1205   /**
1206    * Raise a dialog or status message for the last call to saveAlignment.
1207    *
1208    * @return true if last call to saveAlignment(file, format) was successful.
1209    */
1210   public boolean isSaveAlignmentSuccessful()
1211   {
1212
1213     if (!lastSaveSuccessful)
1214     {
1215       if (!Platform.isHeadless())
1216       {
1217         JvOptionPane.showInternalMessageDialog(this, MessageManager
1218                 .formatMessage("label.couldnt_save_file", new Object[]
1219                 { lastFilenameSaved }),
1220                 MessageManager.getString("label.error_saving_file"),
1221                 JvOptionPane.WARNING_MESSAGE);
1222       }
1223       else
1224       {
1225         Console.error(MessageManager
1226                 .formatMessage("label.couldnt_save_file", new Object[]
1227                 { lastFilenameSaved }));
1228       }
1229     }
1230     else
1231     {
1232
1233       setStatus(MessageManager.formatMessage(
1234               "label.successfully_saved_to_file_in_format", new Object[]
1235               { lastFilenameSaved, lastFormatSaved }));
1236
1237     }
1238     return lastSaveSuccessful;
1239   }
1240
1241   /**
1242    * Saves the alignment to the specified file path, in the specified format,
1243    * which may be an alignment format, or Jalview project format. If the
1244    * alignment has hidden regions, or the format is one capable of including
1245    * non-sequence data (features, annotations, groups), then the user may be
1246    * prompted to specify what to include in the output.
1247    *
1248    * @param file
1249    * @param format
1250    */
1251   public void saveAlignment(String file, FileFormatI format)
1252   {
1253     lastSaveSuccessful = true;
1254     lastFilenameSaved = file;
1255     lastFormatSaved = format;
1256
1257     if (FileFormat.Jalview.equals(format))
1258     {
1259       String shortName = title;
1260       if (shortName.indexOf(File.separatorChar) > -1)
1261       {
1262         shortName = shortName
1263                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1264       }
1265       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1266               shortName);
1267
1268       Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1269       if (lastSaveSuccessful)
1270       {
1271         this.getViewport().setSavedUpToDate(true);
1272       }
1273
1274       statusBar.setText(MessageManager.formatMessage(
1275               "label.successfully_saved_to_file_in_format", new Object[]
1276               { file, format }));
1277
1278       return;
1279     }
1280
1281     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1282     Runnable cancelAction = () -> {
1283       lastSaveSuccessful = false;
1284     };
1285     Runnable outputAction = () -> {
1286       // todo defer this to inside formatSequences (or later)
1287       AlignmentExportData exportData = viewport.getAlignExportData(options);
1288       String output = new FormatAdapter(alignPanel, options)
1289               .formatSequences(format, exportData.getAlignment(),
1290                       exportData.getOmitHidden(),
1291                       exportData.getStartEndPostions(),
1292                       viewport.getAlignment().getHiddenColumns());
1293       if (output == null)
1294       {
1295         lastSaveSuccessful = false;
1296       }
1297       else
1298       {
1299         // create backupfiles object and get new temp filename destination
1300         boolean doBackup = BackupFiles.getEnabled();
1301         BackupFiles backupfiles = null;
1302         if (doBackup)
1303         {
1304           Console.trace("ALIGNFRAME making backupfiles object for " + file);
1305           backupfiles = new BackupFiles(file);
1306         }
1307         try
1308         {
1309           String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1310                   : file;
1311           Console.trace("ALIGNFRAME setting PrintWriter");
1312           PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1313
1314           if (backupfiles != null)
1315           {
1316             Console.trace("ALIGNFRAME about to write to temp file "
1317                     + backupfiles.getTempFilePath());
1318           }
1319
1320           out.print(output);
1321           Console.trace("ALIGNFRAME about to close file");
1322           out.close();
1323           Console.trace("ALIGNFRAME closed file");
1324           AlignFrame.this.setTitle(file);
1325           statusBar.setText(MessageManager.formatMessage(
1326                   "label.successfully_saved_to_file_in_format", new Object[]
1327                   { fileName, format.getName() }));
1328           lastSaveSuccessful = true;
1329         } catch (IOException e)
1330         {
1331           lastSaveSuccessful = false;
1332           Console.error(
1333                   "ALIGNFRAME Something happened writing the temp file");
1334           Console.error(e.getMessage());
1335           Console.debug(Cache.getStackTraceString(e));
1336         } catch (Exception ex)
1337         {
1338           lastSaveSuccessful = false;
1339           Console.error(
1340                   "ALIGNFRAME Something unexpected happened writing the temp file");
1341           Console.error(ex.getMessage());
1342           Console.debug(Cache.getStackTraceString(ex));
1343         }
1344
1345         if (doBackup)
1346         {
1347           backupfiles.setWriteSuccess(lastSaveSuccessful);
1348           Console.debug("ALIGNFRAME writing temp file was "
1349                   + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1350           // do the backup file roll and rename the temp file to actual file
1351           Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1352           lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1353           Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1354                   + (lastSaveSuccessful ? "" : "un") + "successfully");
1355         }
1356
1357         Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1358         if (lastSaveSuccessful)
1359         {
1360           AlignFrame.this.getViewport().setSavedUpToDate(true);
1361         }
1362       }
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.run();
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     Runnable 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     };
1425
1426     /*
1427      * show dialog with export options if applicable; else just do it
1428      */
1429     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1430     {
1431       AlignExportOptions choices = new AlignExportOptions(
1432               alignPanel.getAlignViewport(), fileFormat, options);
1433       choices.setResponseAction(0, outputAction);
1434       choices.showDialog();
1435     }
1436     else
1437     {
1438       try
1439       {
1440         outputAction.run();
1441       } catch (Exception e)
1442       {
1443         e.printStackTrace();
1444       }
1445     }
1446   }
1447
1448   /**
1449    * DOCUMENT ME!
1450    *
1451    * @param e
1452    *          DOCUMENT ME!
1453    */
1454   @Override
1455   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1456   {
1457     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1458     try
1459     {
1460       htmlSVG.exportHTML(null);
1461     } catch (ImageOutputException x)
1462     {
1463       // report problem to console and raise dialog
1464     }
1465   }
1466
1467   @Override
1468   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1469   {
1470     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1471     try
1472     {
1473       bjs.exportHTML(null);
1474     } catch (ImageOutputException x)
1475     {
1476       // report problem to console and raise dialog
1477     }
1478   }
1479
1480   public void createImageMap(File file, String image)
1481   {
1482     try
1483     {
1484       alignPanel.makePNGImageMap(file, image);
1485     } catch (ImageOutputException x)
1486     {
1487       // report problem to console and raise dialog
1488     }
1489   }
1490
1491   @Override
1492   public void createPNG_actionPerformed(ActionEvent e)
1493   {
1494     try
1495     {
1496       createPNG(null);
1497     } catch (ImageOutputException ioex)
1498     {
1499       // raise dialog, and report via console
1500     }
1501   }
1502
1503   @Override
1504   public void createEPS_actionPerformed(ActionEvent e)
1505   {
1506     try
1507     {
1508       createEPS(null);
1509     } catch (ImageOutputException ioex)
1510     {
1511       // raise dialog, and report via console
1512     }
1513
1514   }
1515
1516   @Override
1517   public void createSVG_actionPerformed(ActionEvent e)
1518   {
1519     try
1520     {
1521       createSVG(null);
1522     } catch (ImageOutputException ioex)
1523     {
1524       // raise dialog, and report via console
1525     }
1526
1527   }
1528
1529   /**
1530    * Creates a PNG image of the alignment and writes it to the given file. If
1531    * the file is null, the user is prompted to choose a file.
1532    *
1533    * @param f
1534    */
1535   public void createPNG(File f) throws ImageOutputException
1536   {
1537     createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
1538   }
1539
1540   public void createPNG(File f, String renderer, BitmapImageSizing userBis)
1541           throws ImageOutputException
1542   {
1543     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
1544   }
1545
1546   /**
1547    * Creates an EPS image of the alignment and writes it to the given file. If
1548    * the file is null, the user is prompted to choose a file.
1549    *
1550    * @param f
1551    */
1552   public void createEPS(File f) throws ImageOutputException
1553   {
1554     createEPS(f, null);
1555   }
1556
1557   public void createEPS(File f, String renderer) throws ImageOutputException
1558   {
1559     alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
1560   }
1561
1562   /**
1563    * Creates an SVG image of the alignment and writes it to the given file. If
1564    * the file is null, the user is prompted to choose a file.
1565    *
1566    * @param f
1567    */
1568   public void createSVG(File f) throws ImageOutputException
1569   {
1570     createSVG(f, null);
1571   }
1572
1573   public void createSVG(File f, String renderer) throws ImageOutputException
1574   {
1575     alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
1576   }
1577
1578   @Override
1579   public void pageSetup_actionPerformed(ActionEvent e)
1580   {
1581     PrinterJob printJob = PrinterJob.getPrinterJob();
1582     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1583   }
1584
1585   /**
1586    * DOCUMENT ME!
1587    *
1588    * @param e
1589    *          DOCUMENT ME!
1590    */
1591   @Override
1592   public void printMenuItem_actionPerformed(ActionEvent e)
1593   {
1594     // Putting in a thread avoids Swing painting problems
1595     PrintThread thread = new PrintThread(alignPanel);
1596     thread.start();
1597   }
1598
1599   @Override
1600   public void exportFeatures_actionPerformed(ActionEvent e)
1601   {
1602     new AnnotationExporter(alignPanel).exportFeatures();
1603   }
1604
1605   @Override
1606   public void exportAnnotations_actionPerformed(ActionEvent e)
1607   {
1608     new AnnotationExporter(alignPanel).exportAnnotations();
1609   }
1610
1611   @Override
1612   public void associatedData_actionPerformed(ActionEvent e)
1613   {
1614     final JalviewFileChooser chooser = new JalviewFileChooser(
1615             Cache.getProperty("LAST_DIRECTORY"));
1616     chooser.setFileView(new JalviewFileView());
1617     String tooltip = MessageManager
1618             .getString("label.load_jalview_annotations");
1619     chooser.setDialogTitle(tooltip);
1620     chooser.setToolTipText(tooltip);
1621     chooser.setResponseHandler(0, () -> {
1622       String choice = chooser.getSelectedFile().getPath();
1623       Cache.setProperty("LAST_DIRECTORY", choice);
1624       loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1625     });
1626
1627     chooser.showOpenDialog(this);
1628   }
1629
1630   /**
1631    * Close the current view or all views in the alignment frame. If the frame
1632    * only contains one view then the alignment will be removed from memory.
1633    *
1634    * @param closeAllTabs
1635    */
1636   @Override
1637   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1638   {
1639     if (alignPanels != null && alignPanels.size() < 2)
1640     {
1641       closeAllTabs = true;
1642     }
1643
1644     try
1645     {
1646       if (alignPanels != null)
1647       {
1648         if (closeAllTabs)
1649         {
1650           if (this.isClosed())
1651           {
1652             // really close all the windows - otherwise wait till
1653             // setClosed(true) is called
1654             for (int i = 0; i < alignPanels.size(); i++)
1655             {
1656               AlignmentPanel ap = alignPanels.get(i);
1657               ap.closePanel();
1658             }
1659           }
1660         }
1661         else
1662         {
1663           closeView(alignPanel);
1664         }
1665       }
1666       if (closeAllTabs)
1667       {
1668         if (featureSettings != null && featureSettings.isOpen())
1669         {
1670           featureSettings.close();
1671           featureSettings = null;
1672         }
1673         /*
1674          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1675          * be called recursively, with the frame now in 'closed' state
1676          */
1677         this.setClosed(true);
1678       }
1679     } catch (Exception ex)
1680     {
1681       ex.printStackTrace();
1682     }
1683   }
1684
1685   /**
1686    * Close the specified panel and close up tabs appropriately.
1687    *
1688    * @param panelToClose
1689    */
1690   public void closeView(AlignmentPanel panelToClose)
1691   {
1692     int index = tabbedPane.getSelectedIndex();
1693     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1694     alignPanels.remove(panelToClose);
1695     panelToClose.closePanel();
1696     panelToClose = null;
1697
1698     tabbedPane.removeTabAt(closedindex);
1699     tabbedPane.validate();
1700
1701     if (index > closedindex || index == tabbedPane.getTabCount())
1702     {
1703       // modify currently selected tab index if necessary.
1704       index--;
1705     }
1706
1707     this.tabSelectionChanged(index);
1708   }
1709
1710   /**
1711    * DOCUMENT ME!
1712    */
1713   void updateEditMenuBar()
1714   {
1715
1716     if (viewport.getHistoryList().size() > 0)
1717     {
1718       undoMenuItem.setEnabled(true);
1719       CommandI command = viewport.getHistoryList().peek();
1720       undoMenuItem.setText(MessageManager
1721               .formatMessage("label.undo_command", new Object[]
1722               { command.getDescription() }));
1723     }
1724     else
1725     {
1726       undoMenuItem.setEnabled(false);
1727       undoMenuItem.setText(MessageManager.getString("action.undo"));
1728     }
1729
1730     if (viewport.getRedoList().size() > 0)
1731     {
1732       redoMenuItem.setEnabled(true);
1733
1734       CommandI command = viewport.getRedoList().peek();
1735       redoMenuItem.setText(MessageManager
1736               .formatMessage("label.redo_command", new Object[]
1737               { command.getDescription() }));
1738     }
1739     else
1740     {
1741       redoMenuItem.setEnabled(false);
1742       redoMenuItem.setText(MessageManager.getString("action.redo"));
1743     }
1744   }
1745
1746   @Override
1747   public void addHistoryItem(CommandI command)
1748   {
1749     if (command.getSize() > 0)
1750     {
1751       viewport.addToHistoryList(command);
1752       viewport.clearRedoList();
1753       updateEditMenuBar();
1754       viewport.updateHiddenColumns();
1755       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1756       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1757       // viewport.getColumnSelection()
1758       // .getHiddenColumns().size() > 0);
1759     }
1760   }
1761
1762   /**
1763    *
1764    * @return alignment objects for all views
1765    */
1766   AlignmentI[] getViewAlignments()
1767   {
1768     if (alignPanels != null)
1769     {
1770       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1771       int i = 0;
1772       for (AlignmentPanel ap : alignPanels)
1773       {
1774         als[i++] = ap.av.getAlignment();
1775       }
1776       return als;
1777     }
1778     if (viewport != null)
1779     {
1780       return new AlignmentI[] { viewport.getAlignment() };
1781     }
1782     return null;
1783   }
1784
1785   /**
1786    * DOCUMENT ME!
1787    *
1788    * @param e
1789    *          DOCUMENT ME!
1790    */
1791   @Override
1792   protected void undoMenuItem_actionPerformed(ActionEvent e)
1793   {
1794     if (viewport.getHistoryList().isEmpty())
1795     {
1796       return;
1797     }
1798     CommandI command = viewport.getHistoryList().pop();
1799     viewport.addToRedoList(command);
1800     command.undoCommand(getViewAlignments());
1801
1802     AlignmentViewport originalSource = getOriginatingSource(command);
1803     updateEditMenuBar();
1804
1805     if (originalSource != null)
1806     {
1807       if (originalSource != viewport)
1808       {
1809         Console.warn(
1810                 "Implementation worry: mismatch of viewport origin for undo");
1811       }
1812       originalSource.updateHiddenColumns();
1813       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1814       // null
1815       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1816       // viewport.getColumnSelection()
1817       // .getHiddenColumns().size() > 0);
1818       originalSource.firePropertyChange("alignment", null,
1819               originalSource.getAlignment().getSequences());
1820     }
1821   }
1822
1823   /**
1824    * DOCUMENT ME!
1825    *
1826    * @param e
1827    *          DOCUMENT ME!
1828    */
1829   @Override
1830   protected void redoMenuItem_actionPerformed(ActionEvent e)
1831   {
1832     if (viewport.getRedoList().size() < 1)
1833     {
1834       return;
1835     }
1836
1837     CommandI command = viewport.getRedoList().pop();
1838     viewport.addToHistoryList(command);
1839     command.doCommand(getViewAlignments());
1840
1841     AlignmentViewport originalSource = getOriginatingSource(command);
1842     updateEditMenuBar();
1843
1844     if (originalSource != null)
1845     {
1846
1847       if (originalSource != viewport)
1848       {
1849         Console.warn(
1850                 "Implementation worry: mismatch of viewport origin for redo");
1851       }
1852       originalSource.updateHiddenColumns();
1853       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1854       // null
1855       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1856       // viewport.getColumnSelection()
1857       // .getHiddenColumns().size() > 0);
1858       originalSource.firePropertyChange("alignment", null,
1859               originalSource.getAlignment().getSequences());
1860     }
1861   }
1862
1863   AlignmentViewport getOriginatingSource(CommandI command)
1864   {
1865     AlignmentViewport originalSource = null;
1866     // For sequence removal and addition, we need to fire
1867     // the property change event FROM the viewport where the
1868     // original alignment was altered
1869     AlignmentI al = null;
1870     if (command instanceof EditCommand)
1871     {
1872       EditCommand editCommand = (EditCommand) command;
1873       al = editCommand.getAlignment();
1874       List<Component> comps = PaintRefresher.components
1875               .get(viewport.getSequenceSetId());
1876
1877       for (Component comp : comps)
1878       {
1879         if (comp instanceof AlignmentPanel)
1880         {
1881           if (al == ((AlignmentPanel) comp).av.getAlignment())
1882           {
1883             originalSource = ((AlignmentPanel) comp).av;
1884             break;
1885           }
1886         }
1887       }
1888     }
1889
1890     if (originalSource == null)
1891     {
1892       // The original view is closed, we must validate
1893       // the current view against the closed view first
1894       if (al != null)
1895       {
1896         PaintRefresher.validateSequences(al, viewport.getAlignment());
1897       }
1898
1899       originalSource = viewport;
1900     }
1901
1902     return originalSource;
1903   }
1904
1905   /**
1906    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1907    * or the sequence under cursor in keyboard mode
1908    *
1909    * @param up
1910    *          or down (if !up)
1911    */
1912   public void moveSelectedSequences(boolean up)
1913   {
1914     SequenceGroup sg = viewport.getSelectionGroup();
1915
1916     if (sg == null)
1917     {
1918       if (viewport.cursorMode)
1919       {
1920         sg = new SequenceGroup();
1921         sg.addSequence(viewport.getAlignment().getSequenceAt(
1922                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1923       }
1924       else
1925       {
1926         return;
1927       }
1928     }
1929
1930     if (sg.getSize() < 1)
1931     {
1932       return;
1933     }
1934
1935     // TODO: JAL-3733 - add an event to the undo buffer for this !
1936
1937     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1938             viewport.getHiddenRepSequences(), up);
1939     alignPanel.paintAlignment(true, false);
1940   }
1941
1942   synchronized void slideSequences(boolean right, int size)
1943   {
1944     List<SequenceI> sg = new ArrayList<>();
1945     if (viewport.cursorMode)
1946     {
1947       sg.add(viewport.getAlignment()
1948               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1949     }
1950     else if (viewport.getSelectionGroup() != null
1951             && viewport.getSelectionGroup().getSize() != viewport
1952                     .getAlignment().getHeight())
1953     {
1954       sg = viewport.getSelectionGroup()
1955               .getSequences(viewport.getHiddenRepSequences());
1956     }
1957
1958     if (sg.size() < 1)
1959     {
1960       return;
1961     }
1962
1963     List<SequenceI> invertGroup = new ArrayList<>();
1964
1965     for (SequenceI seq : viewport.getAlignment().getSequences())
1966     {
1967       if (!sg.contains(seq))
1968       {
1969         invertGroup.add(seq);
1970       }
1971     }
1972
1973     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1974
1975     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1976     for (int i = 0; i < invertGroup.size(); i++)
1977     {
1978       seqs2[i] = invertGroup.get(i);
1979     }
1980
1981     SlideSequencesCommand ssc;
1982     if (right)
1983     {
1984       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1985               viewport.getGapCharacter());
1986     }
1987     else
1988     {
1989       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1990               viewport.getGapCharacter());
1991     }
1992
1993     int groupAdjustment = 0;
1994     if (ssc.getGapsInsertedBegin() && right)
1995     {
1996       if (viewport.cursorMode)
1997       {
1998         alignPanel.getSeqPanel().moveCursor(size, 0);
1999       }
2000       else
2001       {
2002         groupAdjustment = size;
2003       }
2004     }
2005     else if (!ssc.getGapsInsertedBegin() && !right)
2006     {
2007       if (viewport.cursorMode)
2008       {
2009         alignPanel.getSeqPanel().moveCursor(-size, 0);
2010       }
2011       else
2012       {
2013         groupAdjustment = -size;
2014       }
2015     }
2016
2017     if (groupAdjustment != 0)
2018     {
2019       viewport.getSelectionGroup().setStartRes(
2020               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2021       viewport.getSelectionGroup().setEndRes(
2022               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2023     }
2024
2025     /*
2026      * just extend the last slide command if compatible; but not if in
2027      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2028      */
2029     boolean appendHistoryItem = false;
2030     Deque<CommandI> historyList = viewport.getHistoryList();
2031     boolean inSplitFrame = getSplitViewContainer() != null;
2032     if (!inSplitFrame && historyList != null && historyList.size() > 0
2033             && historyList.peek() instanceof SlideSequencesCommand)
2034     {
2035       appendHistoryItem = ssc.appendSlideCommand(
2036               (SlideSequencesCommand) historyList.peek());
2037     }
2038
2039     if (!appendHistoryItem)
2040     {
2041       addHistoryItem(ssc);
2042     }
2043
2044     repaint();
2045   }
2046
2047   /**
2048    * DOCUMENT ME!
2049    *
2050    * @param e
2051    *          DOCUMENT ME!
2052    */
2053   @Override
2054   protected void copy_actionPerformed()
2055   {
2056     if (viewport.getSelectionGroup() == null)
2057     {
2058       return;
2059     }
2060     // TODO: preserve the ordering of displayed alignment annotation in any
2061     // internal paste (particularly sequence associated annotation)
2062     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2063     String[] omitHidden = null;
2064
2065     if (viewport.hasHiddenColumns())
2066     {
2067       omitHidden = viewport.getViewAsString(true);
2068     }
2069
2070     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2071             seqs, omitHidden, null);
2072
2073     StringSelection ss = new StringSelection(output);
2074
2075     try
2076     {
2077       jalview.gui.Desktop.internalCopy = true;
2078       // Its really worth setting the clipboard contents
2079       // to empty before setting the large StringSelection!!
2080       Toolkit.getDefaultToolkit().getSystemClipboard()
2081               .setContents(new StringSelection(""), null);
2082
2083       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2084               Desktop.instance);
2085     } catch (OutOfMemoryError er)
2086     {
2087       new OOMWarning("copying region", er);
2088       return;
2089     }
2090
2091     HiddenColumns hiddenColumns = null;
2092     if (viewport.hasHiddenColumns())
2093     {
2094       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2095       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2096
2097       // create new HiddenColumns object with copy of hidden regions
2098       // between startRes and endRes, offset by startRes
2099       hiddenColumns = new HiddenColumns(
2100               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2101               hiddenCutoff, hiddenOffset);
2102     }
2103
2104     Desktop.jalviewClipboard = new Object[] { seqs,
2105         viewport.getAlignment().getDataset(), hiddenColumns };
2106     setStatus(MessageManager.formatMessage(
2107             "label.copied_sequences_to_clipboard", new Object[]
2108             { Integer.valueOf(seqs.length).toString() }));
2109   }
2110
2111   /**
2112    * DOCUMENT ME!
2113    *
2114    * @param e
2115    *          DOCUMENT ME!
2116    */
2117   @Override
2118   protected void pasteNew_actionPerformed(ActionEvent e)
2119   {
2120     paste(true);
2121   }
2122
2123   /**
2124    * DOCUMENT ME!
2125    *
2126    * @param e
2127    *          DOCUMENT ME!
2128    */
2129   @Override
2130   protected void pasteThis_actionPerformed(ActionEvent e)
2131   {
2132     paste(false);
2133   }
2134
2135   /**
2136    * Paste contents of Jalview clipboard
2137    *
2138    * @param newAlignment
2139    *          true to paste to a new alignment, otherwise add to this.
2140    */
2141   void paste(boolean newAlignment)
2142   {
2143     boolean externalPaste = true;
2144     try
2145     {
2146       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2147       Transferable contents = c.getContents(this);
2148
2149       if (contents == null)
2150       {
2151         return;
2152       }
2153
2154       String str;
2155       FileFormatI format;
2156       try
2157       {
2158         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2159         if (str.length() < 1)
2160         {
2161           return;
2162         }
2163
2164         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2165
2166       } catch (OutOfMemoryError er)
2167       {
2168         new OOMWarning("Out of memory pasting sequences!!", er);
2169         return;
2170       }
2171
2172       SequenceI[] sequences;
2173       boolean annotationAdded = false;
2174       AlignmentI alignment = null;
2175
2176       if (Desktop.jalviewClipboard != null)
2177       {
2178         // The clipboard was filled from within Jalview, we must use the
2179         // sequences
2180         // And dataset from the copied alignment
2181         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2182         // be doubly sure that we create *new* sequence objects.
2183         sequences = new SequenceI[newseq.length];
2184         for (int i = 0; i < newseq.length; i++)
2185         {
2186           sequences[i] = new Sequence(newseq[i]);
2187         }
2188         alignment = new Alignment(sequences);
2189         externalPaste = false;
2190       }
2191       else
2192       {
2193         // parse the clipboard as an alignment.
2194         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2195                 format);
2196         sequences = alignment.getSequencesArray();
2197       }
2198
2199       int alwidth = 0;
2200       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2201       int fgroup = -1;
2202
2203       if (newAlignment)
2204       {
2205
2206         if (Desktop.jalviewClipboard != null)
2207         {
2208           // dataset is inherited
2209           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2210         }
2211         else
2212         {
2213           // new dataset is constructed
2214           alignment.setDataset(null);
2215         }
2216         alwidth = alignment.getWidth() + 1;
2217       }
2218       else
2219       {
2220         AlignmentI pastedal = alignment; // preserve pasted alignment object
2221         // Add pasted sequences and dataset into existing alignment.
2222         alignment = viewport.getAlignment();
2223         alwidth = alignment.getWidth() + 1;
2224         // decide if we need to import sequences from an existing dataset
2225         boolean importDs = Desktop.jalviewClipboard != null
2226                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2227         // importDs==true instructs us to copy over new dataset sequences from
2228         // an existing alignment
2229         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2230                                                                       // create
2231         // minimum dataset set
2232
2233         for (int i = 0; i < sequences.length; i++)
2234         {
2235           if (importDs)
2236           {
2237             newDs.addElement(null);
2238           }
2239           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2240           // paste
2241           if (importDs && ds != null)
2242           {
2243             if (!newDs.contains(ds))
2244             {
2245               newDs.setElementAt(ds, i);
2246               ds = new Sequence(ds);
2247               // update with new dataset sequence
2248               sequences[i].setDatasetSequence(ds);
2249             }
2250             else
2251             {
2252               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2253             }
2254           }
2255           else
2256           {
2257             // copy and derive new dataset sequence
2258             sequences[i] = sequences[i].deriveSequence();
2259             alignment.getDataset()
2260                     .addSequence(sequences[i].getDatasetSequence());
2261             // TODO: avoid creation of duplicate dataset sequences with a
2262             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2263           }
2264           alignment.addSequence(sequences[i]); // merges dataset
2265         }
2266         if (newDs != null)
2267         {
2268           newDs.clear(); // tidy up
2269         }
2270         if (alignment.getAlignmentAnnotation() != null)
2271         {
2272           for (AlignmentAnnotation alan : alignment
2273                   .getAlignmentAnnotation())
2274           {
2275             if (alan.graphGroup > fgroup)
2276             {
2277               fgroup = alan.graphGroup;
2278             }
2279           }
2280         }
2281         if (pastedal.getAlignmentAnnotation() != null)
2282         {
2283           // Add any annotation attached to alignment.
2284           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2285           for (int i = 0; i < alann.length; i++)
2286           {
2287             annotationAdded = true;
2288             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2289             {
2290               AlignmentAnnotation newann = new AlignmentAnnotation(
2291                       alann[i]);
2292               if (newann.graphGroup > -1)
2293               {
2294                 if (newGraphGroups.size() <= newann.graphGroup
2295                         || newGraphGroups.get(newann.graphGroup) == null)
2296                 {
2297                   for (int q = newGraphGroups
2298                           .size(); q <= newann.graphGroup; q++)
2299                   {
2300                     newGraphGroups.add(q, null);
2301                   }
2302                   newGraphGroups.set(newann.graphGroup,
2303                           Integer.valueOf(++fgroup));
2304                 }
2305                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2306                         .intValue();
2307               }
2308
2309               newann.padAnnotation(alwidth);
2310               alignment.addAnnotation(newann);
2311             }
2312           }
2313         }
2314       }
2315       if (!newAlignment)
2316       {
2317         // /////
2318         // ADD HISTORY ITEM
2319         //
2320         addHistoryItem(new EditCommand(
2321                 MessageManager.getString("label.add_sequences"),
2322                 Action.PASTE, sequences, 0, alignment.getWidth(),
2323                 alignment));
2324       }
2325       // Add any annotations attached to sequences
2326       for (int i = 0; i < sequences.length; i++)
2327       {
2328         if (sequences[i].getAnnotation() != null)
2329         {
2330           AlignmentAnnotation newann;
2331           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2332           {
2333             annotationAdded = true;
2334             newann = sequences[i].getAnnotation()[a];
2335             newann.adjustForAlignment();
2336             newann.padAnnotation(alwidth);
2337             if (newann.graphGroup > -1)
2338             {
2339               if (newann.graphGroup > -1)
2340               {
2341                 if (newGraphGroups.size() <= newann.graphGroup
2342                         || newGraphGroups.get(newann.graphGroup) == null)
2343                 {
2344                   for (int q = newGraphGroups
2345                           .size(); q <= newann.graphGroup; q++)
2346                   {
2347                     newGraphGroups.add(q, null);
2348                   }
2349                   newGraphGroups.set(newann.graphGroup,
2350                           Integer.valueOf(++fgroup));
2351                 }
2352                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2353                         .intValue();
2354               }
2355             }
2356             // annotation was duplicated earlier
2357             alignment.addAnnotation(sequences[i].getAnnotation()[a]);
2358             // take care of contact matrix too
2359             ContactMatrixI cm = sequences[i]
2360                     .getContactMatrixFor(sequences[i].getAnnotation()[a]);
2361             if (cm != null)
2362             {
2363               alignment.addContactListFor(sequences[i].getAnnotation()[a],
2364                       cm);
2365             }
2366
2367             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2368                     a);
2369           }
2370         }
2371       }
2372       if (!newAlignment)
2373       {
2374
2375         // propagate alignment changed.
2376         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2377         if (annotationAdded)
2378         {
2379           // Duplicate sequence annotation in all views.
2380           AlignmentI[] alview = this.getViewAlignments();
2381           for (int i = 0; i < sequences.length; i++)
2382           {
2383             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2384             if (sann == null)
2385             {
2386               continue;
2387             }
2388             for (int avnum = 0; avnum < alview.length; avnum++)
2389             {
2390               if (alview[avnum] != alignment)
2391               {
2392                 // duplicate in a view other than the one with input focus
2393                 int avwidth = alview[avnum].getWidth() + 1;
2394                 // this relies on sann being preserved after we
2395                 // modify the sequence's annotation array for each duplication
2396                 for (int a = 0; a < sann.length; a++)
2397                 {
2398                   AlignmentAnnotation newann = new AlignmentAnnotation(
2399                           sann[a]);
2400                   sequences[i].addAlignmentAnnotation(newann);
2401                   newann.padAnnotation(avwidth);
2402                   alview[avnum].addAnnotation(newann); // annotation was
2403                   // duplicated earlier
2404                   // TODO JAL-1145 graphGroups are not updated for sequence
2405                   // annotation added to several views. This may cause
2406                   // strangeness
2407                   alview[avnum].setAnnotationIndex(newann, a);
2408                 }
2409               }
2410             }
2411           }
2412           buildSortByAnnotationScoresMenu();
2413         }
2414         viewport.firePropertyChange("alignment", null,
2415                 alignment.getSequences());
2416         if (alignPanels != null)
2417         {
2418           for (AlignmentPanel ap : alignPanels)
2419           {
2420             ap.validateAnnotationDimensions(false);
2421           }
2422         }
2423         else
2424         {
2425           alignPanel.validateAnnotationDimensions(false);
2426         }
2427
2428       }
2429       else
2430       {
2431         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2432                 DEFAULT_HEIGHT);
2433         String newtitle = new String("Copied sequences");
2434
2435         if (Desktop.jalviewClipboard != null
2436                 && Desktop.jalviewClipboard[2] != null)
2437         {
2438           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2439           af.viewport.setHiddenColumns(hc);
2440         }
2441
2442         // >>>This is a fix for the moment, until a better solution is
2443         // found!!<<<
2444         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2445                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2446                         .getFeatureRenderer());
2447
2448         // TODO: maintain provenance of an alignment, rather than just make the
2449         // title a concatenation of operations.
2450         if (!externalPaste)
2451         {
2452           if (title.startsWith("Copied sequences"))
2453           {
2454             newtitle = title;
2455           }
2456           else
2457           {
2458             newtitle = newtitle.concat("- from " + title);
2459           }
2460         }
2461         else
2462         {
2463           newtitle = new String("Pasted sequences");
2464         }
2465
2466         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2467                 DEFAULT_HEIGHT);
2468
2469       }
2470
2471     } catch (Exception ex)
2472     {
2473       ex.printStackTrace();
2474       System.out.println("Exception whilst pasting: " + ex);
2475       // could be anything being pasted in here
2476     }
2477
2478   }
2479
2480   @Override
2481   protected void expand_newalign(ActionEvent e)
2482   {
2483     try
2484     {
2485       AlignmentI alignment = AlignmentUtils
2486               .expandContext(getViewport().getAlignment(), -1);
2487       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2488               DEFAULT_HEIGHT);
2489       String newtitle = new String("Flanking alignment");
2490
2491       if (Desktop.jalviewClipboard != null
2492               && Desktop.jalviewClipboard[2] != null)
2493       {
2494         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2495         af.viewport.setHiddenColumns(hc);
2496       }
2497
2498       // >>>This is a fix for the moment, until a better solution is
2499       // found!!<<<
2500       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2501               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2502                       .getFeatureRenderer());
2503
2504       // TODO: maintain provenance of an alignment, rather than just make the
2505       // title a concatenation of operations.
2506       {
2507         if (title.startsWith("Copied sequences"))
2508         {
2509           newtitle = title;
2510         }
2511         else
2512         {
2513           newtitle = newtitle.concat("- from " + title);
2514         }
2515       }
2516
2517       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2518
2519     } catch (Exception ex)
2520     {
2521       ex.printStackTrace();
2522       System.out.println("Exception whilst pasting: " + ex);
2523       // could be anything being pasted in here
2524     } catch (OutOfMemoryError oom)
2525     {
2526       new OOMWarning("Viewing flanking region of alignment", oom);
2527     }
2528   }
2529
2530   /**
2531    * Action Cut (delete and copy) the selected region
2532    */
2533   @Override
2534   protected void cut_actionPerformed()
2535   {
2536     copy_actionPerformed();
2537     delete_actionPerformed();
2538   }
2539
2540   /**
2541    * Performs menu option to Delete the currently selected region
2542    */
2543   @Override
2544   protected void delete_actionPerformed()
2545   {
2546
2547     SequenceGroup sg = viewport.getSelectionGroup();
2548     if (sg == null)
2549     {
2550       return;
2551     }
2552
2553     Runnable okAction = () -> {
2554       SequenceI[] cut = sg.getSequences()
2555               .toArray(new SequenceI[sg.getSize()]);
2556
2557       addHistoryItem(new EditCommand(
2558               MessageManager.getString("label.cut_sequences"), Action.CUT,
2559               cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2560               viewport.getAlignment()));
2561
2562       viewport.setSelectionGroup(null);
2563       viewport.sendSelection();
2564       viewport.getAlignment().deleteGroup(sg);
2565
2566       viewport.firePropertyChange("alignment", null,
2567               viewport.getAlignment().getSequences());
2568       if (viewport.getAlignment().getHeight() < 1)
2569       {
2570         try
2571         {
2572           AlignFrame.this.setClosed(true);
2573         } catch (Exception ex)
2574         {
2575         }
2576       }
2577     };
2578
2579     /*
2580      * If the cut affects all sequences, prompt for confirmation
2581      */
2582     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2583             .getHeight();
2584     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2585             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2586     if (wholeHeight && wholeWidth)
2587     {
2588       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2589       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2590       Object[] options = new Object[] {
2591           MessageManager.getString("action.ok"),
2592           MessageManager.getString("action.cancel") };
2593       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2594               MessageManager.getString("label.delete_all"),
2595               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2596               options, options[0]);
2597     }
2598     else
2599     {
2600       try
2601       {
2602         okAction.run();
2603       } catch (Exception e)
2604       {
2605         e.printStackTrace();
2606       }
2607     }
2608   }
2609
2610   /**
2611    * DOCUMENT ME!
2612    *
2613    * @param e
2614    *          DOCUMENT ME!
2615    */
2616   @Override
2617   protected void deleteGroups_actionPerformed(ActionEvent e)
2618   {
2619     if (avc.deleteGroups())
2620     {
2621       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2622       alignPanel.updateAnnotation();
2623       alignPanel.paintAlignment(true, true);
2624     }
2625   }
2626
2627   /**
2628    * DOCUMENT ME!
2629    *
2630    * @param e
2631    *          DOCUMENT ME!
2632    */
2633   @Override
2634   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2635   {
2636     SequenceGroup sg = new SequenceGroup(
2637             viewport.getAlignment().getSequences());
2638
2639     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2640     viewport.setSelectionGroup(sg);
2641     viewport.isSelectionGroupChanged(true);
2642     viewport.sendSelection();
2643     // JAL-2034 - should delegate to
2644     // alignPanel to decide if overview needs
2645     // updating.
2646     alignPanel.paintAlignment(false, false);
2647     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2648   }
2649
2650   /**
2651    * DOCUMENT ME!
2652    *
2653    * @param e
2654    *          DOCUMENT ME!
2655    */
2656   @Override
2657   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2658   {
2659     if (viewport.cursorMode)
2660     {
2661       alignPanel.getSeqPanel().keyboardNo1 = null;
2662       alignPanel.getSeqPanel().keyboardNo2 = null;
2663     }
2664     viewport.setSelectionGroup(null);
2665     viewport.getColumnSelection().clear();
2666     viewport.setSearchResults(null);
2667     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2668     // JAL-2034 - should delegate to
2669     // alignPanel to decide if overview needs
2670     // updating.
2671     alignPanel.paintAlignment(false, false);
2672     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2673     viewport.sendSelection();
2674   }
2675
2676   /**
2677    * DOCUMENT ME!
2678    *
2679    * @param e
2680    *          DOCUMENT ME!
2681    */
2682   @Override
2683   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2684   {
2685     SequenceGroup sg = viewport.getSelectionGroup();
2686
2687     if (sg == null)
2688     {
2689       selectAllSequenceMenuItem_actionPerformed(null);
2690
2691       return;
2692     }
2693
2694     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2695     {
2696       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2697     }
2698     // JAL-2034 - should delegate to
2699     // alignPanel to decide if overview needs
2700     // updating.
2701
2702     alignPanel.paintAlignment(true, false);
2703     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2704     viewport.sendSelection();
2705   }
2706
2707   @Override
2708   public void invertColSel_actionPerformed(ActionEvent e)
2709   {
2710     viewport.invertColumnSelection();
2711     alignPanel.paintAlignment(true, false);
2712     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2713     viewport.sendSelection();
2714   }
2715
2716   /**
2717    * DOCUMENT ME!
2718    *
2719    * @param e
2720    *          DOCUMENT ME!
2721    */
2722   @Override
2723   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2724   {
2725     trimAlignment(true);
2726   }
2727
2728   /**
2729    * DOCUMENT ME!
2730    *
2731    * @param e
2732    *          DOCUMENT ME!
2733    */
2734   @Override
2735   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2736   {
2737     trimAlignment(false);
2738   }
2739
2740   void trimAlignment(boolean trimLeft)
2741   {
2742     ColumnSelection colSel = viewport.getColumnSelection();
2743     int column;
2744
2745     if (!colSel.isEmpty())
2746     {
2747       if (trimLeft)
2748       {
2749         column = colSel.getMin();
2750       }
2751       else
2752       {
2753         column = colSel.getMax();
2754       }
2755
2756       SequenceI[] seqs;
2757       if (viewport.getSelectionGroup() != null)
2758       {
2759         seqs = viewport.getSelectionGroup()
2760                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2761       }
2762       else
2763       {
2764         seqs = viewport.getAlignment().getSequencesArray();
2765       }
2766
2767       TrimRegionCommand trimRegion;
2768       if (trimLeft)
2769       {
2770         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2771                 column, viewport.getAlignment());
2772         viewport.getRanges().setStartRes(0);
2773       }
2774       else
2775       {
2776         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2777                 column, viewport.getAlignment());
2778       }
2779
2780       setStatus(MessageManager.formatMessage("label.removed_columns",
2781               new String[]
2782               { Integer.valueOf(trimRegion.getSize()).toString() }));
2783
2784       addHistoryItem(trimRegion);
2785
2786       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2787       {
2788         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2789                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2790         {
2791           viewport.getAlignment().deleteGroup(sg);
2792         }
2793       }
2794
2795       viewport.firePropertyChange("alignment", null,
2796               viewport.getAlignment().getSequences());
2797     }
2798   }
2799
2800   /**
2801    * DOCUMENT ME!
2802    *
2803    * @param e
2804    *          DOCUMENT ME!
2805    */
2806   @Override
2807   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2808   {
2809     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2810
2811     SequenceI[] seqs;
2812     if (viewport.getSelectionGroup() != null)
2813     {
2814       seqs = viewport.getSelectionGroup()
2815               .getSequencesAsArray(viewport.getHiddenRepSequences());
2816       start = viewport.getSelectionGroup().getStartRes();
2817       end = viewport.getSelectionGroup().getEndRes();
2818     }
2819     else
2820     {
2821       seqs = viewport.getAlignment().getSequencesArray();
2822     }
2823
2824     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2825             "Remove Gapped Columns", seqs, start, end,
2826             viewport.getAlignment());
2827
2828     addHistoryItem(removeGapCols);
2829
2830     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2831             new Object[]
2832             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2833
2834     // This is to maintain viewport position on first residue
2835     // of first sequence
2836     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2837     ViewportRanges ranges = viewport.getRanges();
2838     int startRes = seq.findPosition(ranges.getStartRes());
2839     // ShiftList shifts;
2840     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2841     // edit.alColumnChanges=shifts.getInverse();
2842     // if (viewport.hasHiddenColumns)
2843     // viewport.getColumnSelection().compensateForEdits(shifts);
2844     ranges.setStartRes(seq.findIndex(startRes) - 1);
2845     viewport.firePropertyChange("alignment", null,
2846             viewport.getAlignment().getSequences());
2847
2848   }
2849
2850   /**
2851    * DOCUMENT ME!
2852    *
2853    * @param e
2854    *          DOCUMENT ME!
2855    */
2856   @Override
2857   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2858   {
2859     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2860
2861     SequenceI[] seqs;
2862     if (viewport.getSelectionGroup() != null)
2863     {
2864       seqs = viewport.getSelectionGroup()
2865               .getSequencesAsArray(viewport.getHiddenRepSequences());
2866       start = viewport.getSelectionGroup().getStartRes();
2867       end = viewport.getSelectionGroup().getEndRes();
2868     }
2869     else
2870     {
2871       seqs = viewport.getAlignment().getSequencesArray();
2872     }
2873
2874     // This is to maintain viewport position on first residue
2875     // of first sequence
2876     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2877     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2878
2879     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2880             viewport.getAlignment()));
2881
2882     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2883
2884     viewport.firePropertyChange("alignment", null,
2885             viewport.getAlignment().getSequences());
2886
2887   }
2888
2889   /**
2890    * DOCUMENT ME!
2891    *
2892    * @param e
2893    *          DOCUMENT ME!
2894    */
2895   @Override
2896   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2897   {
2898     viewport.setPadGaps(padGapsMenuitem.isSelected());
2899     viewport.firePropertyChange("alignment", null,
2900             viewport.getAlignment().getSequences());
2901   }
2902
2903   /**
2904    * Opens a Finder dialog
2905    *
2906    * @param e
2907    */
2908   @Override
2909   public void findMenuItem_actionPerformed(ActionEvent e)
2910   {
2911     new Finder(alignPanel, false, null);
2912   }
2913
2914   /**
2915    * Create a new view of the current alignment.
2916    */
2917   @Override
2918   public void newView_actionPerformed(ActionEvent e)
2919   {
2920     newView(null, true);
2921   }
2922
2923   /**
2924    * Creates and shows a new view of the current alignment.
2925    *
2926    * @param viewTitle
2927    *          title of newly created view; if null, one will be generated
2928    * @param copyAnnotation
2929    *          if true then duplicate all annnotation, groups and settings
2930    * @return new alignment panel, already displayed.
2931    */
2932   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2933   {
2934     /*
2935      * Create a new AlignmentPanel (with its own, new Viewport)
2936      */
2937     AlignmentPanel newap = new jalview.project.Jalview2XML()
2938             .copyAlignPanel(alignPanel);
2939     if (!copyAnnotation)
2940     {
2941       /*
2942        * remove all groups and annotation except for the automatic stuff
2943        */
2944       newap.av.getAlignment().deleteAllGroups();
2945       newap.av.getAlignment().deleteAllAnnotations(false);
2946     }
2947
2948     newap.av.setGatherViewsHere(false);
2949
2950     if (viewport.getViewName() == null)
2951     {
2952       viewport.setViewName(
2953               MessageManager.getString("label.view_name_original"));
2954     }
2955
2956     /*
2957      * Views share the same edits undo and redo stacks
2958      */
2959     newap.av.setHistoryList(viewport.getHistoryList());
2960     newap.av.setRedoList(viewport.getRedoList());
2961
2962     /*
2963      * copy any visualisation settings that are not saved in the project
2964      */
2965     newap.av.setColourAppliesToAllGroups(
2966             viewport.getColourAppliesToAllGroups());
2967
2968     /*
2969      * Views share the same mappings; need to deregister any new mappings
2970      * created by copyAlignPanel, and register the new reference to the shared
2971      * mappings
2972      */
2973     newap.av.replaceMappings(viewport.getAlignment());
2974
2975     /*
2976      * start up cDNA consensus (if applicable) now mappings are in place
2977      */
2978     if (newap.av.initComplementConsensus())
2979     {
2980       newap.refresh(true); // adjust layout of annotations
2981     }
2982
2983     newap.av.setViewName(getNewViewName(viewTitle));
2984
2985     addAlignmentPanel(newap, true);
2986     newap.alignmentChanged();
2987
2988     if (alignPanels.size() == 2)
2989     {
2990       viewport.setGatherViewsHere(true);
2991     }
2992     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2993
2994     return newap;
2995   }
2996
2997   /**
2998    * Make a new name for the view, ensuring it is unique within the current
2999    * sequenceSetId. (This used to be essential for Jalview Project archives, but
3000    * these now use viewId. Unique view names are still desirable for usability.)
3001    *
3002    * @param viewTitle
3003    * @return
3004    */
3005   protected String getNewViewName(String viewTitle)
3006   {
3007     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3008     boolean addFirstIndex = false;
3009     if (viewTitle == null || viewTitle.trim().length() == 0)
3010     {
3011       viewTitle = MessageManager.getString("action.view");
3012       addFirstIndex = true;
3013     }
3014     else
3015     {
3016       index = 1;// we count from 1 if given a specific name
3017     }
3018     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3019
3020     List<Component> comps = PaintRefresher.components
3021             .get(viewport.getSequenceSetId());
3022
3023     List<String> existingNames = getExistingViewNames(comps);
3024
3025     while (existingNames.contains(newViewName))
3026     {
3027       newViewName = viewTitle + " " + (++index);
3028     }
3029     return newViewName;
3030   }
3031
3032   /**
3033    * Returns a list of distinct view names found in the given list of
3034    * components. View names are held on the viewport of an AlignmentPanel.
3035    *
3036    * @param comps
3037    * @return
3038    */
3039   protected List<String> getExistingViewNames(List<Component> comps)
3040   {
3041     List<String> existingNames = new ArrayList<>();
3042     for (Component comp : comps)
3043     {
3044       if (comp instanceof AlignmentPanel)
3045       {
3046         AlignmentPanel ap = (AlignmentPanel) comp;
3047         if (!existingNames.contains(ap.av.getViewName()))
3048         {
3049           existingNames.add(ap.av.getViewName());
3050         }
3051       }
3052     }
3053     return existingNames;
3054   }
3055
3056   /**
3057    * Explode tabbed views into separate windows.
3058    */
3059   @Override
3060   public void expandViews_actionPerformed(ActionEvent e)
3061   {
3062     Desktop.explodeViews(this);
3063   }
3064
3065   /**
3066    * Gather views in separate windows back into a tabbed presentation.
3067    */
3068   @Override
3069   public void gatherViews_actionPerformed(ActionEvent e)
3070   {
3071     Desktop.instance.gatherViews(this);
3072   }
3073
3074   /**
3075    * DOCUMENT ME!
3076    *
3077    * @param e
3078    *          DOCUMENT ME!
3079    */
3080   @Override
3081   public void font_actionPerformed(ActionEvent e)
3082   {
3083     new FontChooser(alignPanel);
3084   }
3085
3086   /**
3087    * DOCUMENT ME!
3088    *
3089    * @param e
3090    *          DOCUMENT ME!
3091    */
3092   @Override
3093   protected void seqLimit_actionPerformed(ActionEvent e)
3094   {
3095     viewport.setShowJVSuffix(seqLimits.isSelected());
3096
3097     alignPanel.getIdPanel().getIdCanvas()
3098             .setPreferredSize(alignPanel.calculateIdWidth());
3099     alignPanel.paintAlignment(true, false);
3100   }
3101
3102   @Override
3103   public void idRightAlign_actionPerformed(ActionEvent e)
3104   {
3105     viewport.setRightAlignIds(idRightAlign.isSelected());
3106     alignPanel.paintAlignment(false, false);
3107   }
3108
3109   @Override
3110   public void centreColumnLabels_actionPerformed(ActionEvent e)
3111   {
3112     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3113     alignPanel.paintAlignment(false, false);
3114   }
3115
3116   /*
3117    * (non-Javadoc)
3118    *
3119    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3120    */
3121   @Override
3122   protected void followHighlight_actionPerformed()
3123   {
3124     /*
3125      * Set the 'follow' flag on the Viewport (and scroll to position if now
3126      * true).
3127      */
3128     final boolean state = this.followHighlightMenuItem.getState();
3129     viewport.setFollowHighlight(state);
3130     if (state)
3131     {
3132       alignPanel.scrollToPosition(viewport.getSearchResults());
3133     }
3134   }
3135
3136   /**
3137    * DOCUMENT ME!
3138    *
3139    * @param e
3140    *          DOCUMENT ME!
3141    */
3142   @Override
3143   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3144   {
3145     viewport.setColourText(colourTextMenuItem.isSelected());
3146     alignPanel.paintAlignment(false, false);
3147   }
3148
3149   /**
3150    * DOCUMENT ME!
3151    *
3152    * @param e
3153    *          DOCUMENT ME!
3154    */
3155   @Override
3156   public void wrapMenuItem_actionPerformed(ActionEvent e)
3157   {
3158     scaleAbove.setVisible(wrapMenuItem.isSelected());
3159     scaleLeft.setVisible(wrapMenuItem.isSelected());
3160     scaleRight.setVisible(wrapMenuItem.isSelected());
3161     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3162     alignPanel.updateLayout();
3163   }
3164
3165   @Override
3166   public void showAllSeqs_actionPerformed(ActionEvent e)
3167   {
3168     viewport.showAllHiddenSeqs();
3169   }
3170
3171   @Override
3172   public void showAllColumns_actionPerformed(ActionEvent e)
3173   {
3174     viewport.showAllHiddenColumns();
3175     alignPanel.paintAlignment(true, true);
3176     viewport.sendSelection();
3177   }
3178
3179   @Override
3180   public void hideSelSequences_actionPerformed(ActionEvent e)
3181   {
3182     viewport.hideAllSelectedSeqs();
3183   }
3184
3185   /**
3186    * called by key handler and the hide all/show all menu items
3187    *
3188    * @param toggleSeqs
3189    * @param toggleCols
3190    */
3191   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3192   {
3193
3194     boolean hide = false;
3195     SequenceGroup sg = viewport.getSelectionGroup();
3196     if (!toggleSeqs && !toggleCols)
3197     {
3198       // Hide everything by the current selection - this is a hack - we do the
3199       // invert and then hide
3200       // first check that there will be visible columns after the invert.
3201       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3202               && sg.getStartRes() <= sg.getEndRes()))
3203       {
3204         // now invert the sequence set, if required - empty selection implies
3205         // that no hiding is required.
3206         if (sg != null)
3207         {
3208           invertSequenceMenuItem_actionPerformed(null);
3209           sg = viewport.getSelectionGroup();
3210           toggleSeqs = true;
3211
3212         }
3213         viewport.expandColSelection(sg, true);
3214         // finally invert the column selection and get the new sequence
3215         // selection.
3216         invertColSel_actionPerformed(null);
3217         toggleCols = true;
3218       }
3219     }
3220
3221     if (toggleSeqs)
3222     {
3223       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3224       {
3225         hideSelSequences_actionPerformed(null);
3226         hide = true;
3227       }
3228       else if (!(toggleCols && viewport.hasSelectedColumns()))
3229       {
3230         showAllSeqs_actionPerformed(null);
3231       }
3232     }
3233
3234     if (toggleCols)
3235     {
3236       if (viewport.hasSelectedColumns())
3237       {
3238         hideSelColumns_actionPerformed(null);
3239         if (!toggleSeqs)
3240         {
3241           viewport.setSelectionGroup(sg);
3242         }
3243       }
3244       else if (!hide)
3245       {
3246         showAllColumns_actionPerformed(null);
3247       }
3248     }
3249   }
3250
3251   /*
3252    * (non-Javadoc)
3253    *
3254    * @see
3255    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3256    * event.ActionEvent)
3257    */
3258   @Override
3259   public void hideAllButSelection_actionPerformed(ActionEvent e)
3260   {
3261     toggleHiddenRegions(false, false);
3262     viewport.sendSelection();
3263   }
3264
3265   /*
3266    * (non-Javadoc)
3267    *
3268    * @see
3269    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3270    * .ActionEvent)
3271    */
3272   @Override
3273   public void hideAllSelection_actionPerformed(ActionEvent e)
3274   {
3275     SequenceGroup sg = viewport.getSelectionGroup();
3276     viewport.expandColSelection(sg, false);
3277     viewport.hideAllSelectedSeqs();
3278     viewport.hideSelectedColumns();
3279     alignPanel.updateLayout();
3280     alignPanel.paintAlignment(true, true);
3281     viewport.sendSelection();
3282   }
3283
3284   /*
3285    * (non-Javadoc)
3286    *
3287    * @see
3288    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3289    * ActionEvent)
3290    */
3291   @Override
3292   public void showAllhidden_actionPerformed(ActionEvent e)
3293   {
3294     viewport.showAllHiddenColumns();
3295     viewport.showAllHiddenSeqs();
3296     alignPanel.paintAlignment(true, true);
3297     viewport.sendSelection();
3298   }
3299
3300   @Override
3301   public void hideSelColumns_actionPerformed(ActionEvent e)
3302   {
3303     viewport.hideSelectedColumns();
3304     alignPanel.updateLayout();
3305     alignPanel.paintAlignment(true, true);
3306     viewport.sendSelection();
3307   }
3308
3309   @Override
3310   public void hiddenMarkers_actionPerformed(ActionEvent e)
3311   {
3312     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3313     repaint();
3314   }
3315
3316   /**
3317    * DOCUMENT ME!
3318    *
3319    * @param e
3320    *          DOCUMENT ME!
3321    */
3322   @Override
3323   protected void scaleAbove_actionPerformed(ActionEvent e)
3324   {
3325     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3326     alignPanel.updateLayout();
3327     alignPanel.paintAlignment(true, false);
3328   }
3329
3330   /**
3331    * DOCUMENT ME!
3332    *
3333    * @param e
3334    *          DOCUMENT ME!
3335    */
3336   @Override
3337   protected void scaleLeft_actionPerformed(ActionEvent e)
3338   {
3339     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3340     alignPanel.updateLayout();
3341     alignPanel.paintAlignment(true, false);
3342   }
3343
3344   /**
3345    * DOCUMENT ME!
3346    *
3347    * @param e
3348    *          DOCUMENT ME!
3349    */
3350   @Override
3351   protected void scaleRight_actionPerformed(ActionEvent e)
3352   {
3353     viewport.setScaleRightWrapped(scaleRight.isSelected());
3354     alignPanel.updateLayout();
3355     alignPanel.paintAlignment(true, false);
3356   }
3357
3358   /**
3359    * DOCUMENT ME!
3360    *
3361    * @param e
3362    *          DOCUMENT ME!
3363    */
3364   @Override
3365   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3366   {
3367     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3368     alignPanel.paintAlignment(false, false);
3369   }
3370
3371   /**
3372    * DOCUMENT ME!
3373    *
3374    * @param e
3375    *          DOCUMENT ME!
3376    */
3377   @Override
3378   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3379   {
3380     viewport.setShowText(viewTextMenuItem.isSelected());
3381     alignPanel.paintAlignment(false, false);
3382   }
3383
3384   /**
3385    * DOCUMENT ME!
3386    *
3387    * @param e
3388    *          DOCUMENT ME!
3389    */
3390   @Override
3391   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3392   {
3393     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3394     alignPanel.paintAlignment(false, false);
3395   }
3396
3397   public FeatureSettings featureSettings;
3398
3399   @Override
3400   public FeatureSettingsControllerI getFeatureSettingsUI()
3401   {
3402     return featureSettings;
3403   }
3404
3405   @Override
3406   public void featureSettings_actionPerformed(ActionEvent e)
3407   {
3408     showFeatureSettingsUI();
3409   }
3410
3411   @Override
3412   public FeatureSettingsControllerI showFeatureSettingsUI()
3413   {
3414     if (featureSettings != null)
3415     {
3416       featureSettings.closeOldSettings();
3417       featureSettings = null;
3418     }
3419     if (!showSeqFeatures.isSelected())
3420     {
3421       // make sure features are actually displayed
3422       showSeqFeatures.setSelected(true);
3423       showSeqFeatures_actionPerformed(null);
3424     }
3425     featureSettings = new FeatureSettings(this);
3426     return featureSettings;
3427   }
3428
3429   /**
3430    * Set or clear 'Show Sequence Features'
3431    *
3432    * @param evt
3433    *          DOCUMENT ME!
3434    */
3435   @Override
3436   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3437   {
3438     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3439     alignPanel.paintAlignment(true, true);
3440   }
3441
3442   /**
3443    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3444    * the annotations panel as a whole.
3445    *
3446    * The options to show/hide all annotations should be enabled when the panel
3447    * is shown, and disabled when the panel is hidden.
3448    *
3449    * @param e
3450    */
3451   @Override
3452   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3453   {
3454     final boolean setVisible = annotationPanelMenuItem.isSelected();
3455     viewport.setShowAnnotation(setVisible);
3456     this.showAllSeqAnnotations.setEnabled(setVisible);
3457     this.hideAllSeqAnnotations.setEnabled(setVisible);
3458     this.showAllAlAnnotations.setEnabled(setVisible);
3459     this.hideAllAlAnnotations.setEnabled(setVisible);
3460     alignPanel.updateLayout();
3461   }
3462
3463   @Override
3464   public void alignmentProperties()
3465   {
3466     JComponent pane;
3467     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3468
3469             .formatAsHtml();
3470     String content = MessageManager.formatMessage("label.html_content",
3471             new Object[]
3472             { contents.toString() });
3473     contents = null;
3474
3475     if (Platform.isJS())
3476     {
3477       JLabel textLabel = new JLabel();
3478       textLabel.setText(content);
3479       textLabel.setBackground(Color.WHITE);
3480
3481       pane = new JPanel(new BorderLayout());
3482       ((JPanel) pane).setOpaque(true);
3483       pane.setBackground(Color.WHITE);
3484       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3485     }
3486     else
3487     /**
3488      * Java only
3489      *
3490      * @j2sIgnore
3491      */
3492     {
3493       JEditorPane editPane = new JEditorPane("text/html", "");
3494       editPane.setEditable(false);
3495       editPane.setText(content);
3496       pane = editPane;
3497     }
3498
3499     JInternalFrame frame = new JInternalFrame();
3500     frame.setFrameIcon(null);
3501     frame.getContentPane().add(new JScrollPane(pane));
3502
3503     Desktop.addInternalFrame(frame, MessageManager
3504             .formatMessage("label.alignment_properties", new Object[]
3505             { getTitle() }), 500, 400);
3506   }
3507
3508   /**
3509    * Opens an Overview panel for the alignment, unless one is open already
3510    *
3511    * @param e
3512    */
3513   @Override
3514   public void overviewMenuItem_actionPerformed(ActionEvent e)
3515   {
3516     boolean showHiddenRegions = Cache
3517             .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
3518     openOverviewPanel(showHiddenRegions);
3519   }
3520
3521   public OverviewPanel openOverviewPanel(boolean showHidden)
3522   {
3523     if (alignPanel.overviewPanel != null)
3524     {
3525       return alignPanel.overviewPanel;
3526     }
3527     JInternalFrame frame = new JInternalFrame();
3528     frame.setFrameIcon(null);
3529     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
3530             showHidden);
3531     frame.setContentPane(overview);
3532     Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
3533             frame.getHeight(), true, true);
3534     frame.pack();
3535     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3536     final AlignmentPanel thePanel = this.alignPanel;
3537     frame.addInternalFrameListener(
3538             new javax.swing.event.InternalFrameAdapter()
3539             {
3540               @Override
3541               public void internalFrameClosed(
3542                       javax.swing.event.InternalFrameEvent evt)
3543               {
3544                 overview.dispose();
3545                 thePanel.setOverviewPanel(null);
3546               }
3547             });
3548     if (getKeyListeners().length > 0)
3549     {
3550       frame.addKeyListener(getKeyListeners()[0]);
3551     }
3552
3553     alignPanel.setOverviewPanel(overview);
3554     alignPanel.setOverviewTitle(this);
3555
3556     return overview;
3557   }
3558
3559   @Override
3560   public void textColour_actionPerformed()
3561   {
3562     new TextColourChooser().chooseColour(alignPanel, null);
3563   }
3564
3565   /*
3566    * public void covariationColour_actionPerformed() {
3567    * changeColour(new
3568    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3569    * ()[0])); }
3570    */
3571   @Override
3572   public void annotationColour_actionPerformed()
3573   {
3574     new AnnotationColourChooser(viewport, alignPanel);
3575   }
3576
3577   @Override
3578   public void annotationColumn_actionPerformed(ActionEvent e)
3579   {
3580     new AnnotationColumnChooser(viewport, alignPanel);
3581   }
3582
3583   /**
3584    * Action on the user checking or unchecking the option to apply the selected
3585    * colour scheme to all groups. If unchecked, groups may have their own
3586    * independent colour schemes.
3587    *
3588    * @param selected
3589    */
3590   @Override
3591   public void applyToAllGroups_actionPerformed(boolean selected)
3592   {
3593     viewport.setColourAppliesToAllGroups(selected);
3594   }
3595
3596   /**
3597    * Action on user selecting a colour from the colour menu
3598    *
3599    * @param name
3600    *          the name (not the menu item label!) of the colour scheme
3601    */
3602   @Override
3603   public void changeColour_actionPerformed(String name)
3604   {
3605     /*
3606      * 'User Defined' opens a panel to configure or load a
3607      * user-defined colour scheme
3608      */
3609     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3610     {
3611       new UserDefinedColours(alignPanel);
3612       return;
3613     }
3614
3615     /*
3616      * otherwise set the chosen colour scheme (or null for 'None')
3617      */
3618     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3619             viewport, viewport.getAlignment(),
3620             viewport.getHiddenRepSequences());
3621     changeColour(cs);
3622   }
3623
3624   /**
3625    * Actions on setting or changing the alignment colour scheme
3626    *
3627    * @param cs
3628    */
3629   @Override
3630   public void changeColour(ColourSchemeI cs)
3631   {
3632     // TODO: pull up to controller method
3633     ColourMenuHelper.setColourSelected(colourMenu, cs);
3634
3635     viewport.setGlobalColourScheme(cs);
3636
3637     alignPanel.paintAlignment(true, true);
3638   }
3639
3640   /**
3641    * Show the PID threshold slider panel
3642    */
3643   @Override
3644   protected void modifyPID_actionPerformed()
3645   {
3646     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3647             alignPanel.getViewName());
3648     SliderPanel.showPIDSlider();
3649   }
3650
3651   /**
3652    * Show the Conservation slider panel
3653    */
3654   @Override
3655   protected void modifyConservation_actionPerformed()
3656   {
3657     SliderPanel.setConservationSlider(alignPanel,
3658             viewport.getResidueShading(), alignPanel.getViewName());
3659     SliderPanel.showConservationSlider();
3660   }
3661
3662   /**
3663    * Action on selecting or deselecting (Colour) By Conservation
3664    */
3665   @Override
3666   public void conservationMenuItem_actionPerformed(boolean selected)
3667   {
3668     modifyConservation.setEnabled(selected);
3669     viewport.setConservationSelected(selected);
3670     viewport.getResidueShading().setConservationApplied(selected);
3671
3672     changeColour(viewport.getGlobalColourScheme());
3673     if (selected)
3674     {
3675       modifyConservation_actionPerformed();
3676     }
3677     else
3678     {
3679       SliderPanel.hideConservationSlider();
3680     }
3681   }
3682
3683   /**
3684    * Action on selecting or deselecting (Colour) Above PID Threshold
3685    */
3686   @Override
3687   public void abovePIDThreshold_actionPerformed(boolean selected)
3688   {
3689     modifyPID.setEnabled(selected);
3690     viewport.setAbovePIDThreshold(selected);
3691     if (!selected)
3692     {
3693       viewport.getResidueShading().setThreshold(0,
3694               viewport.isIgnoreGapsConsensus());
3695     }
3696
3697     changeColour(viewport.getGlobalColourScheme());
3698     if (selected)
3699     {
3700       modifyPID_actionPerformed();
3701     }
3702     else
3703     {
3704       SliderPanel.hidePIDSlider();
3705     }
3706   }
3707
3708   /**
3709    * DOCUMENT ME!
3710    *
3711    * @param e
3712    *          DOCUMENT ME!
3713    */
3714   @Override
3715   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3716   {
3717     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3718     AlignmentSorter.sortByPID(viewport.getAlignment(),
3719             viewport.getAlignment().getSequenceAt(0));
3720     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3721             viewport.getAlignment()));
3722     alignPanel.paintAlignment(true, false);
3723   }
3724
3725   /**
3726    * DOCUMENT ME!
3727    *
3728    * @param e
3729    *          DOCUMENT ME!
3730    */
3731   @Override
3732   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3733   {
3734     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3735     AlignmentSorter.sortByID(viewport.getAlignment());
3736     addHistoryItem(
3737             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3738     alignPanel.paintAlignment(true, false);
3739   }
3740
3741   /**
3742    * DOCUMENT ME!
3743    *
3744    * @param e
3745    *          DOCUMENT ME!
3746    */
3747   @Override
3748   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3749   {
3750     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751     AlignmentSorter.sortByLength(viewport.getAlignment());
3752     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3753             viewport.getAlignment()));
3754     alignPanel.paintAlignment(true, false);
3755   }
3756
3757   /**
3758    * DOCUMENT ME!
3759    *
3760    * @param e
3761    *          DOCUMENT ME!
3762    */
3763   @Override
3764   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3765   {
3766     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3767     AlignmentSorter.sortByGroup(viewport.getAlignment());
3768     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3769             viewport.getAlignment()));
3770
3771     alignPanel.paintAlignment(true, false);
3772   }
3773
3774   /**
3775    * DOCUMENT ME!
3776    *
3777    * @param e
3778    *          DOCUMENT ME!
3779    */
3780   @Override
3781   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3782   {
3783     new RedundancyPanel(alignPanel, this);
3784   }
3785
3786   /**
3787    * DOCUMENT ME!
3788    *
3789    * @param e
3790    *          DOCUMENT ME!
3791    */
3792   @Override
3793   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3794   {
3795     if ((viewport.getSelectionGroup() == null)
3796             || (viewport.getSelectionGroup().getSize() < 2))
3797     {
3798       JvOptionPane.showInternalMessageDialog(this,
3799               MessageManager.getString(
3800                       "label.you_must_select_least_two_sequences"),
3801               MessageManager.getString("label.invalid_selection"),
3802               JvOptionPane.WARNING_MESSAGE);
3803     }
3804     else
3805     {
3806       JInternalFrame frame = new JInternalFrame();
3807       frame.setFrameIcon(null);
3808       frame.setContentPane(new PairwiseAlignPanel(viewport));
3809       Desktop.addInternalFrame(frame,
3810               MessageManager.getString("action.pairwise_alignment"), 600,
3811               500);
3812     }
3813   }
3814
3815   @Override
3816   public void autoCalculate_actionPerformed(ActionEvent e)
3817   {
3818     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3819     if (viewport.autoCalculateConsensus)
3820     {
3821       viewport.firePropertyChange("alignment", null,
3822               viewport.getAlignment().getSequences());
3823     }
3824   }
3825
3826   @Override
3827   public void sortByTreeOption_actionPerformed(ActionEvent e)
3828   {
3829     viewport.sortByTree = sortByTree.isSelected();
3830   }
3831
3832   @Override
3833   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3834   {
3835     viewport.followSelection = listenToViewSelections.isSelected();
3836   }
3837
3838   /**
3839    * Constructs a tree panel and adds it to the desktop
3840    *
3841    * @param type
3842    *          tree type (NJ or AV)
3843    * @param modelName
3844    *          name of score model used to compute the tree
3845    * @param options
3846    *          parameters for the distance or similarity calculation
3847    */
3848   void newTreePanel(String type, String modelName,
3849           SimilarityParamsI options)
3850   {
3851     String frameTitle = "";
3852     TreePanel tp;
3853
3854     boolean onSelection = false;
3855     if (viewport.getSelectionGroup() != null
3856             && viewport.getSelectionGroup().getSize() > 0)
3857     {
3858       SequenceGroup sg = viewport.getSelectionGroup();
3859
3860       /* Decide if the selection is a column region */
3861       for (SequenceI _s : sg.getSequences())
3862       {
3863         if (_s.getLength() < sg.getEndRes())
3864         {
3865           JvOptionPane.showMessageDialog(Desktop.desktop,
3866                   MessageManager.getString(
3867                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3868                   MessageManager.getString(
3869                           "label.sequences_selection_not_aligned"),
3870                   JvOptionPane.WARNING_MESSAGE);
3871
3872           return;
3873         }
3874       }
3875       onSelection = true;
3876     }
3877     else
3878     {
3879       if (viewport.getAlignment().getHeight() < 2)
3880       {
3881         return;
3882       }
3883     }
3884
3885     tp = new TreePanel(alignPanel, type, modelName, options);
3886     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3887
3888     frameTitle += " from ";
3889
3890     if (viewport.getViewName() != null)
3891     {
3892       frameTitle += viewport.getViewName() + " of ";
3893     }
3894
3895     frameTitle += this.title;
3896
3897     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3898   }
3899
3900   /**
3901    * DOCUMENT ME!
3902    *
3903    * @param title
3904    *          DOCUMENT ME!
3905    * @param order
3906    *          DOCUMENT ME!
3907    */
3908   public void addSortByOrderMenuItem(String title,
3909           final AlignmentOrder order)
3910   {
3911     final JMenuItem item = new JMenuItem(MessageManager
3912             .formatMessage("action.by_title_param", new Object[]
3913             { title }));
3914     sort.add(item);
3915     item.addActionListener(new java.awt.event.ActionListener()
3916     {
3917       @Override
3918       public void actionPerformed(ActionEvent e)
3919       {
3920         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3921
3922         // TODO: JBPNote - have to map order entries to curent SequenceI
3923         // pointers
3924         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3925
3926         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3927                 viewport.getAlignment()));
3928
3929         alignPanel.paintAlignment(true, false);
3930       }
3931     });
3932   }
3933
3934   /**
3935    * Add a new sort by annotation score menu item
3936    *
3937    * @param sort
3938    *          the menu to add the option to
3939    * @param scoreLabel
3940    *          the label used to retrieve scores for each sequence on the
3941    *          alignment
3942    */
3943   public void addSortByAnnotScoreMenuItem(JMenu sort,
3944           final String scoreLabel)
3945   {
3946     final JMenuItem item = new JMenuItem(scoreLabel);
3947     sort.add(item);
3948     item.addActionListener(new java.awt.event.ActionListener()
3949     {
3950       @Override
3951       public void actionPerformed(ActionEvent e)
3952       {
3953         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3954         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3955                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3956         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3957                 viewport.getAlignment()));
3958         alignPanel.paintAlignment(true, false);
3959       }
3960     });
3961   }
3962
3963   /**
3964    * last hash for alignment's annotation array - used to minimise cost of
3965    * rebuild.
3966    */
3967   protected int _annotationScoreVectorHash;
3968
3969   /**
3970    * search the alignment and rebuild the sort by annotation score submenu the
3971    * last alignment annotation vector hash is stored to minimize cost of
3972    * rebuilding in subsequence calls.
3973    *
3974    */
3975   @Override
3976   public void buildSortByAnnotationScoresMenu()
3977   {
3978     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3979     {
3980       return;
3981     }
3982
3983     if (viewport.getAlignment().getAlignmentAnnotation()
3984             .hashCode() != _annotationScoreVectorHash)
3985     {
3986       sortByAnnotScore.removeAll();
3987       // almost certainly a quicker way to do this - but we keep it simple
3988       Hashtable<String, String> scoreSorts = new Hashtable<>();
3989       AlignmentAnnotation aann[];
3990       for (SequenceI sqa : viewport.getAlignment().getSequences())
3991       {
3992         aann = sqa.getAnnotation();
3993         for (int i = 0; aann != null && i < aann.length; i++)
3994         {
3995           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3996           {
3997             scoreSorts.put(aann[i].label, aann[i].label);
3998           }
3999         }
4000       }
4001       Enumeration<String> labels = scoreSorts.keys();
4002       while (labels.hasMoreElements())
4003       {
4004         addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
4005       }
4006       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4007       scoreSorts.clear();
4008
4009       _annotationScoreVectorHash = viewport.getAlignment()
4010               .getAlignmentAnnotation().hashCode();
4011     }
4012   }
4013
4014   /**
4015    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4016    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4017    * call. Listeners are added to remove the menu item when the treePanel is
4018    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4019    * modified.
4020    */
4021   @Override
4022   public void buildTreeSortMenu()
4023   {
4024     sortByTreeMenu.removeAll();
4025
4026     List<Component> comps = PaintRefresher.components
4027             .get(viewport.getSequenceSetId());
4028     List<TreePanel> treePanels = new ArrayList<>();
4029     for (Component comp : comps)
4030     {
4031       if (comp instanceof TreePanel)
4032       {
4033         treePanels.add((TreePanel) comp);
4034       }
4035     }
4036
4037     if (treePanels.size() < 1)
4038     {
4039       sortByTreeMenu.setVisible(false);
4040       return;
4041     }
4042
4043     sortByTreeMenu.setVisible(true);
4044
4045     for (final TreePanel tp : treePanels)
4046     {
4047       final JMenuItem item = new JMenuItem(tp.getTitle());
4048       item.addActionListener(new java.awt.event.ActionListener()
4049       {
4050         @Override
4051         public void actionPerformed(ActionEvent e)
4052         {
4053           tp.sortByTree_actionPerformed();
4054           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4055
4056         }
4057       });
4058
4059       sortByTreeMenu.add(item);
4060     }
4061   }
4062
4063   public boolean sortBy(AlignmentOrder alorder, String undoname)
4064   {
4065     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4066     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4067     if (undoname != null)
4068     {
4069       addHistoryItem(new OrderCommand(undoname, oldOrder,
4070               viewport.getAlignment()));
4071     }
4072     alignPanel.paintAlignment(true, false);
4073     return true;
4074   }
4075
4076   /**
4077    * Work out whether the whole set of sequences or just the selected set will
4078    * be submitted for multiple alignment.
4079    *
4080    */
4081   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4082   {
4083     // Now, check we have enough sequences
4084     AlignmentView msa = null;
4085
4086     if ((viewport.getSelectionGroup() != null)
4087             && (viewport.getSelectionGroup().getSize() > 1))
4088     {
4089       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4090       // some common interface!
4091       /*
4092        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4093        * SequenceI[sz = seqs.getSize(false)];
4094        *
4095        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4096        * seqs.getSequenceAt(i); }
4097        */
4098       msa = viewport.getAlignmentView(true);
4099     }
4100     else if (viewport.getSelectionGroup() != null
4101             && viewport.getSelectionGroup().getSize() == 1)
4102     {
4103       int option = JvOptionPane.showConfirmDialog(this,
4104               MessageManager.getString("warn.oneseq_msainput_selection"),
4105               MessageManager.getString("label.invalid_selection"),
4106               JvOptionPane.OK_CANCEL_OPTION);
4107       if (option == JvOptionPane.OK_OPTION)
4108       {
4109         msa = viewport.getAlignmentView(false);
4110       }
4111     }
4112     else
4113     {
4114       msa = viewport.getAlignmentView(false);
4115     }
4116     return msa;
4117   }
4118
4119   /**
4120    * Decides what is submitted to a secondary structure prediction service: the
4121    * first sequence in the alignment, or in the current selection, or, if the
4122    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4123    * region or the whole alignment. (where the first sequence in the set is the
4124    * one that the prediction will be for).
4125    */
4126   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4127   {
4128     AlignmentView seqs = null;
4129
4130     if ((viewport.getSelectionGroup() != null)
4131             && (viewport.getSelectionGroup().getSize() > 0))
4132     {
4133       seqs = viewport.getAlignmentView(true);
4134     }
4135     else
4136     {
4137       seqs = viewport.getAlignmentView(false);
4138     }
4139     // limit sequences - JBPNote in future - could spawn multiple prediction
4140     // jobs
4141     // TODO: viewport.getAlignment().isAligned is a global state - the local
4142     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4143     if (!viewport.getAlignment().isAligned(false))
4144     {
4145       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4146       // TODO: if seqs.getSequences().length>1 then should really have warned
4147       // user!
4148
4149     }
4150     return seqs;
4151   }
4152
4153   /**
4154    * DOCUMENT ME!
4155    *
4156    * @param e
4157    *          DOCUMENT ME!
4158    */
4159   @Override
4160   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4161   {
4162     // Pick the tree file
4163     JalviewFileChooser chooser = new JalviewFileChooser(
4164             Cache.getProperty("LAST_DIRECTORY"));
4165     chooser.setFileView(new JalviewFileView());
4166     chooser.setDialogTitle(
4167             MessageManager.getString("label.select_newick_like_tree_file"));
4168     chooser.setToolTipText(
4169             MessageManager.getString("label.load_tree_file"));
4170
4171     chooser.setResponseHandler(0, () -> {
4172       String filePath = chooser.getSelectedFile().getPath();
4173       Cache.setProperty("LAST_DIRECTORY", filePath);
4174       NewickFile fin = null;
4175       try
4176       {
4177         fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4178                 DataSourceType.FILE));
4179         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4180       } catch (Exception ex)
4181       {
4182         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4183                 MessageManager.getString("label.problem_reading_tree_file"),
4184                 JvOptionPane.WARNING_MESSAGE);
4185         ex.printStackTrace();
4186       }
4187       if (fin != null && fin.hasWarningMessage())
4188       {
4189         JvOptionPane.showMessageDialog(Desktop.desktop,
4190                 fin.getWarningMessage(),
4191                 MessageManager
4192                         .getString("label.possible_problem_with_tree_file"),
4193                 JvOptionPane.WARNING_MESSAGE);
4194       }
4195     });
4196     chooser.showOpenDialog(this);
4197   }
4198
4199   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4200   {
4201     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4202   }
4203
4204   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4205           int h, int x, int y)
4206   {
4207     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4208   }
4209
4210   /**
4211    * Add a treeviewer for the tree extracted from a Newick file object to the
4212    * current alignment view
4213    *
4214    * @param nf
4215    *          the tree
4216    * @param title
4217    *          tree viewer title
4218    * @param input
4219    *          Associated alignment input data (or null)
4220    * @param w
4221    *          width
4222    * @param h
4223    *          height
4224    * @param x
4225    *          position
4226    * @param y
4227    *          position
4228    * @return TreePanel handle
4229    */
4230   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4231           AlignmentView input, int w, int h, int x, int y)
4232   {
4233     TreePanel tp = null;
4234
4235     try
4236     {
4237       nf.parse();
4238
4239       if (nf.getTree() != null)
4240       {
4241         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4242
4243         tp.setSize(w, h);
4244
4245         if (x > 0 && y > 0)
4246         {
4247           tp.setLocation(x, y);
4248         }
4249
4250         Desktop.addInternalFrame(tp, treeTitle, w, h);
4251       }
4252     } catch (Exception ex)
4253     {
4254       ex.printStackTrace();
4255     }
4256
4257     return tp;
4258   }
4259
4260   public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
4261   {
4262     int x = 4, y = 5;
4263     int w = 400, h = 500;
4264
4265     try
4266     {
4267       NewickFile fin = new NewickFile(
4268               new FileParse(cm.getNewick(), DataSourceType.PASTE));
4269       String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree"
4270               + aa.sequenceRef != null
4271                       ? (" for " + aa.sequenceRef.getDisplayId(false))
4272                       : "";
4273
4274       showColumnWiseTree(fin, aa, title, w, h, x, y);
4275     } catch (Throwable xx)
4276     {
4277       Console.error("Unexpected exception showing tree for contact matrix",
4278               xx);
4279     }
4280   }
4281
4282   public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
4283           String treeTitle, int w, int h, int x, int y)
4284   {
4285     try
4286     {
4287       nf.parse();
4288       if (nf.getTree() == null)
4289       {
4290         return null;
4291       }
4292       TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
4293
4294       tp.setSize(w, h);
4295
4296       if (x > 0 && y > 0)
4297       {
4298         tp.setLocation(x, y);
4299       }
4300
4301       Desktop.addInternalFrame(tp, title, w, h);
4302       return tp;
4303     } catch (Throwable xx)
4304     {
4305       Console.error("Unexpected exception showing tree for contact matrix",
4306               xx);
4307     }
4308     return null;
4309   }
4310
4311   private boolean buildingMenu = false;
4312
4313   /**
4314    * Generates menu items and listener event actions for web service clients
4315    *
4316    */
4317   public void BuildWebServiceMenu()
4318   {
4319     while (buildingMenu)
4320     {
4321       try
4322       {
4323         System.err.println("Waiting for building menu to finish.");
4324         Thread.sleep(10);
4325       } catch (Exception e)
4326       {
4327       }
4328     }
4329     final AlignFrame me = this;
4330     buildingMenu = true;
4331     new Thread(new Runnable()
4332     {
4333       @Override
4334       public void run()
4335       {
4336         final List<JMenuItem> legacyItems = new ArrayList<>();
4337         try
4338         {
4339           // System.err.println("Building ws menu again "
4340           // + Thread.currentThread());
4341           // TODO: add support for context dependent disabling of services based
4342           // on
4343           // alignment and current selection
4344           // TODO: add additional serviceHandle parameter to specify abstract
4345           // handler
4346           // class independently of AbstractName
4347           // TODO: add in rediscovery GUI function to restart discoverer
4348           // TODO: group services by location as well as function and/or
4349           // introduce
4350           // object broker mechanism.
4351           final Vector<JMenu> wsmenu = new Vector<>();
4352           final IProgressIndicator af = me;
4353
4354           /*
4355            * do not i18n these strings - they are hard-coded in class
4356            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4357            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4358            */
4359           final JMenu msawsmenu = new JMenu("Alignment");
4360           final JMenu secstrmenu = new JMenu(
4361                   "Secondary Structure Prediction");
4362           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4363           final JMenu analymenu = new JMenu("Analysis");
4364           final JMenu dismenu = new JMenu("Protein Disorder");
4365           // JAL-940 - only show secondary structure prediction services from
4366           // the legacy server
4367           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4368               // &&
4369           Discoverer.services != null && (Discoverer.services.size() > 0))
4370           {
4371             // TODO: refactor to allow list of AbstractName/Handler bindings to
4372             // be
4373             // stored or retrieved from elsewhere
4374             // No MSAWS used any more:
4375             // Vector msaws = null; // (Vector)
4376             // Discoverer.services.get("MsaWS");
4377             Vector<ServiceHandle> secstrpr = Discoverer.services
4378                     .get("SecStrPred");
4379             if (secstrpr != null)
4380             {
4381               // Add any secondary structure prediction services
4382               for (int i = 0, j = secstrpr.size(); i < j; i++)
4383               {
4384                 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4385                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4386                         .getServiceClient(sh);
4387                 int p = secstrmenu.getItemCount();
4388                 impl.attachWSMenuEntry(secstrmenu, me);
4389                 int q = secstrmenu.getItemCount();
4390                 for (int litm = p; litm < q; litm++)
4391                 {
4392                   legacyItems.add(secstrmenu.getItem(litm));
4393                 }
4394               }
4395             }
4396           }
4397
4398           // Add all submenus in the order they should appear on the web
4399           // services menu
4400           wsmenu.add(msawsmenu);
4401           wsmenu.add(secstrmenu);
4402           wsmenu.add(dismenu);
4403           wsmenu.add(analymenu);
4404           // No search services yet
4405           // wsmenu.add(seqsrchmenu);
4406
4407           javax.swing.SwingUtilities.invokeLater(new Runnable()
4408           {
4409             @Override
4410             public void run()
4411             {
4412               try
4413               {
4414                 webService.removeAll();
4415                 // first, add discovered services onto the webservices menu
4416                 if (wsmenu.size() > 0)
4417                 {
4418                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4419                   {
4420                     webService.add(wsmenu.get(i));
4421                   }
4422                 }
4423                 else
4424                 {
4425                   webService.add(me.webServiceNoServices);
4426                 }
4427                 // TODO: move into separate menu builder class.
4428                 {
4429                   // logic for 2.11.1.4 is
4430                   // always look to see if there is a discover. if there isn't
4431                   // we can't show any Jws2 services
4432                   // if there are services available, show them - regardless of
4433                   // the 'show JWS2 preference'
4434                   // if the discoverer is running then say so
4435                   // otherwise offer to trigger discovery if 'show JWS2' is not
4436                   // enabled
4437                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4438                   if (jws2servs != null)
4439                   {
4440                     if (jws2servs.hasServices())
4441                     {
4442                       jws2servs.attachWSMenuEntry(webService, me);
4443                       for (Jws2Instance sv : jws2servs.getServices())
4444                       {
4445                         if (sv.description.toLowerCase(Locale.ROOT)
4446                                 .contains("jpred"))
4447                         {
4448                           for (JMenuItem jmi : legacyItems)
4449                           {
4450                             jmi.setVisible(false);
4451                           }
4452                         }
4453                       }
4454                     }
4455
4456                     if (jws2servs.isRunning())
4457                     {
4458                       JMenuItem tm = new JMenuItem(
4459                               "Still discovering JABA Services");
4460                       tm.setEnabled(false);
4461                       webService.add(tm);
4462                     }
4463                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4464                     {
4465                       JMenuItem enableJws2 = new JMenuItem(
4466                               "Discover Web Services");
4467                       enableJws2.setToolTipText(
4468                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4469                       enableJws2.setEnabled(true);
4470                       enableJws2.addActionListener(new ActionListener()
4471                       {
4472
4473                         @Override
4474                         public void actionPerformed(ActionEvent e)
4475                         {
4476                           // start service discoverer, but ignore preference
4477                           Desktop.instance.startServiceDiscovery(false,
4478                                   true);
4479                         }
4480                       });
4481                       webService.add(enableJws2);
4482                     }
4483                   }
4484                 }
4485                 build_urlServiceMenu(me.webService);
4486                 build_fetchdbmenu(webService);
4487                 for (JMenu item : wsmenu)
4488                 {
4489                   if (item.getItemCount() == 0)
4490                   {
4491                     item.setEnabled(false);
4492                   }
4493                   else
4494                   {
4495                     item.setEnabled(true);
4496                   }
4497                 }
4498               } catch (Exception e)
4499               {
4500                 Console.debug(
4501                         "Exception during web service menu building process.",
4502                         e);
4503               }
4504             }
4505           });
4506         } catch (Exception e)
4507         {
4508         }
4509         buildingMenu = false;
4510       }
4511     }).start();
4512
4513   }
4514
4515   /**
4516    * construct any groupURL type service menu entries.
4517    *
4518    * @param webService
4519    */
4520   protected void build_urlServiceMenu(JMenu webService)
4521   {
4522     // TODO: remove this code when 2.7 is released
4523     // DEBUG - alignmentView
4524     /*
4525      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4526      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4527      *
4528      * @Override public void actionPerformed(ActionEvent e) {
4529      * jalview.datamodel.AlignmentView
4530      * .testSelectionViews(af.viewport.getAlignment(),
4531      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4532      *
4533      * }); webService.add(testAlView);
4534      */
4535     // TODO: refactor to RestClient discoverer and merge menu entries for
4536     // rest-style services with other types of analysis/calculation service
4537     // SHmmr test client - still being implemented.
4538     // DEBUG - alignmentView
4539
4540     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4541             .getRestClients())
4542     {
4543       client.attachWSMenuEntry(
4544               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4545               this);
4546     }
4547   }
4548
4549   /**
4550    * Searches the alignment sequences for xRefs and builds the Show
4551    * Cross-References menu (formerly called Show Products), with database
4552    * sources for which cross-references are found (protein sources for a
4553    * nucleotide alignment and vice versa)
4554    *
4555    * @return true if Show Cross-references menu should be enabled
4556    */
4557   public boolean canShowProducts()
4558   {
4559     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4560     AlignmentI dataset = viewport.getAlignment().getDataset();
4561
4562     showProducts.removeAll();
4563     final boolean dna = viewport.getAlignment().isNucleotide();
4564
4565     if (seqs == null || seqs.length == 0)
4566     {
4567       // nothing to see here.
4568       return false;
4569     }
4570
4571     boolean showp = false;
4572     try
4573     {
4574       List<String> ptypes = new CrossRef(seqs, dataset)
4575               .findXrefSourcesForSequences(dna);
4576
4577       for (final String source : ptypes)
4578       {
4579         showp = true;
4580         final AlignFrame af = this;
4581         JMenuItem xtype = new JMenuItem(source);
4582         xtype.addActionListener(new ActionListener()
4583         {
4584           @Override
4585           public void actionPerformed(ActionEvent e)
4586           {
4587             showProductsFor(af.viewport.getSequenceSelection(), dna,
4588                     source);
4589           }
4590         });
4591         showProducts.add(xtype);
4592       }
4593       showProducts.setVisible(showp);
4594       showProducts.setEnabled(showp);
4595     } catch (Exception e)
4596     {
4597       Console.warn(
4598               "canShowProducts threw an exception - please report to help@jalview.org",
4599               e);
4600       return false;
4601     }
4602     return showp;
4603   }
4604
4605   /**
4606    * Finds and displays cross-references for the selected sequences (protein
4607    * products for nucleotide sequences, dna coding sequences for peptides).
4608    *
4609    * @param sel
4610    *          the sequences to show cross-references for
4611    * @param dna
4612    *          true if from a nucleotide alignment (so showing proteins)
4613    * @param source
4614    *          the database to show cross-references for
4615    */
4616   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4617           final String source)
4618   {
4619     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4620             .start();
4621   }
4622
4623   /**
4624    * Construct and display a new frame containing the translation of this
4625    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4626    */
4627   @Override
4628   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4629   {
4630     AlignmentI al = null;
4631     try
4632     {
4633       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4634
4635       al = dna.translateCdna(codeTable);
4636     } catch (Exception ex)
4637     {
4638       Console.error("Exception during translation. Please report this !",
4639               ex);
4640       final String msg = MessageManager.getString(
4641               "label.error_when_translating_sequences_submit_bug_report");
4642       final String errorTitle = MessageManager
4643               .getString("label.implementation_error")
4644               + MessageManager.getString("label.translation_failed");
4645       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4646               JvOptionPane.ERROR_MESSAGE);
4647       return;
4648     }
4649     if (al == null || al.getHeight() == 0)
4650     {
4651       final String msg = MessageManager.getString(
4652               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4653       final String errorTitle = MessageManager
4654               .getString("label.translation_failed");
4655       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4656               JvOptionPane.WARNING_MESSAGE);
4657     }
4658     else
4659     {
4660       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4661       af.setFileFormat(this.currentFileFormat);
4662       final String newTitle = MessageManager
4663               .formatMessage("label.translation_of_params", new Object[]
4664               { this.getTitle(), codeTable.getId() });
4665       af.setTitle(newTitle);
4666       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4667       {
4668         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4669         viewport.openSplitFrame(af, new Alignment(seqs));
4670       }
4671       else
4672       {
4673         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4674                 DEFAULT_HEIGHT);
4675       }
4676     }
4677   }
4678
4679   /**
4680    * Set the file format
4681    *
4682    * @param format
4683    */
4684   public void setFileFormat(FileFormatI format)
4685   {
4686     this.currentFileFormat = format;
4687   }
4688
4689   /**
4690    * Try to load a features file onto the alignment.
4691    *
4692    * @param file
4693    *          contents or path to retrieve file or a File object
4694    * @param sourceType
4695    *          access mode of file (see jalview.io.AlignFile)
4696    * @return true if features file was parsed correctly.
4697    */
4698   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4699   {
4700     // BH 2018
4701     return avc.parseFeaturesFile(file, sourceType,
4702             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4703
4704   }
4705
4706   @Override
4707   public void refreshFeatureUI(boolean enableIfNecessary)
4708   {
4709     // note - currently this is only still here rather than in the controller
4710     // because of the featureSettings hard reference that is yet to be
4711     // abstracted
4712     if (enableIfNecessary)
4713     {
4714       viewport.setShowSequenceFeatures(true);
4715       showSeqFeatures.setSelected(true);
4716     }
4717
4718   }
4719
4720   @Override
4721   public void dragEnter(DropTargetDragEvent evt)
4722   {
4723   }
4724
4725   @Override
4726   public void dragExit(DropTargetEvent evt)
4727   {
4728   }
4729
4730   @Override
4731   public void dragOver(DropTargetDragEvent evt)
4732   {
4733   }
4734
4735   @Override
4736   public void dropActionChanged(DropTargetDragEvent evt)
4737   {
4738   }
4739
4740   @Override
4741   public void drop(DropTargetDropEvent evt)
4742   {
4743     // JAL-1552 - acceptDrop required before getTransferable call for
4744     // Java's Transferable for native dnd
4745     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4746     Transferable t = evt.getTransferable();
4747
4748     final AlignFrame thisaf = this;
4749     final List<Object> files = new ArrayList<>();
4750     List<DataSourceType> protocols = new ArrayList<>();
4751
4752     try
4753     {
4754       Desktop.transferFromDropTarget(files, protocols, evt, t);
4755     } catch (Exception e)
4756     {
4757       e.printStackTrace();
4758     }
4759     if (files != null)
4760     {
4761       new Thread(new Runnable()
4762       {
4763         @Override
4764         public void run()
4765         {
4766           try
4767           {
4768             // check to see if any of these files have names matching sequences
4769             // in
4770             // the alignment
4771             SequenceIdMatcher idm = new SequenceIdMatcher(
4772                     viewport.getAlignment().getSequencesArray());
4773             /**
4774              * Object[] { String,SequenceI}
4775              */
4776             ArrayList<Object[]> filesmatched = new ArrayList<>();
4777             ArrayList<Object> filesnotmatched = new ArrayList<>();
4778             for (int i = 0; i < files.size(); i++)
4779             {
4780               // BH 2018
4781               Object file = files.get(i);
4782               String fileName = file.toString();
4783               String pdbfn = "";
4784               DataSourceType protocol = (file instanceof File
4785                       ? DataSourceType.FILE
4786                       : FormatAdapter.checkProtocol(fileName));
4787               if (protocol == DataSourceType.FILE)
4788               {
4789                 File fl;
4790                 if (file instanceof File)
4791                 {
4792                   fl = (File) file;
4793                   Platform.cacheFileData(fl);
4794                 }
4795                 else
4796                 {
4797                   fl = new File(fileName);
4798                 }
4799                 pdbfn = fl.getName();
4800               }
4801               else if (protocol == DataSourceType.URL)
4802               {
4803                 URL url = new URL(fileName);
4804                 pdbfn = url.getFile();
4805               }
4806               if (pdbfn.length() > 0)
4807               {
4808                 // attempt to find a match in the alignment
4809                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4810                 int l = 0, c = pdbfn.indexOf(".");
4811                 while (mtch == null && c != -1)
4812                 {
4813                   do
4814                   {
4815                     l = c;
4816                   } while ((c = pdbfn.indexOf(".", l)) > l);
4817                   if (l > -1)
4818                   {
4819                     pdbfn = pdbfn.substring(0, l);
4820                   }
4821                   mtch = idm.findAllIdMatches(pdbfn);
4822                 }
4823                 if (mtch != null)
4824                 {
4825                   FileFormatI type;
4826                   try
4827                   {
4828                     type = new IdentifyFile().identify(file, protocol);
4829                   } catch (Exception ex)
4830                   {
4831                     type = null;
4832                   }
4833                   if (type != null && type.isStructureFile())
4834                   {
4835                     filesmatched.add(new Object[] { file, protocol, mtch });
4836                     continue;
4837                   }
4838                 }
4839                 // File wasn't named like one of the sequences or wasn't a PDB
4840                 // file.
4841                 filesnotmatched.add(file);
4842               }
4843             }
4844             int assocfiles = 0;
4845             if (filesmatched.size() > 0)
4846             {
4847               boolean autoAssociate = Cache
4848                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4849               if (!autoAssociate)
4850               {
4851                 String msg = MessageManager.formatMessage(
4852                         "label.automatically_associate_structure_files_with_sequences_same_name",
4853                         new Object[]
4854                         { Integer.valueOf(filesmatched.size())
4855                                 .toString() });
4856                 String ttl = MessageManager.getString(
4857                         "label.automatically_associate_structure_files_by_name");
4858                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4859                         ttl, JvOptionPane.YES_NO_OPTION);
4860                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4861               }
4862               if (autoAssociate)
4863               {
4864                 for (Object[] fm : filesmatched)
4865                 {
4866                   // try and associate
4867                   // TODO: may want to set a standard ID naming formalism for
4868                   // associating PDB files which have no IDs.
4869                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4870                   {
4871                     PDBEntry pe = new AssociatePdbFileWithSeq()
4872                             .associatePdbWithSeq(fm[0].toString(),
4873                                     (DataSourceType) fm[1], toassoc, false,
4874                                     Desktop.instance);
4875                     if (pe != null)
4876                     {
4877                       System.err.println("Associated file : "
4878                               + (fm[0].toString()) + " with "
4879                               + toassoc.getDisplayId(true));
4880                       assocfiles++;
4881                     }
4882                   }
4883                   // TODO: do we need to update overview ? only if features are
4884                   // shown I guess
4885                   alignPanel.paintAlignment(true, false);
4886                 }
4887               }
4888               else
4889               {
4890                 /*
4891                  * add declined structures as sequences
4892                  */
4893                 for (Object[] o : filesmatched)
4894                 {
4895                   filesnotmatched.add(o[0]);
4896                 }
4897               }
4898             }
4899             if (filesnotmatched.size() > 0)
4900             {
4901               if (assocfiles > 0 && (Cache.getDefault(
4902                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4903                       || JvOptionPane.showConfirmDialog(thisaf,
4904                               "<html>" + MessageManager.formatMessage(
4905                                       "label.ignore_unmatched_dropped_files_info",
4906                                       new Object[]
4907                                       { Integer.valueOf(
4908                                               filesnotmatched.size())
4909                                               .toString() })
4910                                       + "</html>",
4911                               MessageManager.getString(
4912                                       "label.ignore_unmatched_dropped_files"),
4913                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4914               {
4915                 return;
4916               }
4917               for (Object fn : filesnotmatched)
4918               {
4919                 loadJalviewDataFile(fn, null, null, null);
4920               }
4921
4922             }
4923           } catch (Exception ex)
4924           {
4925             ex.printStackTrace();
4926           }
4927         }
4928       }).start();
4929     }
4930   }
4931
4932   /**
4933    * Attempt to load a "dropped" file or URL string, by testing in turn for
4934    * <ul>
4935    * <li>an Annotation file</li>
4936    * <li>a JNet file</li>
4937    * <li>a features file</li>
4938    * <li>else try to interpret as an alignment file</li>
4939    * </ul>
4940    *
4941    * @param file
4942    *          either a filename or a URL string.
4943    */
4944   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4945           FileFormatI format, SequenceI assocSeq)
4946   {
4947     // BH 2018 was String file
4948     try
4949     {
4950       if (sourceType == null)
4951       {
4952         sourceType = FormatAdapter.checkProtocol(file);
4953       }
4954       // if the file isn't identified, or not positively identified as some
4955       // other filetype (PFAM is default unidentified alignment file type) then
4956       // try to parse as annotation.
4957       boolean isAnnotation = (format == null
4958               || FileFormat.Pfam.equals(format))
4959                       ? new AnnotationFile().annotateAlignmentView(viewport,
4960                               file, sourceType)
4961                       : false;
4962
4963       if (!isAnnotation)
4964       {
4965         // first see if its a T-COFFEE score file
4966         TCoffeeScoreFile tcf = null;
4967         try
4968         {
4969           tcf = new TCoffeeScoreFile(file, sourceType);
4970           if (tcf.isValid())
4971           {
4972             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4973             {
4974               buildColourMenu();
4975               changeColour(
4976                       new TCoffeeColourScheme(viewport.getAlignment()));
4977               isAnnotation = true;
4978               setStatus(MessageManager.getString(
4979                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4980             }
4981             else
4982             {
4983               // some problem - if no warning its probable that the ID matching
4984               // process didn't work
4985               JvOptionPane.showMessageDialog(Desktop.desktop,
4986                       tcf.getWarningMessage() == null
4987                               ? MessageManager.getString(
4988                                       "label.check_file_matches_sequence_ids_alignment")
4989                               : tcf.getWarningMessage(),
4990                       MessageManager.getString(
4991                               "label.problem_reading_tcoffee_score_file"),
4992                       JvOptionPane.WARNING_MESSAGE);
4993             }
4994           }
4995           else
4996           {
4997             tcf = null;
4998           }
4999         } catch (Exception x)
5000         {
5001           Console.debug(
5002                   "Exception when processing data source as T-COFFEE score file",
5003                   x);
5004           tcf = null;
5005         }
5006         if (tcf == null)
5007         {
5008           // try to see if its a JNet 'concise' style annotation file *before*
5009           // we
5010           // try to parse it as a features file
5011           if (format == null)
5012           {
5013             format = new IdentifyFile().identify(file, sourceType);
5014           }
5015           if (FileFormat.ScoreMatrix == format)
5016           {
5017             ScoreMatrixFile sm = new ScoreMatrixFile(
5018                     new FileParse(file, sourceType));
5019             sm.parse();
5020             // todo: i18n this message
5021             setStatus(MessageManager.formatMessage(
5022                     "label.successfully_loaded_matrix",
5023                     sm.getMatrixName()));
5024           }
5025           else if (FileFormat.Jnet.equals(format))
5026           {
5027             JPredFile predictions = new JPredFile(file, sourceType);
5028             new JnetAnnotationMaker();
5029             JnetAnnotationMaker.add_annotation(predictions,
5030                     viewport.getAlignment(), 0, false);
5031             viewport.getAlignment().setupJPredAlignment();
5032             isAnnotation = true;
5033           }
5034           // else if (IdentifyFile.FeaturesFile.equals(format))
5035           else if (FileFormat.Features.equals(format))
5036           {
5037             if (parseFeaturesFile(file, sourceType))
5038             {
5039               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
5040               if (splitFrame != null)
5041               {
5042                 splitFrame.repaint();
5043               }
5044               else
5045               {
5046                 alignPanel.paintAlignment(true, true);
5047               }
5048             }
5049           }
5050           else
5051           {
5052             new FileLoader().LoadFile(viewport, file, sourceType, format);
5053           }
5054         }
5055       }
5056       if (isAnnotation)
5057       {
5058
5059         alignPanel.adjustAnnotationHeight();
5060         viewport.updateSequenceIdColours();
5061         buildSortByAnnotationScoresMenu();
5062         alignPanel.paintAlignment(true, true);
5063       }
5064     } catch (Exception ex)
5065     {
5066       ex.printStackTrace();
5067     } catch (OutOfMemoryError oom)
5068     {
5069       try
5070       {
5071         System.gc();
5072       } catch (Exception x)
5073       {
5074       }
5075       new OOMWarning(
5076               "loading data "
5077                       + (sourceType != null
5078                               ? (sourceType == DataSourceType.PASTE
5079                                       ? "from clipboard."
5080                                       : "using " + sourceType + " from "
5081                                               + file)
5082                               : ".")
5083                       + (format != null
5084                               ? "(parsing as '" + format + "' file)"
5085                               : ""),
5086               oom, Desktop.desktop);
5087     }
5088   }
5089
5090   /**
5091    * Method invoked by the ChangeListener on the tabbed pane, in other words
5092    * when a different tabbed pane is selected by the user or programmatically.
5093    */
5094   @Override
5095   public void tabSelectionChanged(int index)
5096   {
5097     if (index > -1)
5098     {
5099       /*
5100        * update current Overview window title (if there is one)
5101        * to add view name "Original" if necessary
5102        */
5103       alignPanel.setOverviewTitle(this);
5104
5105       /*
5106        * switch panels and set Overview title (if there is one
5107        * because it was opened automatically)
5108        */
5109       alignPanel = alignPanels.get(index);
5110       alignPanel.setOverviewTitle(this);
5111
5112       viewport = alignPanel.av;
5113       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5114       setMenusFromViewport(viewport);
5115       if (featureSettings != null && featureSettings.isOpen()
5116               && featureSettings.fr.getViewport() != viewport)
5117       {
5118         if (viewport.isShowSequenceFeatures())
5119         {
5120           // refresh the featureSettings to reflect UI change
5121           showFeatureSettingsUI();
5122         }
5123         else
5124         {
5125           // close feature settings for this view.
5126           featureSettings.close();
5127         }
5128       }
5129
5130     }
5131
5132     /*
5133      * 'focus' any colour slider that is open to the selected viewport
5134      */
5135     if (viewport.getConservationSelected())
5136     {
5137       SliderPanel.setConservationSlider(alignPanel,
5138               viewport.getResidueShading(), alignPanel.getViewName());
5139     }
5140     else
5141     {
5142       SliderPanel.hideConservationSlider();
5143     }
5144     if (viewport.getAbovePIDThreshold())
5145     {
5146       SliderPanel.setPIDSliderSource(alignPanel,
5147               viewport.getResidueShading(), alignPanel.getViewName());
5148     }
5149     else
5150     {
5151       SliderPanel.hidePIDSlider();
5152     }
5153
5154     /*
5155      * If there is a frame linked to this one in a SplitPane, switch it to the
5156      * same view tab index. No infinite recursion of calls should happen, since
5157      * tabSelectionChanged() should not get invoked on setting the selected
5158      * index to an unchanged value. Guard against setting an invalid index
5159      * before the new view peer tab has been created.
5160      */
5161     final AlignViewportI peer = viewport.getCodingComplement();
5162     if (peer != null)
5163     {
5164       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5165               .getAlignPanel().alignFrame;
5166       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5167       {
5168         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5169       }
5170     }
5171   }
5172
5173   /**
5174    * On right mouse click on view tab, prompt for and set new view name.
5175    */
5176   @Override
5177   public void tabbedPane_mousePressed(MouseEvent e)
5178   {
5179     if (e.isPopupTrigger())
5180     {
5181       String msg = MessageManager.getString("label.enter_view_name");
5182       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5183       String reply = JvOptionPane.showInputDialog(msg, ttl);
5184
5185       if (reply != null)
5186       {
5187         viewport.setViewName(reply);
5188         // TODO warn if reply is in getExistingViewNames()?
5189         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5190       }
5191     }
5192   }
5193
5194   public AlignViewport getCurrentView()
5195   {
5196     return viewport;
5197   }
5198
5199   /**
5200    * Open the dialog for regex description parsing.
5201    */
5202   @Override
5203   protected void extractScores_actionPerformed(ActionEvent e)
5204   {
5205     ParseProperties pp = new jalview.analysis.ParseProperties(
5206             viewport.getAlignment());
5207     // TODO: verify regex and introduce GUI dialog for version 2.5
5208     // if (pp.getScoresFromDescription("col", "score column ",
5209     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5210     // true)>0)
5211     if (pp.getScoresFromDescription("description column",
5212             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5213     {
5214       buildSortByAnnotationScoresMenu();
5215     }
5216   }
5217
5218   /*
5219    * (non-Javadoc)
5220    *
5221    * @see
5222    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5223    * )
5224    */
5225   @Override
5226   protected void showDbRefs_actionPerformed(ActionEvent e)
5227   {
5228     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5229   }
5230
5231   /*
5232    * (non-Javadoc)
5233    *
5234    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5235    * ActionEvent)
5236    */
5237   @Override
5238   protected void showNpFeats_actionPerformed(ActionEvent e)
5239   {
5240     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5241   }
5242
5243   /**
5244    * find the viewport amongst the tabs in this alignment frame and close that
5245    * tab
5246    *
5247    * @param av
5248    */
5249   public boolean closeView(AlignViewportI av)
5250   {
5251     if (viewport == av)
5252     {
5253       this.closeMenuItem_actionPerformed(false);
5254       return true;
5255     }
5256     Component[] comp = tabbedPane.getComponents();
5257     for (int i = 0; comp != null && i < comp.length; i++)
5258     {
5259       if (comp[i] instanceof AlignmentPanel)
5260       {
5261         if (((AlignmentPanel) comp[i]).av == av)
5262         {
5263           // close the view.
5264           closeView((AlignmentPanel) comp[i]);
5265           return true;
5266         }
5267       }
5268     }
5269     return false;
5270   }
5271
5272   protected void build_fetchdbmenu(JMenu webService)
5273   {
5274     // Temporary hack - DBRef Fetcher always top level ws entry.
5275     // TODO We probably want to store a sequence database checklist in
5276     // preferences and have checkboxes.. rather than individual sources selected
5277     // here
5278     final JMenu rfetch = new JMenu(
5279             MessageManager.getString("action.fetch_db_references"));
5280     rfetch.setToolTipText(MessageManager.getString(
5281             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5282     webService.add(rfetch);
5283
5284     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5285             MessageManager.getString("option.trim_retrieved_seqs"));
5286     trimrs.setToolTipText(
5287             MessageManager.getString("label.trim_retrieved_sequences"));
5288     trimrs.setSelected(
5289             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5290     trimrs.addActionListener(new ActionListener()
5291     {
5292       @Override
5293       public void actionPerformed(ActionEvent e)
5294       {
5295         trimrs.setSelected(trimrs.isSelected());
5296         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5297                 Boolean.valueOf(trimrs.isSelected()).toString());
5298       }
5299     });
5300     rfetch.add(trimrs);
5301     JMenuItem fetchr = new JMenuItem(
5302             MessageManager.getString("label.standard_databases"));
5303     fetchr.setToolTipText(
5304             MessageManager.getString("label.fetch_embl_uniprot"));
5305     fetchr.addActionListener(new ActionListener()
5306     {
5307
5308       @Override
5309       public void actionPerformed(ActionEvent e)
5310       {
5311         new Thread(new Runnable()
5312         {
5313           @Override
5314           public void run()
5315           {
5316             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5317                     .getAlignment().isNucleotide();
5318             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5319                     alignPanel.av.getSequenceSelection(),
5320                     alignPanel.alignFrame, null,
5321                     alignPanel.alignFrame.featureSettings, isNucleotide);
5322             dbRefFetcher.addListener(new FetchFinishedListenerI()
5323             {
5324               @Override
5325               public void finished()
5326               {
5327
5328                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5329                         .getFeatureSettingsModels())
5330                 {
5331
5332                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5333                 }
5334                 AlignFrame.this.setMenusForViewport();
5335               }
5336             });
5337             dbRefFetcher.fetchDBRefs(false);
5338           }
5339         }).start();
5340
5341       }
5342
5343     });
5344     rfetch.add(fetchr);
5345     new Thread(new Runnable()
5346     {
5347       @Override
5348       public void run()
5349       {
5350         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5351                 .getSequenceFetcherSingleton();
5352         javax.swing.SwingUtilities.invokeLater(new Runnable()
5353         {
5354           @Override
5355           public void run()
5356           {
5357             String[] dbclasses = sf.getNonAlignmentSources();
5358             List<DbSourceProxy> otherdb;
5359             JMenu dfetch = new JMenu();
5360             JMenu ifetch = new JMenu();
5361             JMenuItem fetchr = null;
5362             int comp = 0, icomp = 0, mcomp = 15;
5363             String mname = null;
5364             int dbi = 0;
5365             for (String dbclass : dbclasses)
5366             {
5367               otherdb = sf.getSourceProxy(dbclass);
5368               // add a single entry for this class, or submenu allowing 'fetch
5369               // all' or pick one
5370               if (otherdb == null || otherdb.size() < 1)
5371               {
5372                 continue;
5373               }
5374               if (mname == null)
5375               {
5376                 mname = "From " + dbclass;
5377               }
5378               if (otherdb.size() == 1)
5379               {
5380                 final DbSourceProxy[] dassource = otherdb
5381                         .toArray(new DbSourceProxy[0]);
5382                 DbSourceProxy src = otherdb.get(0);
5383                 fetchr = new JMenuItem(src.getDbSource());
5384                 fetchr.addActionListener(new ActionListener()
5385                 {
5386
5387                   @Override
5388                   public void actionPerformed(ActionEvent e)
5389                   {
5390                     new Thread(new Runnable()
5391                     {
5392
5393                       @Override
5394                       public void run()
5395                       {
5396                         boolean isNucleotide = alignPanel.alignFrame
5397                                 .getViewport().getAlignment()
5398                                 .isNucleotide();
5399                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5400                                 alignPanel.av.getSequenceSelection(),
5401                                 alignPanel.alignFrame, dassource,
5402                                 alignPanel.alignFrame.featureSettings,
5403                                 isNucleotide);
5404                         dbRefFetcher
5405                                 .addListener(new FetchFinishedListenerI()
5406                                 {
5407                                   @Override
5408                                   public void finished()
5409                                   {
5410                                     FeatureSettingsModelI srcSettings = dassource[0]
5411                                             .getFeatureColourScheme();
5412                                     alignPanel.av.mergeFeaturesStyle(
5413                                             srcSettings);
5414                                     AlignFrame.this.setMenusForViewport();
5415                                   }
5416                                 });
5417                         dbRefFetcher.fetchDBRefs(false);
5418                       }
5419                     }).start();
5420                   }
5421
5422                 });
5423                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5424                         MessageManager.formatMessage(
5425                                 "label.fetch_retrieve_from", new Object[]
5426                                 { src.getDbName() })));
5427                 dfetch.add(fetchr);
5428                 comp++;
5429               }
5430               else
5431               {
5432                 final DbSourceProxy[] dassource = otherdb
5433                         .toArray(new DbSourceProxy[0]);
5434                 // fetch all entry
5435                 DbSourceProxy src = otherdb.get(0);
5436                 fetchr = new JMenuItem(MessageManager
5437                         .formatMessage("label.fetch_all_param", new Object[]
5438                         { src.getDbSource() }));
5439                 fetchr.addActionListener(new ActionListener()
5440                 {
5441                   @Override
5442                   public void actionPerformed(ActionEvent e)
5443                   {
5444                     new Thread(new Runnable()
5445                     {
5446
5447                       @Override
5448                       public void run()
5449                       {
5450                         boolean isNucleotide = alignPanel.alignFrame
5451                                 .getViewport().getAlignment()
5452                                 .isNucleotide();
5453                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5454                                 alignPanel.av.getSequenceSelection(),
5455                                 alignPanel.alignFrame, dassource,
5456                                 alignPanel.alignFrame.featureSettings,
5457                                 isNucleotide);
5458                         dbRefFetcher
5459                                 .addListener(new FetchFinishedListenerI()
5460                                 {
5461                                   @Override
5462                                   public void finished()
5463                                   {
5464                                     AlignFrame.this.setMenusForViewport();
5465                                   }
5466                                 });
5467                         dbRefFetcher.fetchDBRefs(false);
5468                       }
5469                     }).start();
5470                   }
5471                 });
5472
5473                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5474                         MessageManager.formatMessage(
5475                                 "label.fetch_retrieve_from_all_sources",
5476                                 new Object[]
5477                                 { Integer.valueOf(otherdb.size())
5478                                         .toString(),
5479                                     src.getDbSource(), src.getDbName() })));
5480                 dfetch.add(fetchr);
5481                 comp++;
5482                 // and then build the rest of the individual menus
5483                 ifetch = new JMenu(MessageManager.formatMessage(
5484                         "label.source_from_db_source", new Object[]
5485                         { src.getDbSource() }));
5486                 icomp = 0;
5487                 String imname = null;
5488                 int i = 0;
5489                 for (DbSourceProxy sproxy : otherdb)
5490                 {
5491                   String dbname = sproxy.getDbName();
5492                   String sname = dbname.length() > 5
5493                           ? dbname.substring(0, 5) + "..."
5494                           : dbname;
5495                   String msname = dbname.length() > 10
5496                           ? dbname.substring(0, 10) + "..."
5497                           : dbname;
5498                   if (imname == null)
5499                   {
5500                     imname = MessageManager
5501                             .formatMessage("label.from_msname", new Object[]
5502                             { sname });
5503                   }
5504                   fetchr = new JMenuItem(msname);
5505                   final DbSourceProxy[] dassrc = { sproxy };
5506                   fetchr.addActionListener(new ActionListener()
5507                   {
5508
5509                     @Override
5510                     public void actionPerformed(ActionEvent e)
5511                     {
5512                       new Thread(new Runnable()
5513                       {
5514
5515                         @Override
5516                         public void run()
5517                         {
5518                           boolean isNucleotide = alignPanel.alignFrame
5519                                   .getViewport().getAlignment()
5520                                   .isNucleotide();
5521                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5522                                   alignPanel.av.getSequenceSelection(),
5523                                   alignPanel.alignFrame, dassrc,
5524                                   alignPanel.alignFrame.featureSettings,
5525                                   isNucleotide);
5526                           dbRefFetcher
5527                                   .addListener(new FetchFinishedListenerI()
5528                                   {
5529                                     @Override
5530                                     public void finished()
5531                                     {
5532                                       AlignFrame.this.setMenusForViewport();
5533                                     }
5534                                   });
5535                           dbRefFetcher.fetchDBRefs(false);
5536                         }
5537                       }).start();
5538                     }
5539
5540                   });
5541                   fetchr.setToolTipText(
5542                           "<html>" + MessageManager.formatMessage(
5543                                   "label.fetch_retrieve_from", new Object[]
5544                                   { dbname }));
5545                   ifetch.add(fetchr);
5546                   ++i;
5547                   if (++icomp >= mcomp || i == (otherdb.size()))
5548                   {
5549                     ifetch.setText(MessageManager.formatMessage(
5550                             "label.source_to_target", imname, sname));
5551                     dfetch.add(ifetch);
5552                     ifetch = new JMenu();
5553                     imname = null;
5554                     icomp = 0;
5555                     comp++;
5556                   }
5557                 }
5558               }
5559               ++dbi;
5560               if (comp >= mcomp || dbi >= (dbclasses.length))
5561               {
5562                 dfetch.setText(MessageManager.formatMessage(
5563                         "label.source_to_target", mname, dbclass));
5564                 rfetch.add(dfetch);
5565                 dfetch = new JMenu();
5566                 mname = null;
5567                 comp = 0;
5568               }
5569             }
5570           }
5571         });
5572       }
5573     }).start();
5574
5575   }
5576
5577   /**
5578    * Left justify the whole alignment.
5579    */
5580   @Override
5581   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5582   {
5583     AlignmentI al = viewport.getAlignment();
5584     al.justify(false);
5585     viewport.firePropertyChange("alignment", null, al);
5586   }
5587
5588   /**
5589    * Right justify the whole alignment.
5590    */
5591   @Override
5592   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5593   {
5594     AlignmentI al = viewport.getAlignment();
5595     al.justify(true);
5596     viewport.firePropertyChange("alignment", null, al);
5597   }
5598
5599   @Override
5600   public void setShowSeqFeatures(boolean b)
5601   {
5602     showSeqFeatures.setSelected(b);
5603     viewport.setShowSequenceFeatures(b);
5604   }
5605
5606   /*
5607    * (non-Javadoc)
5608    *
5609    * @see
5610    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5611    * awt.event.ActionEvent)
5612    */
5613   @Override
5614   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5615   {
5616     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5617     alignPanel.paintAlignment(false, false);
5618   }
5619
5620   /*
5621    * (non-Javadoc)
5622    *
5623    * @see
5624    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5625    * .ActionEvent)
5626    */
5627   @Override
5628   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5629   {
5630     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5631     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5632
5633   }
5634
5635   /*
5636    * (non-Javadoc)
5637    *
5638    * @see
5639    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5640    * .event.ActionEvent)
5641    */
5642   @Override
5643   protected void showGroupConservation_actionPerformed(ActionEvent e)
5644   {
5645     viewport.setShowGroupConservation(showGroupConservation.getState());
5646     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5647   }
5648
5649   /*
5650    * (non-Javadoc)
5651    *
5652    * @see
5653    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5654    * .event.ActionEvent)
5655    */
5656   @Override
5657   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5658   {
5659     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5660     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5661   }
5662
5663   /*
5664    * (non-Javadoc)
5665    *
5666    * @see
5667    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5668    * .event.ActionEvent)
5669    */
5670   @Override
5671   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5672   {
5673     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5674     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5675   }
5676
5677   @Override
5678   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5679   {
5680     showSequenceLogo.setState(true);
5681     viewport.setShowSequenceLogo(true);
5682     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5683     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5684   }
5685
5686   @Override
5687   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5688   {
5689     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5690   }
5691
5692   /*
5693    * (non-Javadoc)
5694    *
5695    * @see
5696    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5697    * .event.ActionEvent)
5698    */
5699   @Override
5700   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5701   {
5702     if (avc.makeGroupsFromSelection())
5703     {
5704       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5705       alignPanel.updateAnnotation();
5706       alignPanel.paintAlignment(true,
5707               viewport.needToUpdateStructureViews());
5708     }
5709   }
5710
5711   public void clearAlignmentSeqRep()
5712   {
5713     // TODO refactor alignmentseqrep to controller
5714     if (viewport.getAlignment().hasSeqrep())
5715     {
5716       viewport.getAlignment().setSeqrep(null);
5717       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5718       alignPanel.updateAnnotation();
5719       alignPanel.paintAlignment(true, true);
5720     }
5721   }
5722
5723   @Override
5724   protected void createGroup_actionPerformed(ActionEvent e)
5725   {
5726     if (avc.createGroup())
5727     {
5728       if (applyAutoAnnotationSettings.isSelected())
5729       {
5730         alignPanel.updateAnnotation(true, false);
5731       }
5732       alignPanel.alignmentChanged();
5733     }
5734   }
5735
5736   @Override
5737   protected void unGroup_actionPerformed(ActionEvent e)
5738   {
5739     if (avc.unGroup())
5740     {
5741       alignPanel.alignmentChanged();
5742     }
5743   }
5744
5745   /**
5746    * make the given alignmentPanel the currently selected tab
5747    *
5748    * @param alignmentPanel
5749    */
5750   public void setDisplayedView(AlignmentPanel alignmentPanel)
5751   {
5752     if (!viewport.getSequenceSetId()
5753             .equals(alignmentPanel.av.getSequenceSetId()))
5754     {
5755       throw new Error(MessageManager.getString(
5756               "error.implementation_error_cannot_show_view_alignment_frame"));
5757     }
5758     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5759             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5760     {
5761       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5762     }
5763   }
5764
5765   /**
5766    * Action on selection of menu options to Show or Hide annotations.
5767    *
5768    * @param visible
5769    * @param forSequences
5770    *          update sequence-related annotations
5771    * @param forAlignment
5772    *          update non-sequence-related annotations
5773    */
5774   @Override
5775   public void setAnnotationsVisibility(boolean visible,
5776           boolean forSequences, boolean forAlignment)
5777   {
5778     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5779             .getAlignmentAnnotation();
5780     if (anns == null)
5781     {
5782       return;
5783     }
5784     for (AlignmentAnnotation aa : anns)
5785     {
5786       /*
5787        * don't display non-positional annotations on an alignment
5788        */
5789       if (aa.annotations == null)
5790       {
5791         continue;
5792       }
5793       boolean apply = (aa.sequenceRef == null && forAlignment)
5794               || (aa.sequenceRef != null && forSequences);
5795       if (apply)
5796       {
5797         aa.visible = visible;
5798       }
5799     }
5800     alignPanel.validateAnnotationDimensions(true);
5801     alignPanel.alignmentChanged();
5802   }
5803
5804   /**
5805    * Store selected annotation sort order for the view and repaint.
5806    */
5807   @Override
5808   protected void sortAnnotations_actionPerformed()
5809   {
5810     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5811     this.alignPanel.av
5812             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5813     alignPanel.paintAlignment(false, false);
5814   }
5815
5816   /**
5817    *
5818    * @return alignment panels in this alignment frame
5819    */
5820   public List<? extends AlignmentViewPanel> getAlignPanels()
5821   {
5822     // alignPanels is never null
5823     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5824     return alignPanels;
5825   }
5826
5827   /**
5828    * Open a new alignment window, with the cDNA associated with this (protein)
5829    * alignment, aligned as is the protein.
5830    */
5831   protected void viewAsCdna_actionPerformed()
5832   {
5833     // TODO no longer a menu action - refactor as required
5834     final AlignmentI alignment = getViewport().getAlignment();
5835     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5836     if (mappings == null)
5837     {
5838       return;
5839     }
5840     List<SequenceI> cdnaSeqs = new ArrayList<>();
5841     for (SequenceI aaSeq : alignment.getSequences())
5842     {
5843       for (AlignedCodonFrame acf : mappings)
5844       {
5845         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5846         if (dnaSeq != null)
5847         {
5848           /*
5849            * There is a cDNA mapping for this protein sequence - add to new
5850            * alignment. It will share the same dataset sequence as other mapped
5851            * cDNA (no new mappings need to be created).
5852            */
5853           final Sequence newSeq = new Sequence(dnaSeq);
5854           newSeq.setDatasetSequence(dnaSeq);
5855           cdnaSeqs.add(newSeq);
5856         }
5857       }
5858     }
5859     if (cdnaSeqs.size() == 0)
5860     {
5861       // show a warning dialog no mapped cDNA
5862       return;
5863     }
5864     AlignmentI cdna = new Alignment(
5865             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5866     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5867             AlignFrame.DEFAULT_HEIGHT);
5868     cdna.alignAs(alignment);
5869     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5870             + this.title;
5871     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5872             AlignFrame.DEFAULT_HEIGHT);
5873   }
5874
5875   /**
5876    * Set visibility of dna/protein complement view (available when shown in a
5877    * split frame).
5878    *
5879    * @param show
5880    */
5881   @Override
5882   protected void showComplement_actionPerformed(boolean show)
5883   {
5884     SplitContainerI sf = getSplitViewContainer();
5885     if (sf != null)
5886     {
5887       sf.setComplementVisible(this, show);
5888     }
5889   }
5890
5891   /**
5892    * Generate the reverse (optionally complemented) of the selected sequences,
5893    * and add them to the alignment
5894    */
5895   @Override
5896   protected void showReverse_actionPerformed(boolean complement)
5897   {
5898     AlignmentI al = null;
5899     try
5900     {
5901       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5902       al = dna.reverseCdna(complement);
5903       viewport.addAlignment(al, "");
5904       addHistoryItem(new EditCommand(
5905               MessageManager.getString("label.add_sequences"), Action.PASTE,
5906               al.getSequencesArray(), 0, al.getWidth(),
5907               viewport.getAlignment()));
5908     } catch (Exception ex)
5909     {
5910       System.err.println(ex.getMessage());
5911       return;
5912     }
5913   }
5914
5915   /**
5916    * Try to run a script in the Groovy console, having first ensured that this
5917    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5918    * be targeted at this alignment.
5919    */
5920   @Override
5921   protected void runGroovy_actionPerformed()
5922   {
5923     Jalview.setCurrentAlignFrame(this);
5924     groovy.ui.Console console = Desktop.getGroovyConsole();
5925     if (console != null)
5926     {
5927       try
5928       {
5929         console.runScript();
5930       } catch (Exception ex)
5931       {
5932         System.err.println((ex.toString()));
5933         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5934                 MessageManager.getString("label.couldnt_run_groovy_script"),
5935                 MessageManager.getString("label.groovy_support_failed"),
5936                 JvOptionPane.ERROR_MESSAGE);
5937       }
5938     }
5939     else
5940     {
5941       System.err.println("Can't run Groovy script as console not found");
5942     }
5943   }
5944
5945   /**
5946    * Hides columns containing (or not containing) a specified feature, provided
5947    * that would not leave all columns hidden
5948    *
5949    * @param featureType
5950    * @param columnsContaining
5951    * @return
5952    */
5953   public boolean hideFeatureColumns(String featureType,
5954           boolean columnsContaining)
5955   {
5956     boolean notForHiding = avc.markColumnsContainingFeatures(
5957             columnsContaining, false, false, featureType);
5958     if (notForHiding)
5959     {
5960       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5961               false, featureType))
5962       {
5963         getViewport().hideSelectedColumns();
5964         return true;
5965       }
5966     }
5967     return false;
5968   }
5969
5970   @Override
5971   protected void selectHighlightedColumns_actionPerformed(
5972           ActionEvent actionEvent)
5973   {
5974     // include key modifier check in case user selects from menu
5975     avc.markHighlightedColumns(
5976             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5977             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5978                     | ActionEvent.CTRL_MASK)) != 0);
5979   }
5980
5981   @Override
5982   protected void copyHighlightedColumns_actionPerformed(
5983           ActionEvent actionEvent)
5984   {
5985     avc.copyHighlightedRegionsToClipboard();
5986   }
5987
5988   /**
5989    * Rebuilds the Colour menu, including any user-defined colours which have
5990    * been loaded either on startup or during the session
5991    */
5992   public void buildColourMenu()
5993   {
5994     colourMenu.removeAll();
5995
5996     colourMenu.add(applyToAllGroups);
5997     colourMenu.add(textColour);
5998     colourMenu.addSeparator();
5999
6000     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
6001             viewport.getAlignment(), false);
6002
6003     colourMenu.add(annotationColour);
6004     bg.add(annotationColour);
6005     colourMenu.addSeparator();
6006     colourMenu.add(conservationMenuItem);
6007     colourMenu.add(modifyConservation);
6008     colourMenu.add(abovePIDThreshold);
6009     colourMenu.add(modifyPID);
6010
6011     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
6012     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
6013   }
6014
6015   /**
6016    * Open a dialog (if not already open) that allows the user to select and
6017    * calculate PCA or Tree analysis
6018    */
6019   protected void openTreePcaDialog()
6020   {
6021     if (alignPanel.getCalculationDialog() == null)
6022     {
6023       new CalculationChooser(AlignFrame.this);
6024     }
6025   }
6026
6027   @Override
6028   protected void loadVcf_actionPerformed()
6029   {
6030     JalviewFileChooser chooser = new JalviewFileChooser(
6031             Cache.getProperty("LAST_DIRECTORY"));
6032     chooser.setFileView(new JalviewFileView());
6033     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
6034     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
6035     final AlignFrame us = this;
6036     chooser.setResponseHandler(0, () -> {
6037       String choice = chooser.getSelectedFile().getPath();
6038       Cache.setProperty("LAST_DIRECTORY", choice);
6039       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
6040       new VCFLoader(choice).loadVCF(seqs, us);
6041     });
6042     chooser.showOpenDialog(null);
6043
6044   }
6045
6046   private Rectangle lastFeatureSettingsBounds = null;
6047
6048   @Override
6049   public void setFeatureSettingsGeometry(Rectangle bounds)
6050   {
6051     lastFeatureSettingsBounds = bounds;
6052   }
6053
6054   @Override
6055   public Rectangle getFeatureSettingsGeometry()
6056   {
6057     return lastFeatureSettingsBounds;
6058   }
6059
6060 }
6061
6062 class PrintThread extends Thread
6063 {
6064   AlignmentPanel ap;
6065
6066   public PrintThread(AlignmentPanel ap)
6067   {
6068     this.ap = ap;
6069   }
6070
6071   static PageFormat pf;
6072
6073   @Override
6074   public void run()
6075   {
6076     PrinterJob printJob = PrinterJob.getPrinterJob();
6077
6078     if (pf != null)
6079     {
6080       printJob.setPrintable(ap, pf);
6081     }
6082     else
6083     {
6084       printJob.setPrintable(ap);
6085     }
6086
6087     if (printJob.printDialog())
6088     {
6089       try
6090       {
6091         printJob.print();
6092       } catch (Exception PrintException)
6093       {
6094         PrintException.printStackTrace();
6095       }
6096     }
6097   }
6098 }