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.JProgressBar;
  74 import javax.swing.JScrollPane;
  75 import javax.swing.SwingUtilities;
  76
  77 import ext.vamsas.ServiceHandle;
  78 import jalview.analysis.AlignmentSorter;
  79 import jalview.analysis.AlignmentUtils;
  80 import jalview.analysis.CrossRef;
  81 import jalview.analysis.Dna;
  82 import jalview.analysis.GeneticCodeI;
  83 import jalview.analysis.ParseProperties;
  84 import jalview.analysis.SequenceIdMatcher;
  85 import jalview.api.AlignExportSettingsI;
  86 import jalview.api.AlignViewControllerGuiI;
  87 import jalview.api.AlignViewControllerI;
  88 import jalview.api.AlignViewportI;
  89 import jalview.api.AlignmentViewPanel;
  90 import jalview.api.FeatureSettingsControllerI;
  91 import jalview.api.FeatureSettingsModelI;
  92 import jalview.api.SplitContainerI;
  93 import jalview.api.ViewStyleI;
  94 import jalview.api.analysis.SimilarityParamsI;
  95 import jalview.bin.Cache;
  96 import jalview.bin.Console;
  97 import jalview.bin.Jalview;
  98 import jalview.commands.CommandI;
  99 import jalview.commands.EditCommand;
 100 import jalview.commands.EditCommand.Action;
 101 import jalview.commands.OrderCommand;
 102 import jalview.commands.RemoveGapColCommand;
 103 import jalview.commands.RemoveGapsCommand;
 104 import jalview.commands.SlideSequencesCommand;
 105 import jalview.commands.TrimRegionCommand;
 106 import jalview.datamodel.AlignExportSettingsAdapter;
 107 import jalview.datamodel.AlignedCodonFrame;
 108 import jalview.datamodel.Alignment;
 109 import jalview.datamodel.AlignmentAnnotation;
 110 import jalview.datamodel.AlignmentExportData;
 111 import jalview.datamodel.AlignmentI;
 112 import jalview.datamodel.AlignmentOrder;
 113 import jalview.datamodel.AlignmentView;
 114 import jalview.datamodel.ColumnSelection;
 115 import jalview.datamodel.ContactMatrixI;
 116 import jalview.datamodel.HiddenColumns;
 117 import jalview.datamodel.PDBEntry;
 118 import jalview.datamodel.SeqCigar;
 119 import jalview.datamodel.Sequence;
 120 import jalview.datamodel.SequenceGroup;
 121 import jalview.datamodel.SequenceI;
 122 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 123 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 124 import jalview.io.AlignmentProperties;
 125 import jalview.io.AnnotationFile;
 126 import jalview.io.BackupFiles;
 127 import jalview.io.BioJsHTMLOutput;
 128 import jalview.io.DataSourceType;
 129 import jalview.io.FileFormat;
 130 import jalview.io.FileFormatI;
 131 import jalview.io.FileFormats;
 132 import jalview.io.FileLoader;
 133 import jalview.io.FileParse;
 134 import jalview.io.FormatAdapter;
 135 import jalview.io.HtmlSvgOutput;
 136 import jalview.io.IdentifyFile;
 137 import jalview.io.JPredFile;
 138 import jalview.io.JalviewFileChooser;
 139 import jalview.io.JalviewFileView;
 140 import jalview.io.JnetAnnotationMaker;
 141 import jalview.io.NewickFile;
 142 import jalview.io.ScoreMatrixFile;
 143 import jalview.io.TCoffeeScoreFile;
 144 import jalview.io.exceptions.ImageOutputException;
 145 import jalview.io.vcf.VCFLoader;
 146 import jalview.jbgui.GAlignFrame;
 147 import jalview.project.Jalview2XML;
 148 import jalview.schemes.ColourSchemeI;
 149 import jalview.schemes.ColourSchemes;
 150 import jalview.schemes.ResidueColourScheme;
 151 import jalview.schemes.TCoffeeColourScheme;
 152 import jalview.util.HttpUtils;
 153 import jalview.util.ImageMaker.TYPE;
 154 import jalview.util.MessageManager;
 155 import jalview.util.Platform;
 156 import jalview.util.imagemaker.BitmapImageSizing;
 157 import jalview.viewmodel.AlignmentViewport;
 158 import jalview.viewmodel.ViewportRanges;
 159 import jalview.ws.DBRefFetcher;
 160 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 161 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 162 import jalview.ws.jws1.Discoverer;
 163 import jalview.ws.jws2.Jws2Discoverer;
 164 import jalview.ws.jws2.jabaws2.Jws2Instance;
 165 import jalview.ws.seqfetcher.DbSourceProxy;
 166
 167 /**
 168  * DOCUMENT ME!
 169  *
 170  * @author $author$
 171  * @version $Revision$
 172  */
 173 @SuppressWarnings("serial")
 174 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 175         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 176 {
 177
 178   public static final int DEFAULT_WIDTH = 700;
 179
 180   public static final int DEFAULT_HEIGHT = 500;
 181
 182   /*
 183    * The currently displayed panel (selected tabbed view if more than one)
 184    */
 185   public AlignmentPanel alignPanel;
 186
 187   AlignViewport viewport;
 188
 189   public AlignViewControllerI avc;
 190
 191   List<AlignmentPanel> alignPanels = new ArrayList<>();
 192
 193   /**
 194    * Last format used to load or save alignments in this window
 195    */
 196   FileFormatI currentFileFormat = null;
 197
 198   /**
 199    * Current filename for this alignment
 200    */
 201   String fileName = null;
 202
 203   File fileObject;
 204
 205   /**
 206    * Creates a new AlignFrame object with specific width and height.
 207    *
 208    * @param al
 209    * @param width
 210    * @param height
 211    */
 212   public AlignFrame(AlignmentI al, int width, int height)
 213   {
 214     this(al, null, width, height);
 215   }
 216
 217   /**
 218    * Creates a new AlignFrame object with specific width, height and
 219    * sequenceSetId
 220    *
 221    * @param al
 222    * @param width
 223    * @param height
 224    * @param sequenceSetId
 225    */
 226   public AlignFrame(AlignmentI al, int width, int height,
 227           String sequenceSetId)
 228   {
 229     this(al, null, width, height, sequenceSetId);
 230   }
 231
 232   /**
 233    * Creates a new AlignFrame object with specific width, height and
 234    * sequenceSetId
 235    *
 236    * @param al
 237    * @param width
 238    * @param height
 239    * @param sequenceSetId
 240    * @param viewId
 241    */
 242   public AlignFrame(AlignmentI al, int width, int height,
 243           String sequenceSetId, String viewId)
 244   {
 245     this(al, null, width, height, sequenceSetId, viewId);
 246   }
 247
 248   /**
 249    * new alignment window with hidden columns
 250    *
 251    * @param al
 252    *          AlignmentI
 253    * @param hiddenColumns
 254    *          ColumnSelection or null
 255    * @param width
 256    *          Width of alignment frame
 257    * @param height
 258    *          height of frame.
 259    */
 260   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 261           int height)
 262   {
 263     this(al, hiddenColumns, width, height, null);
 264   }
 265
 266   /**
 267    * Create alignment frame for al with hiddenColumns, a specific width and
 268    * height, and specific sequenceId
 269    *
 270    * @param al
 271    * @param hiddenColumns
 272    * @param width
 273    * @param height
 274    * @param sequenceSetId
 275    *          (may be null)
 276    */
 277   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 278           int height, String sequenceSetId)
 279   {
 280     this(al, hiddenColumns, width, height, sequenceSetId, null);
 281   }
 282
 283   /**
 284    * Create alignment frame for al with hiddenColumns, a specific width and
 285    * height, and specific sequenceId
 286    *
 287    * @param al
 288    * @param hiddenColumns
 289    * @param width
 290    * @param height
 291    * @param sequenceSetId
 292    *          (may be null)
 293    * @param viewId
 294    *          (may be null)
 295    */
 296   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 297           int height, String sequenceSetId, String viewId)
 298   {
 299     setSize(width, height);
 300
 301     if (al.getDataset() == null)
 302     {
 303       al.setDataset(null);
 304     }
 305
 306     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 307
 308     alignPanel = new AlignmentPanel(this, viewport);
 309
 310     addAlignmentPanel(alignPanel, true);
 311     init();
 312   }
 313
 314   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 315           HiddenColumns hiddenColumns, int width, int height)
 316   {
 317     setSize(width, height);
 318
 319     if (al.getDataset() == null)
 320     {
 321       al.setDataset(null);
 322     }
 323
 324     viewport = new AlignViewport(al, hiddenColumns);
 325
 326     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 327     {
 328       viewport.hideSequence(hiddenSeqs);
 329     }
 330     alignPanel = new AlignmentPanel(this, viewport);
 331     addAlignmentPanel(alignPanel, true);
 332     init();
 333   }
 334
 335   /**
 336    * Make a new AlignFrame from existing alignmentPanels
 337    *
 338    * @param ap
 339    *          AlignmentPanel
 340    * @param av
 341    *          AlignViewport
 342    */
 343   public AlignFrame(AlignmentPanel ap)
 344   {
 345     viewport = ap.av;
 346     alignPanel = ap;
 347     addAlignmentPanel(ap, false);
 348     init();
 349   }
 350
 351   /**
 352    * initalise the alignframe from the underlying viewport data and the
 353    * configurations
 354    */
 355   void init()
 356   {
 357     setFrameIcon(null);
 358
 359     // setBackground(Color.white); // BH 2019
 360
 361     if (!Jalview.isHeadlessMode())
 362     {
 363       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 364     }
 365
 366     avc = new jalview.controller.AlignViewController(this, viewport,
 367             alignPanel);
 368     if (viewport.getAlignmentConservationAnnotation() == null)
 369     {
 370       // BLOSUM62Colour.setEnabled(false);
 371       conservationMenuItem.setEnabled(false);
 372       modifyConservation.setEnabled(false);
 373       // PIDColour.setEnabled(false);
 374       // abovePIDThreshold.setEnabled(false);
 375       // modifyPID.setEnabled(false);
 376     }
 377
 378     String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 379
 380     if (sortby.equals("Id"))
 381     {
 382       sortIDMenuItem_actionPerformed(null);
 383     }
 384     else if (sortby.equals("Pairwise Identity"))
 385     {
 386       sortPairwiseMenuItem_actionPerformed(null);
 387     }
 388
 389     this.alignPanel.av
 390             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 391
 392     setMenusFromViewport(viewport);
 393     buildSortByAnnotationScoresMenu();
 394     calculateTree.addActionListener(new ActionListener()
 395     {
 396
 397       @Override
 398       public void actionPerformed(ActionEvent e)
 399       {
 400         openTreePcaDialog();
 401       }
 402     });
 403     buildColourMenu();
 404
 405     if (Desktop.desktop != null)
 406     {
 407       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 408       if (!Platform.isJS())
 409       {
 410         addServiceListeners();
 411       }
 412       setGUINucleotide();
 413     }
 414
 415     if (viewport.getWrapAlignment())
 416     {
 417       wrapMenuItem_actionPerformed(null);
 418     }
 419
 420     if (Cache.getDefault("SHOW_OVERVIEW", false))
 421     {
 422       this.overviewMenuItem_actionPerformed(null);
 423     }
 424
 425     addKeyListener();
 426
 427     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 428     final List<AlignmentPanel> origview = new ArrayList<>();
 429     final String menuLabel = MessageManager
 430             .getString("label.copy_format_from");
 431     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 432             new ViewSetProvider()
 433             {
 434
 435               @Override
 436               public AlignmentPanel[] getAllAlignmentPanels()
 437               {
 438                 origview.clear();
 439                 origview.add(alignPanel);
 440                 // make an array of all alignment panels except for this one
 441                 List<AlignmentPanel> aps = new ArrayList<>(
 442                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 443                 aps.remove(AlignFrame.this.alignPanel);
 444                 return aps.toArray(new AlignmentPanel[aps.size()]);
 445               }
 446             }, selviews, new ItemListener()
 447             {
 448
 449               @Override
 450               public void itemStateChanged(ItemEvent e)
 451               {
 452                 if (origview.size() > 0)
 453                 {
 454                   final AlignmentPanel ap = origview.get(0);
 455
 456                   /*
 457                    * Copy the ViewStyle of the selected panel to 'this one'.
 458                    * Don't change value of 'scaleProteinAsCdna' unless copying
 459                    * from a SplitFrame.
 460                    */
 461                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 462                           .getViewStyle();
 463                   boolean fromSplitFrame = selviews.get(0)
 464                           .getAlignViewport().getCodingComplement() != null;
 465                   if (!fromSplitFrame)
 466                   {
 467                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 468                             .getViewStyle().isScaleProteinAsCdna());
 469                   }
 470                   ap.getAlignViewport().setViewStyle(vs);
 471
 472                   /*
 473                    * Also rescale ViewStyle of SplitFrame complement if there is
 474                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 475                    * the whole ViewStyle (allow cDNA protein to have different
 476                    * fonts)
 477                    */
 478                   AlignViewportI complement = ap.getAlignViewport()
 479                           .getCodingComplement();
 480                   if (complement != null && vs.isScaleProteinAsCdna())
 481                   {
 482                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 483                     ((SplitFrame) af.getSplitViewContainer())
 484                             .adjustLayout();
 485                     af.setMenusForViewport();
 486                   }
 487
 488                   ap.updateLayout();
 489                   ap.setSelected(true);
 490                   ap.alignFrame.setMenusForViewport();
 491
 492                 }
 493               }
 494             });
 495     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
 496             .indexOf("devel") > -1
 497             || Cache.getDefault("VERSION", "DEVELOPMENT")
 498                     .toLowerCase(Locale.ROOT).indexOf("test") > -1)
 499     {
 500       formatMenu.add(vsel);
 501     }
 502     addFocusListener(new FocusAdapter()
 503     {
 504       @Override
 505       public void focusGained(FocusEvent e)
 506       {
 507         Jalview.setCurrentAlignFrame(AlignFrame.this);
 508       }
 509     });
 510
 511   }
 512
 513   /**
 514    * Change the filename and format for the alignment, and enable the 'reload'
 515    * button functionality.
 516    *
 517    * @param file
 518    *          valid filename
 519    * @param format
 520    *          format of file
 521    */
 522   public void setFileName(String file, FileFormatI format)
 523   {
 524     fileName = file;
 525     setFileFormat(format);
 526     reload.setEnabled(true);
 527   }
 528
 529   /**
 530    * JavaScript will have this, maybe others. More dependable than a file name
 531    * and maintains a reference to the actual bytes loaded.
 532    *
 533    * @param file
 534    */
 535   public void setFileObject(File file)
 536   {
 537     this.fileObject = file;
 538   }
 539
 540   /**
 541    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 542    * events
 543    */
 544   void addKeyListener()
 545   {
 546     addKeyListener(new KeyAdapter()
 547     {
 548       @Override
 549       public void keyPressed(KeyEvent evt)
 550       {
 551         if (viewport.cursorMode
 552                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 553                         && evt.getKeyCode() <= KeyEvent.VK_9)
 554                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 555                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 556                 && Character.isDigit(evt.getKeyChar()))
 557         {
 558           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 559         }
 560
 561         switch (evt.getKeyCode())
 562         {
 563
 564         case 27: // escape key
 565           deselectAllSequenceMenuItem_actionPerformed(null);
 566
 567           break;
 568
 569         case KeyEvent.VK_DOWN:
 570           if (evt.isAltDown() || !viewport.cursorMode)
 571           {
 572             moveSelectedSequences(false);
 573           }
 574           if (viewport.cursorMode)
 575           {
 576             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 577           }
 578           break;
 579
 580         case KeyEvent.VK_UP:
 581           if (evt.isAltDown() || !viewport.cursorMode)
 582           {
 583             moveSelectedSequences(true);
 584           }
 585           if (viewport.cursorMode)
 586           {
 587             alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
 588           }
 589
 590           break;
 591
 592         case KeyEvent.VK_LEFT:
 593           if (evt.isAltDown() || !viewport.cursorMode)
 594           {
 595             slideSequences(false,
 596                     alignPanel.getSeqPanel().getKeyboardNo1());
 597           }
 598           else
 599           {
 600             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 601           }
 602
 603           break;
 604
 605         case KeyEvent.VK_RIGHT:
 606           if (evt.isAltDown() || !viewport.cursorMode)
 607           {
 608             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 609           }
 610           else
 611           {
 612             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 613           }
 614           break;
 615
 616         case KeyEvent.VK_SPACE:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 620                     || evt.isShiftDown() || evt.isAltDown());
 621           }
 622           break;
 623
 624         // case KeyEvent.VK_A:
 625         // if (viewport.cursorMode)
 626         // {
 627         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 628         // //System.out.println("A");
 629         // }
 630         // break;
 631         /*
 632          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 633          * System.out.println("closing bracket"); } break;
 634          */
 635         case KeyEvent.VK_DELETE:
 636         case KeyEvent.VK_BACK_SPACE:
 637           if (!viewport.cursorMode)
 638           {
 639             cut_actionPerformed();
 640           }
 641           else
 642           {
 643             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 644                     || evt.isShiftDown() || evt.isAltDown());
 645           }
 646
 647           break;
 648
 649         case KeyEvent.VK_S:
 650           if (viewport.cursorMode)
 651           {
 652             alignPanel.getSeqPanel().setCursorRow();
 653           }
 654           break;
 655         case KeyEvent.VK_C:
 656           if (viewport.cursorMode && !evt.isControlDown())
 657           {
 658             alignPanel.getSeqPanel().setCursorColumn();
 659           }
 660           break;
 661         case KeyEvent.VK_P:
 662           if (viewport.cursorMode)
 663           {
 664             alignPanel.getSeqPanel().setCursorPosition();
 665           }
 666           break;
 667
 668         case KeyEvent.VK_ENTER:
 669         case KeyEvent.VK_COMMA:
 670           if (viewport.cursorMode)
 671           {
 672             alignPanel.getSeqPanel().setCursorRowAndColumn();
 673           }
 674           break;
 675
 676         case KeyEvent.VK_Q:
 677           if (viewport.cursorMode)
 678           {
 679             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 680           }
 681           break;
 682         case KeyEvent.VK_M:
 683           if (viewport.cursorMode)
 684           {
 685             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 686           }
 687           break;
 688
 689         case KeyEvent.VK_F2:
 690           viewport.cursorMode = !viewport.cursorMode;
 691           setStatus(MessageManager
 692                   .formatMessage("label.keyboard_editing_mode", new String[]
 693                   { (viewport.cursorMode ? "on" : "off") }));
 694           if (viewport.cursorMode)
 695           {
 696             ViewportRanges ranges = viewport.getRanges();
 697             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 698                     .getStartRes();
 699             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 700                     .getStartSeq();
 701           }
 702           alignPanel.getSeqPanel().seqCanvas.repaint();
 703           break;
 704
 705         case KeyEvent.VK_F1:
 706           try
 707           {
 708             Help.showHelpWindow();
 709           } catch (Exception ex)
 710           {
 711             ex.printStackTrace();
 712           }
 713           break;
 714         case KeyEvent.VK_H:
 715         {
 716           boolean toggleSeqs = !evt.isControlDown();
 717           boolean toggleCols = !evt.isShiftDown();
 718           toggleHiddenRegions(toggleSeqs, toggleCols);
 719           break;
 720         }
 721         case KeyEvent.VK_B:
 722         {
 723           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 724           boolean modifyExisting = true; // always modify, don't clear
 725                                          // evt.isShiftDown();
 726           boolean invertHighlighted = evt.isAltDown();
 727           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 728                   toggleSel);
 729           break;
 730         }
 731         case KeyEvent.VK_PAGE_UP:
 732           viewport.getRanges().pageUp();
 733           break;
 734         case KeyEvent.VK_PAGE_DOWN:
 735           viewport.getRanges().pageDown();
 736           break;
 737         }
 738       }
 739
 740       @Override
 741       public void keyReleased(KeyEvent evt)
 742       {
 743         switch (evt.getKeyCode())
 744         {
 745         case KeyEvent.VK_LEFT:
 746           if (evt.isAltDown() || !viewport.cursorMode)
 747           {
 748             viewport.firePropertyChange("alignment", null,
 749                     viewport.getAlignment().getSequences());
 750           }
 751           break;
 752
 753         case KeyEvent.VK_RIGHT:
 754           if (evt.isAltDown() || !viewport.cursorMode)
 755           {
 756             viewport.firePropertyChange("alignment", null,
 757                     viewport.getAlignment().getSequences());
 758           }
 759           break;
 760         }
 761       }
 762     });
 763   }
 764
 765   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 766   {
 767     ap.alignFrame = this;
 768     avc = new jalview.controller.AlignViewController(this, viewport,
 769             alignPanel);
 770
 771     alignPanels.add(ap);
 772
 773     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 774
 775     int aSize = alignPanels.size();
 776
 777     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 778
 779     if (aSize == 1 && ap.av.getViewName() == null)
 780     {
 781       this.getContentPane().add(ap, BorderLayout.CENTER);
 782     }
 783     else
 784     {
 785       if (aSize == 2)
 786       {
 787         setInitialTabVisible();
 788       }
 789
 790       expandViews.setEnabled(true);
 791       gatherViews.setEnabled(true);
 792       tabbedPane.addTab(ap.av.getViewName(), ap);
 793
 794       ap.setVisible(false);
 795     }
 796
 797     if (newPanel)
 798     {
 799       if (ap.av.isPadGaps())
 800       {
 801         ap.av.getAlignment().padGaps();
 802       }
 803       ap.av.updateConservation(ap);
 804       ap.av.updateConsensus(ap);
 805       ap.av.updateStrucConsensus(ap);
 806     }
 807   }
 808
 809   public void setInitialTabVisible()
 810   {
 811     expandViews.setEnabled(true);
 812     gatherViews.setEnabled(true);
 813     tabbedPane.setVisible(true);
 814     AlignmentPanel first = alignPanels.get(0);
 815     tabbedPane.addTab(first.av.getViewName(), first);
 816     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 817   }
 818
 819   public AlignViewport getViewport()
 820   {
 821     return viewport;
 822   }
 823
 824   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 825   private void addServiceListeners()
 826   {
 827     final java.beans.PropertyChangeListener thisListener;
 828     Desktop.instance.addJalviewPropertyChangeListener("services",
 829             thisListener = new java.beans.PropertyChangeListener()
 830             {
 831               @Override
 832               public void propertyChange(PropertyChangeEvent evt)
 833               {
 834                 // // System.out.println("Discoverer property change.");
 835                 // if (evt.getPropertyName().equals("services"))
 836                 {
 837                   SwingUtilities.invokeLater(new Runnable()
 838                   {
 839
 840                     @Override
 841                     public void run()
 842                     {
 843                       System.err.println(
 844                               "Rebuild WS Menu for service change");
 845                       BuildWebServiceMenu();
 846                     }
 847
 848                   });
 849                 }
 850               }
 851             });
 852     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 853     {
 854       @Override
 855       public void internalFrameClosed(
 856               javax.swing.event.InternalFrameEvent evt)
 857       {
 858         // System.out.println("deregistering discoverer listener");
 859         Desktop.instance.removeJalviewPropertyChangeListener("services",
 860                 thisListener);
 861         closeMenuItem_actionPerformed(true);
 862       }
 863     });
 864     // Finally, build the menu once to get current service state
 865     new Thread(new Runnable()
 866     {
 867       @Override
 868       public void run()
 869       {
 870         BuildWebServiceMenu();
 871       }
 872     }).start();
 873   }
 874
 875   /**
 876    * Configure menu items that vary according to whether the alignment is
 877    * nucleotide or protein
 878    */
 879   public void setGUINucleotide()
 880   {
 881     AlignmentI al = getViewport().getAlignment();
 882     boolean nucleotide = al.isNucleotide();
 883
 884     loadVcf.setVisible(nucleotide);
 885     showTranslation.setVisible(nucleotide);
 886     showReverse.setVisible(nucleotide);
 887     showReverseComplement.setVisible(nucleotide);
 888     conservationMenuItem.setEnabled(!nucleotide);
 889     modifyConservation
 890             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 891     showGroupConservation.setEnabled(!nucleotide);
 892
 893     showComplementMenuItem
 894             .setText(nucleotide ? MessageManager.getString("label.protein")
 895                     : MessageManager.getString("label.nucleotide"));
 896   }
 897
 898   /**
 899    * set up menus for the current viewport. This may be called after any
 900    * operation that affects the data in the current view (selection changed,
 901    * etc) to update the menus to reflect the new state.
 902    */
 903   @Override
 904   public void setMenusForViewport()
 905   {
 906     setMenusFromViewport(viewport);
 907   }
 908
 909   /**
 910    * Need to call this method when tabs are selected for multiple views, or when
 911    * loading from Jalview2XML.java
 912    *
 913    * @param av
 914    *          AlignViewport
 915    */
 916   public void setMenusFromViewport(AlignViewport av)
 917   {
 918     padGapsMenuitem.setSelected(av.isPadGaps());
 919     colourTextMenuItem.setSelected(av.isShowColourText());
 920     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 921     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 922     conservationMenuItem.setSelected(av.getConservationSelected());
 923     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 924     seqLimits.setSelected(av.getShowJVSuffix());
 925     idRightAlign.setSelected(av.isRightAlignIds());
 926     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 927     renderGapsMenuItem.setSelected(av.isRenderGaps());
 928     wrapMenuItem.setSelected(av.getWrapAlignment());
 929     scaleAbove.setVisible(av.getWrapAlignment());
 930     scaleLeft.setVisible(av.getWrapAlignment());
 931     scaleRight.setVisible(av.getWrapAlignment());
 932     annotationPanelMenuItem.setState(av.isShowAnnotation());
 933     /*
 934      * Show/hide annotations only enabled if annotation panel is shown
 935      */
 936     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 937     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 938     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 939     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 940     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 941     viewTextMenuItem.setSelected(av.getShowText());
 942     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 943     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 944     showGroupConservation.setSelected(av.isShowGroupConservation());
 945     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 946     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 947     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 948
 949     ColourMenuHelper.setColourSelected(colourMenu,
 950             av.getGlobalColourScheme());
 951
 952     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 953     hiddenMarkers.setState(av.getShowHiddenMarkers());
 954     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 955     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 956     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 957     autoCalculate.setSelected(av.autoCalculateConsensus);
 958     sortByTree.setSelected(av.sortByTree);
 959     listenToViewSelections.setSelected(av.followSelection);
 960
 961     showProducts.setEnabled(canShowProducts());
 962     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 963
 964     updateEditMenuBar();
 965   }
 966
 967   /**
 968    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 969    *
 970    * @param b
 971    */
 972   public void setGroovyEnabled(boolean b)
 973   {
 974     runGroovy.setEnabled(b);
 975   }
 976
 977   private IProgressIndicator progressBar;
 978
 979   /*
 980    * (non-Javadoc)
 981    *
 982    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 983    */
 984   @Override
 985   public void setProgressBar(String message, long id)
 986   {
 987     if (!Platform.isHeadless() && progressBar != null)
 988       progressBar.setProgressBar(message, id);
 989   }
 990
 991   @Override
 992   public JProgressBar getProgressBar(long id)
 993   {
 994     if (progressBar != null)
 995       return progressBar.getProgressBar(id);
 996     return null;
 997   }
 998
 999   @Override
1000   public void registerHandler(final long id,
1001           final IProgressIndicatorHandler handler)
1002   {
1003     if (progressBar != null)
1004       progressBar.registerHandler(id, handler);
1005   }
1006
1007   /**
1008    *
1009    * @return true if any progress bars are still active
1010    */
1011   @Override
1012   public boolean operationInProgress()
1013   {
1014     return progressBar == null ? false : progressBar.operationInProgress();
1015   }
1016
1017   /**
1018    * Sets the text of the status bar. Note that setting a null or empty value
1019    * will cause the status bar to be hidden, with possibly undesirable flicker
1020    * of the screen layout.
1021    */
1022   @Override
1023   public void setStatus(String text)
1024   {
1025     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1026   }
1027
1028   /*
1029    * Added so Castor Mapping file can obtain Jalview Version
1030    */
1031   public String getVersion()
1032   {
1033     return Cache.getProperty("VERSION");
1034   }
1035
1036   public FeatureRenderer getFeatureRenderer()
1037   {
1038     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1039   }
1040
1041   @Override
1042   public void fetchSequence_actionPerformed()
1043   {
1044     new SequenceFetcher(this);
1045   }
1046
1047   @Override
1048   public void addFromFile_actionPerformed(ActionEvent e)
1049   {
1050     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1051   }
1052
1053   @Override
1054   public void reload_actionPerformed(ActionEvent e)
1055   {
1056     if (fileName != null)
1057     {
1058       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1059       // originating file's format
1060       // TODO: work out how to recover feature settings for correct view(s) when
1061       // file is reloaded.
1062       if (FileFormat.Jalview.equals(currentFileFormat))
1063       {
1064         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1065         for (int i = 0; i < frames.length; i++)
1066         {
1067           if (frames[i] instanceof AlignFrame && frames[i] != this
1068                   && ((AlignFrame) frames[i]).fileName != null
1069                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1070           {
1071             try
1072             {
1073               frames[i].setSelected(true);
1074               Desktop.instance.closeAssociatedWindows();
1075             } catch (java.beans.PropertyVetoException ex)
1076             {
1077             }
1078           }
1079
1080         }
1081         Desktop.instance.closeAssociatedWindows();
1082
1083         FileLoader loader = new FileLoader();
1084         DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1085                 ? DataSourceType.URL
1086                 : DataSourceType.FILE;
1087         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1088       }
1089       else
1090       {
1091         Rectangle bounds = this.getBounds();
1092
1093         FileLoader loader = new FileLoader();
1094
1095         AlignFrame newframe = null;
1096
1097         if (fileObject == null)
1098         {
1099
1100           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1101                   fileName) ? DataSourceType.URL : DataSourceType.FILE;
1102           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1103                   currentFileFormat);
1104         }
1105         else
1106         {
1107           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1108                   DataSourceType.FILE, currentFileFormat);
1109         }
1110
1111         newframe.setBounds(bounds);
1112         if (featureSettings != null && featureSettings.isShowing())
1113         {
1114           final Rectangle fspos = featureSettings.frame.getBounds();
1115           // TODO: need a 'show feature settings' function that takes bounds -
1116           // need to refactor Desktop.addFrame
1117           newframe.featureSettings_actionPerformed(null);
1118           final FeatureSettings nfs = newframe.featureSettings;
1119           SwingUtilities.invokeLater(new Runnable()
1120           {
1121             @Override
1122             public void run()
1123             {
1124               nfs.frame.setBounds(fspos);
1125             }
1126           });
1127           this.featureSettings.close();
1128           this.featureSettings = null;
1129         }
1130         this.closeMenuItem_actionPerformed(true);
1131       }
1132     }
1133   }
1134
1135   @Override
1136   public void addFromText_actionPerformed(ActionEvent e)
1137   {
1138     Desktop.instance
1139             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1140   }
1141
1142   @Override
1143   public void addFromURL_actionPerformed(ActionEvent e)
1144   {
1145     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1146   }
1147
1148   @Override
1149   public void save_actionPerformed(ActionEvent e)
1150   {
1151     if (fileName == null || (currentFileFormat == null)
1152             || HttpUtils.startsWithHttpOrHttps(fileName))
1153     {
1154       saveAs_actionPerformed();
1155     }
1156     else
1157     {
1158       saveAlignment(fileName, currentFileFormat);
1159     }
1160   }
1161
1162   /**
1163    * Saves the alignment to a file with a name chosen by the user, if necessary
1164    * warning if a file would be overwritten
1165    */
1166   @Override
1167   public void saveAs_actionPerformed()
1168   {
1169     String format = currentFileFormat == null ? null
1170             : currentFileFormat.getName();
1171     JalviewFileChooser chooser = JalviewFileChooser
1172             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1173
1174     chooser.setFileView(new JalviewFileView());
1175     chooser.setDialogTitle(
1176             MessageManager.getString("label.save_alignment_to_file"));
1177     chooser.setToolTipText(MessageManager.getString("action.save"));
1178
1179     int value = chooser.showSaveDialog(this);
1180
1181     if (value != JalviewFileChooser.APPROVE_OPTION)
1182     {
1183       return;
1184     }
1185     currentFileFormat = chooser.getSelectedFormat();
1186     // todo is this (2005) test now obsolete - value is never null?
1187     while (currentFileFormat == null)
1188     {
1189       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1190               MessageManager
1191                       .getString("label.select_file_format_before_saving"),
1192               MessageManager.getString("label.file_format_not_specified"),
1193               JvOptionPane.WARNING_MESSAGE);
1194       currentFileFormat = chooser.getSelectedFormat();
1195       value = chooser.showSaveDialog(this);
1196       if (value != JalviewFileChooser.APPROVE_OPTION)
1197       {
1198         return;
1199       }
1200     }
1201
1202     fileName = chooser.getSelectedFile().getPath();
1203
1204     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1205     Cache.setProperty("LAST_DIRECTORY", fileName);
1206     saveAlignment(fileName, currentFileFormat);
1207   }
1208
1209   boolean lastSaveSuccessful = false;
1210
1211   FileFormatI lastFormatSaved;
1212
1213   String lastFilenameSaved;
1214
1215   /**
1216    * Raise a dialog or status message for the last call to saveAlignment.
1217    *
1218    * @return true if last call to saveAlignment(file, format) was successful.
1219    */
1220   public boolean isSaveAlignmentSuccessful()
1221   {
1222
1223     if (!lastSaveSuccessful)
1224     {
1225       if (!Platform.isHeadless())
1226       {
1227         JvOptionPane.showInternalMessageDialog(this, MessageManager
1228                 .formatMessage("label.couldnt_save_file", new Object[]
1229                 { lastFilenameSaved }),
1230                 MessageManager.getString("label.error_saving_file"),
1231                 JvOptionPane.WARNING_MESSAGE);
1232       }
1233       else
1234       {
1235         Console.error(MessageManager
1236                 .formatMessage("label.couldnt_save_file", new Object[]
1237                 { lastFilenameSaved }));
1238       }
1239     }
1240     else
1241     {
1242
1243       setStatus(MessageManager.formatMessage(
1244               "label.successfully_saved_to_file_in_format", new Object[]
1245               { lastFilenameSaved, lastFormatSaved }));
1246
1247     }
1248     return lastSaveSuccessful;
1249   }
1250
1251   /**
1252    * Saves the alignment to the specified file path, in the specified format,
1253    * which may be an alignment format, or Jalview project format. If the
1254    * alignment has hidden regions, or the format is one capable of including
1255    * non-sequence data (features, annotations, groups), then the user may be
1256    * prompted to specify what to include in the output.
1257    *
1258    * @param file
1259    * @param format
1260    */
1261   public void saveAlignment(String file, FileFormatI format)
1262   {
1263     lastSaveSuccessful = true;
1264     lastFilenameSaved = file;
1265     lastFormatSaved = format;
1266
1267     if (FileFormat.Jalview.equals(format))
1268     {
1269       String shortName = title;
1270       if (shortName.indexOf(File.separatorChar) > -1)
1271       {
1272         shortName = shortName
1273                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1274       }
1275       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1276               shortName);
1277
1278       Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1279       if (lastSaveSuccessful)
1280       {
1281         this.getViewport().setSavedUpToDate(true);
1282       }
1283
1284       statusBar.setText(MessageManager.formatMessage(
1285               "label.successfully_saved_to_file_in_format", new Object[]
1286               { file, format }));
1287
1288       return;
1289     }
1290
1291     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1292     Runnable cancelAction = () -> {
1293       lastSaveSuccessful = false;
1294     };
1295     Runnable outputAction = () -> {
1296       // todo defer this to inside formatSequences (or later)
1297       AlignmentExportData exportData = viewport.getAlignExportData(options);
1298       String output = new FormatAdapter(alignPanel, options)
1299               .formatSequences(format, exportData.getAlignment(),
1300                       exportData.getOmitHidden(),
1301                       exportData.getStartEndPostions(),
1302                       viewport.getAlignment().getHiddenColumns());
1303       if (output == null)
1304       {
1305         lastSaveSuccessful = false;
1306       }
1307       else
1308       {
1309         // create backupfiles object and get new temp filename destination
1310         boolean doBackup = BackupFiles.getEnabled();
1311         BackupFiles backupfiles = null;
1312         if (doBackup)
1313         {
1314           Console.trace("ALIGNFRAME making backupfiles object for " + file);
1315           backupfiles = new BackupFiles(file);
1316         }
1317         try
1318         {
1319           String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1320                   : file;
1321           Console.trace("ALIGNFRAME setting PrintWriter");
1322           PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1323
1324           if (backupfiles != null)
1325           {
1326             Console.trace("ALIGNFRAME about to write to temp file "
1327                     + backupfiles.getTempFilePath());
1328           }
1329
1330           out.print(output);
1331           Console.trace("ALIGNFRAME about to close file");
1332           out.close();
1333           Console.trace("ALIGNFRAME closed file");
1334           AlignFrame.this.setTitle(file);
1335           statusBar.setText(MessageManager.formatMessage(
1336                   "label.successfully_saved_to_file_in_format", new Object[]
1337                   { fileName, format.getName() }));
1338           lastSaveSuccessful = true;
1339         } catch (IOException e)
1340         {
1341           lastSaveSuccessful = false;
1342           Console.error(
1343                   "ALIGNFRAME Something happened writing the temp file");
1344           Console.error(e.getMessage());
1345           Console.debug(Cache.getStackTraceString(e));
1346         } catch (Exception ex)
1347         {
1348           lastSaveSuccessful = false;
1349           Console.error(
1350                   "ALIGNFRAME Something unexpected happened writing the temp file");
1351           Console.error(ex.getMessage());
1352           Console.debug(Cache.getStackTraceString(ex));
1353         }
1354
1355         if (doBackup)
1356         {
1357           backupfiles.setWriteSuccess(lastSaveSuccessful);
1358           Console.debug("ALIGNFRAME writing temp file was "
1359                   + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1360           // do the backup file roll and rename the temp file to actual file
1361           Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1362           lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1363           Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1364                   + (lastSaveSuccessful ? "" : "un") + "successfully");
1365         }
1366
1367         Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1368         if (lastSaveSuccessful)
1369         {
1370           AlignFrame.this.getViewport().setSavedUpToDate(true);
1371         }
1372       }
1373     };
1374
1375     /*
1376      * show dialog with export options if applicable; else just do it
1377      */
1378     if (AlignExportOptions.isNeeded(viewport, format))
1379     {
1380       AlignExportOptions choices = new AlignExportOptions(
1381               alignPanel.getAlignViewport(), format, options);
1382       choices.setResponseAction(0, outputAction);
1383       choices.setResponseAction(1, cancelAction);
1384       choices.showDialog();
1385     }
1386     else
1387     {
1388       try
1389       {
1390         outputAction.run();
1391       } catch (Exception e)
1392       {
1393         // TODO Auto-generated catch block
1394         e.printStackTrace();
1395       }
1396     }
1397   }
1398
1399   /**
1400    * Outputs the alignment to textbox in the requested format, if necessary
1401    * first prompting the user for whether to include hidden regions or
1402    * non-sequence data
1403    *
1404    * @param fileFormatName
1405    */
1406   @Override
1407   protected void outputText_actionPerformed(String fileFormatName)
1408   {
1409     FileFormatI fileFormat = FileFormats.getInstance()
1410             .forName(fileFormatName);
1411     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1412     Runnable outputAction = () -> {
1413       // todo defer this to inside formatSequences (or later)
1414       AlignmentExportData exportData = viewport.getAlignExportData(options);
1415       CutAndPasteTransfer cap = new CutAndPasteTransfer();
1416       cap.setForInput(null);
1417       try
1418       {
1419         FileFormatI format = fileFormat;
1420         cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
1421                 format, exportData.getAlignment(),
1422                 exportData.getOmitHidden(),
1423                 exportData.getStartEndPostions(),
1424                 viewport.getAlignment().getHiddenColumns()));
1425         Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1426                 "label.alignment_output_command", new Object[]
1427                 { fileFormat.getName() }), 600, 500);
1428       } catch (OutOfMemoryError oom)
1429       {
1430         new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1431                 oom);
1432         cap.dispose();
1433       }
1434     };
1435
1436     /*
1437      * show dialog with export options if applicable; else just do it
1438      */
1439     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1440     {
1441       AlignExportOptions choices = new AlignExportOptions(
1442               alignPanel.getAlignViewport(), fileFormat, options);
1443       choices.setResponseAction(0, outputAction);
1444       choices.showDialog();
1445     }
1446     else
1447     {
1448       try
1449       {
1450         outputAction.run();
1451       } catch (Exception e)
1452       {
1453         e.printStackTrace();
1454       }
1455     }
1456   }
1457
1458   /**
1459    * DOCUMENT ME!
1460    *
1461    * @param e
1462    *          DOCUMENT ME!
1463    */
1464   @Override
1465   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1466   {
1467     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1468     try {
1469       htmlSVG.exportHTML(null);
1470     } catch (ImageOutputException x) {
1471       // report problem to console and raise dialog
1472     }
1473   }
1474
1475   @Override
1476   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1477   {
1478     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1479     try {
1480     bjs.exportHTML(null);
1481   } catch (ImageOutputException x) {
1482     // report problem to console and raise dialog
1483   }
1484   }
1485
1486   public void createImageMap(File file, String image)
1487   {
1488     try {
1489     alignPanel.makePNGImageMap(file, image);
1490     } catch (ImageOutputException x) {
1491       // report problem to console and raise dialog
1492     }
1493   }
1494
1495   @Override
1496   public void createPNG_actionPerformed(ActionEvent e) {
1497     try{
1498       createPNG(null);
1499     } catch (ImageOutputException ioex)
1500     {
1501       // raise dialog, and report via console
1502     }
1503   }
1504   @Override
1505   public void createEPS_actionPerformed(ActionEvent e) {
1506     try{
1507       createEPS(null);
1508     } catch (ImageOutputException ioex)
1509     {
1510       // raise dialog, and report via console
1511     }
1512
1513   }
1514   @Override
1515   public void createSVG_actionPerformed(ActionEvent e) {
1516     try{
1517       createSVG(null);
1518     } catch (ImageOutputException ioex)
1519     {
1520       // raise dialog, and report via console
1521     }
1522
1523   }
1524   /**
1525    * Creates a PNG image of the alignment and writes it to the given file. If
1526    * the file is null, the user is prompted to choose a file.
1527    *
1528    * @param f
1529    */
1530   public void createPNG(File f) throws ImageOutputException
1531   {
1532     createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
1533   }
1534
1535   public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException
1536   {
1537     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
1538   }
1539
1540   /**
1541    * Creates an EPS image of the alignment and writes it to the given file. If
1542    * the file is null, the user is prompted to choose a file.
1543    *
1544    * @param f
1545    */
1546   public void createEPS(File f)  throws ImageOutputException
1547   {
1548     createEPS(f, null);
1549   }
1550
1551   public void createEPS(File f, String renderer) throws ImageOutputException
1552   {
1553     alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
1554   }
1555
1556   /**
1557    * Creates an SVG image of the alignment and writes it to the given file. If
1558    * the file is null, the user is prompted to choose a file.
1559    *
1560    * @param f
1561    */
1562   public void createSVG(File f)  throws ImageOutputException
1563   {
1564     createSVG(f, null);
1565   }
1566
1567   public void createSVG(File f, String renderer) throws ImageOutputException
1568   {
1569     alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
1570   }
1571
1572   @Override
1573   public void pageSetup_actionPerformed(ActionEvent e)
1574   {
1575     PrinterJob printJob = PrinterJob.getPrinterJob();
1576     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1577   }
1578
1579   /**
1580    * DOCUMENT ME!
1581    *
1582    * @param e
1583    *          DOCUMENT ME!
1584    */
1585   @Override
1586   public void printMenuItem_actionPerformed(ActionEvent e)
1587   {
1588     // Putting in a thread avoids Swing painting problems
1589     PrintThread thread = new PrintThread(alignPanel);
1590     thread.start();
1591   }
1592
1593   @Override
1594   public void exportFeatures_actionPerformed(ActionEvent e)
1595   {
1596     new AnnotationExporter(alignPanel).exportFeatures();
1597   }
1598
1599   @Override
1600   public void exportAnnotations_actionPerformed(ActionEvent e)
1601   {
1602     new AnnotationExporter(alignPanel).exportAnnotations();
1603   }
1604
1605   @Override
1606   public void associatedData_actionPerformed(ActionEvent e)
1607   {
1608     final JalviewFileChooser chooser = new JalviewFileChooser(
1609             Cache.getProperty("LAST_DIRECTORY"));
1610     chooser.setFileView(new JalviewFileView());
1611     String tooltip = MessageManager
1612             .getString("label.load_jalview_annotations");
1613     chooser.setDialogTitle(tooltip);
1614     chooser.setToolTipText(tooltip);
1615     chooser.setResponseHandler(0, () -> {
1616       String choice = chooser.getSelectedFile().getPath();
1617       Cache.setProperty("LAST_DIRECTORY", choice);
1618       loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1619     });
1620
1621     chooser.showOpenDialog(this);
1622   }
1623
1624   /**
1625    * Close the current view or all views in the alignment frame. If the frame
1626    * only contains one view then the alignment will be removed from memory.
1627    *
1628    * @param closeAllTabs
1629    */
1630   @Override
1631   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1632   {
1633     if (alignPanels != null && alignPanels.size() < 2)
1634     {
1635       closeAllTabs = true;
1636     }
1637
1638     try
1639     {
1640       if (alignPanels != null)
1641       {
1642         if (closeAllTabs)
1643         {
1644           if (this.isClosed())
1645           {
1646             // really close all the windows - otherwise wait till
1647             // setClosed(true) is called
1648             for (int i = 0; i < alignPanels.size(); i++)
1649             {
1650               AlignmentPanel ap = alignPanels.get(i);
1651               ap.closePanel();
1652             }
1653           }
1654         }
1655         else
1656         {
1657           closeView(alignPanel);
1658         }
1659       }
1660       if (closeAllTabs)
1661       {
1662         if (featureSettings != null && featureSettings.isOpen())
1663         {
1664           featureSettings.close();
1665           featureSettings = null;
1666         }
1667         /*
1668          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1669          * be called recursively, with the frame now in 'closed' state
1670          */
1671         this.setClosed(true);
1672       }
1673     } catch (Exception ex)
1674     {
1675       ex.printStackTrace();
1676     }
1677   }
1678
1679   /**
1680    * Close the specified panel and close up tabs appropriately.
1681    *
1682    * @param panelToClose
1683    */
1684   public void closeView(AlignmentPanel panelToClose)
1685   {
1686     int index = tabbedPane.getSelectedIndex();
1687     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1688     alignPanels.remove(panelToClose);
1689     panelToClose.closePanel();
1690     panelToClose = null;
1691
1692     tabbedPane.removeTabAt(closedindex);
1693     tabbedPane.validate();
1694
1695     if (index > closedindex || index == tabbedPane.getTabCount())
1696     {
1697       // modify currently selected tab index if necessary.
1698       index--;
1699     }
1700
1701     this.tabSelectionChanged(index);
1702   }
1703
1704   /**
1705    * DOCUMENT ME!
1706    */
1707   void updateEditMenuBar()
1708   {
1709
1710     if (viewport.getHistoryList().size() > 0)
1711     {
1712       undoMenuItem.setEnabled(true);
1713       CommandI command = viewport.getHistoryList().peek();
1714       undoMenuItem.setText(MessageManager
1715               .formatMessage("label.undo_command", new Object[]
1716               { command.getDescription() }));
1717     }
1718     else
1719     {
1720       undoMenuItem.setEnabled(false);
1721       undoMenuItem.setText(MessageManager.getString("action.undo"));
1722     }
1723
1724     if (viewport.getRedoList().size() > 0)
1725     {
1726       redoMenuItem.setEnabled(true);
1727
1728       CommandI command = viewport.getRedoList().peek();
1729       redoMenuItem.setText(MessageManager
1730               .formatMessage("label.redo_command", new Object[]
1731               { command.getDescription() }));
1732     }
1733     else
1734     {
1735       redoMenuItem.setEnabled(false);
1736       redoMenuItem.setText(MessageManager.getString("action.redo"));
1737     }
1738   }
1739
1740   @Override
1741   public void addHistoryItem(CommandI command)
1742   {
1743     if (command.getSize() > 0)
1744     {
1745       viewport.addToHistoryList(command);
1746       viewport.clearRedoList();
1747       updateEditMenuBar();
1748       viewport.updateHiddenColumns();
1749       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1750       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1751       // viewport.getColumnSelection()
1752       // .getHiddenColumns().size() > 0);
1753     }
1754   }
1755
1756   /**
1757    *
1758    * @return alignment objects for all views
1759    */
1760   AlignmentI[] getViewAlignments()
1761   {
1762     if (alignPanels != null)
1763     {
1764       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1765       int i = 0;
1766       for (AlignmentPanel ap : alignPanels)
1767       {
1768         als[i++] = ap.av.getAlignment();
1769       }
1770       return als;
1771     }
1772     if (viewport != null)
1773     {
1774       return new AlignmentI[] { viewport.getAlignment() };
1775     }
1776     return null;
1777   }
1778
1779   /**
1780    * DOCUMENT ME!
1781    *
1782    * @param e
1783    *          DOCUMENT ME!
1784    */
1785   @Override
1786   protected void undoMenuItem_actionPerformed(ActionEvent e)
1787   {
1788     if (viewport.getHistoryList().isEmpty())
1789     {
1790       return;
1791     }
1792     CommandI command = viewport.getHistoryList().pop();
1793     viewport.addToRedoList(command);
1794     command.undoCommand(getViewAlignments());
1795
1796     AlignmentViewport originalSource = getOriginatingSource(command);
1797     updateEditMenuBar();
1798
1799     if (originalSource != null)
1800     {
1801       if (originalSource != viewport)
1802       {
1803         Console.warn(
1804                 "Implementation worry: mismatch of viewport origin for undo");
1805       }
1806       originalSource.updateHiddenColumns();
1807       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1808       // null
1809       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1810       // viewport.getColumnSelection()
1811       // .getHiddenColumns().size() > 0);
1812       originalSource.firePropertyChange("alignment", null,
1813               originalSource.getAlignment().getSequences());
1814     }
1815   }
1816
1817   /**
1818    * DOCUMENT ME!
1819    *
1820    * @param e
1821    *          DOCUMENT ME!
1822    */
1823   @Override
1824   protected void redoMenuItem_actionPerformed(ActionEvent e)
1825   {
1826     if (viewport.getRedoList().size() < 1)
1827     {
1828       return;
1829     }
1830
1831     CommandI command = viewport.getRedoList().pop();
1832     viewport.addToHistoryList(command);
1833     command.doCommand(getViewAlignments());
1834
1835     AlignmentViewport originalSource = getOriginatingSource(command);
1836     updateEditMenuBar();
1837
1838     if (originalSource != null)
1839     {
1840
1841       if (originalSource != viewport)
1842       {
1843         Console.warn(
1844                 "Implementation worry: mismatch of viewport origin for redo");
1845       }
1846       originalSource.updateHiddenColumns();
1847       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1848       // null
1849       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1850       // viewport.getColumnSelection()
1851       // .getHiddenColumns().size() > 0);
1852       originalSource.firePropertyChange("alignment", null,
1853               originalSource.getAlignment().getSequences());
1854     }
1855   }
1856
1857   AlignmentViewport getOriginatingSource(CommandI command)
1858   {
1859     AlignmentViewport originalSource = null;
1860     // For sequence removal and addition, we need to fire
1861     // the property change event FROM the viewport where the
1862     // original alignment was altered
1863     AlignmentI al = null;
1864     if (command instanceof EditCommand)
1865     {
1866       EditCommand editCommand = (EditCommand) command;
1867       al = editCommand.getAlignment();
1868       List<Component> comps = PaintRefresher.components
1869               .get(viewport.getSequenceSetId());
1870
1871       for (Component comp : comps)
1872       {
1873         if (comp instanceof AlignmentPanel)
1874         {
1875           if (al == ((AlignmentPanel) comp).av.getAlignment())
1876           {
1877             originalSource = ((AlignmentPanel) comp).av;
1878             break;
1879           }
1880         }
1881       }
1882     }
1883
1884     if (originalSource == null)
1885     {
1886       // The original view is closed, we must validate
1887       // the current view against the closed view first
1888       if (al != null)
1889       {
1890         PaintRefresher.validateSequences(al, viewport.getAlignment());
1891       }
1892
1893       originalSource = viewport;
1894     }
1895
1896     return originalSource;
1897   }
1898
1899   /**
1900    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1901    * or the sequence under cursor in keyboard mode
1902    *
1903    * @param up
1904    *          or down (if !up)
1905    */
1906   public void moveSelectedSequences(boolean up)
1907   {
1908     SequenceGroup sg = viewport.getSelectionGroup();
1909
1910     if (sg == null)
1911     {
1912       if (viewport.cursorMode)
1913       {
1914         sg = new SequenceGroup();
1915         sg.addSequence(viewport.getAlignment().getSequenceAt(
1916                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1917       }
1918       else
1919       {
1920         return;
1921       }
1922     }
1923
1924     if (sg.getSize() < 1)
1925     {
1926       return;
1927     }
1928
1929     // TODO: JAL-3733 - add an event to the undo buffer for this !
1930
1931     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1932             viewport.getHiddenRepSequences(), up);
1933     alignPanel.paintAlignment(true, false);
1934   }
1935
1936   synchronized void slideSequences(boolean right, int size)
1937   {
1938     List<SequenceI> sg = new ArrayList<>();
1939     if (viewport.cursorMode)
1940     {
1941       sg.add(viewport.getAlignment()
1942               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1943     }
1944     else if (viewport.getSelectionGroup() != null
1945             && viewport.getSelectionGroup().getSize() != viewport
1946                     .getAlignment().getHeight())
1947     {
1948       sg = viewport.getSelectionGroup()
1949               .getSequences(viewport.getHiddenRepSequences());
1950     }
1951
1952     if (sg.size() < 1)
1953     {
1954       return;
1955     }
1956
1957     List<SequenceI> invertGroup = new ArrayList<>();
1958
1959     for (SequenceI seq : viewport.getAlignment().getSequences())
1960     {
1961       if (!sg.contains(seq))
1962       {
1963         invertGroup.add(seq);
1964       }
1965     }
1966
1967     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1968
1969     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1970     for (int i = 0; i < invertGroup.size(); i++)
1971     {
1972       seqs2[i] = invertGroup.get(i);
1973     }
1974
1975     SlideSequencesCommand ssc;
1976     if (right)
1977     {
1978       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1979               viewport.getGapCharacter());
1980     }
1981     else
1982     {
1983       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1984               viewport.getGapCharacter());
1985     }
1986
1987     int groupAdjustment = 0;
1988     if (ssc.getGapsInsertedBegin() && right)
1989     {
1990       if (viewport.cursorMode)
1991       {
1992         alignPanel.getSeqPanel().moveCursor(size, 0);
1993       }
1994       else
1995       {
1996         groupAdjustment = size;
1997       }
1998     }
1999     else if (!ssc.getGapsInsertedBegin() && !right)
2000     {
2001       if (viewport.cursorMode)
2002       {
2003         alignPanel.getSeqPanel().moveCursor(-size, 0);
2004       }
2005       else
2006       {
2007         groupAdjustment = -size;
2008       }
2009     }
2010
2011     if (groupAdjustment != 0)
2012     {
2013       viewport.getSelectionGroup().setStartRes(
2014               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2015       viewport.getSelectionGroup().setEndRes(
2016               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2017     }
2018
2019     /*
2020      * just extend the last slide command if compatible; but not if in
2021      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2022      */
2023     boolean appendHistoryItem = false;
2024     Deque<CommandI> historyList = viewport.getHistoryList();
2025     boolean inSplitFrame = getSplitViewContainer() != null;
2026     if (!inSplitFrame && historyList != null && historyList.size() > 0
2027             && historyList.peek() instanceof SlideSequencesCommand)
2028     {
2029       appendHistoryItem = ssc.appendSlideCommand(
2030               (SlideSequencesCommand) historyList.peek());
2031     }
2032
2033     if (!appendHistoryItem)
2034     {
2035       addHistoryItem(ssc);
2036     }
2037
2038     repaint();
2039   }
2040
2041   /**
2042    * DOCUMENT ME!
2043    *
2044    * @param e
2045    *          DOCUMENT ME!
2046    */
2047   @Override
2048   protected void copy_actionPerformed()
2049   {
2050     if (viewport.getSelectionGroup() == null)
2051     {
2052       return;
2053     }
2054     // TODO: preserve the ordering of displayed alignment annotation in any
2055     // internal paste (particularly sequence associated annotation)
2056     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2057     String[] omitHidden = null;
2058
2059     if (viewport.hasHiddenColumns())
2060     {
2061       omitHidden = viewport.getViewAsString(true);
2062     }
2063
2064     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2065             seqs, omitHidden, null);
2066
2067     StringSelection ss = new StringSelection(output);
2068
2069     try
2070     {
2071       jalview.gui.Desktop.internalCopy = true;
2072       // Its really worth setting the clipboard contents
2073       // to empty before setting the large StringSelection!!
2074       Toolkit.getDefaultToolkit().getSystemClipboard()
2075               .setContents(new StringSelection(""), null);
2076
2077       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2078               Desktop.instance);
2079     } catch (OutOfMemoryError er)
2080     {
2081       new OOMWarning("copying region", er);
2082       return;
2083     }
2084
2085     HiddenColumns hiddenColumns = null;
2086     if (viewport.hasHiddenColumns())
2087     {
2088       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2089       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2090
2091       // create new HiddenColumns object with copy of hidden regions
2092       // between startRes and endRes, offset by startRes
2093       hiddenColumns = new HiddenColumns(
2094               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2095               hiddenCutoff, hiddenOffset);
2096     }
2097
2098     Desktop.jalviewClipboard = new Object[] { seqs,
2099         viewport.getAlignment().getDataset(), hiddenColumns };
2100     setStatus(MessageManager.formatMessage(
2101             "label.copied_sequences_to_clipboard", new Object[]
2102             { Integer.valueOf(seqs.length).toString() }));
2103   }
2104
2105   /**
2106    * DOCUMENT ME!
2107    *
2108    * @param e
2109    *          DOCUMENT ME!
2110    */
2111   @Override
2112   protected void pasteNew_actionPerformed(ActionEvent e)
2113   {
2114     paste(true);
2115   }
2116
2117   /**
2118    * DOCUMENT ME!
2119    *
2120    * @param e
2121    *          DOCUMENT ME!
2122    */
2123   @Override
2124   protected void pasteThis_actionPerformed(ActionEvent e)
2125   {
2126     paste(false);
2127   }
2128
2129   /**
2130    * Paste contents of Jalview clipboard
2131    *
2132    * @param newAlignment
2133    *          true to paste to a new alignment, otherwise add to this.
2134    */
2135   void paste(boolean newAlignment)
2136   {
2137     boolean externalPaste = true;
2138     try
2139     {
2140       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2141       Transferable contents = c.getContents(this);
2142
2143       if (contents == null)
2144       {
2145         return;
2146       }
2147
2148       String str;
2149       FileFormatI format;
2150       try
2151       {
2152         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2153         if (str.length() < 1)
2154         {
2155           return;
2156         }
2157
2158         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2159
2160       } catch (OutOfMemoryError er)
2161       {
2162         new OOMWarning("Out of memory pasting sequences!!", er);
2163         return;
2164       }
2165
2166       SequenceI[] sequences;
2167       boolean annotationAdded = false;
2168       AlignmentI alignment = null;
2169
2170       if (Desktop.jalviewClipboard != null)
2171       {
2172         // The clipboard was filled from within Jalview, we must use the
2173         // sequences
2174         // And dataset from the copied alignment
2175         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2176         // be doubly sure that we create *new* sequence objects.
2177         sequences = new SequenceI[newseq.length];
2178         for (int i = 0; i < newseq.length; i++)
2179         {
2180           sequences[i] = new Sequence(newseq[i]);
2181         }
2182         alignment = new Alignment(sequences);
2183         externalPaste = false;
2184       }
2185       else
2186       {
2187         // parse the clipboard as an alignment.
2188         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2189                 format);
2190         sequences = alignment.getSequencesArray();
2191       }
2192
2193       int alwidth = 0;
2194       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2195       int fgroup = -1;
2196
2197       if (newAlignment)
2198       {
2199
2200         if (Desktop.jalviewClipboard != null)
2201         {
2202           // dataset is inherited
2203           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2204         }
2205         else
2206         {
2207           // new dataset is constructed
2208           alignment.setDataset(null);
2209         }
2210         alwidth = alignment.getWidth() + 1;
2211       }
2212       else
2213       {
2214         AlignmentI pastedal = alignment; // preserve pasted alignment object
2215         // Add pasted sequences and dataset into existing alignment.
2216         alignment = viewport.getAlignment();
2217         alwidth = alignment.getWidth() + 1;
2218         // decide if we need to import sequences from an existing dataset
2219         boolean importDs = Desktop.jalviewClipboard != null
2220                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2221         // importDs==true instructs us to copy over new dataset sequences from
2222         // an existing alignment
2223         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2224                                                                       // create
2225         // minimum dataset set
2226
2227         for (int i = 0; i < sequences.length; i++)
2228         {
2229           if (importDs)
2230           {
2231             newDs.addElement(null);
2232           }
2233           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2234           // paste
2235           if (importDs && ds != null)
2236           {
2237             if (!newDs.contains(ds))
2238             {
2239               newDs.setElementAt(ds, i);
2240               ds = new Sequence(ds);
2241               // update with new dataset sequence
2242               sequences[i].setDatasetSequence(ds);
2243             }
2244             else
2245             {
2246               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2247             }
2248           }
2249           else
2250           {
2251             // copy and derive new dataset sequence
2252             sequences[i] = sequences[i].deriveSequence();
2253             alignment.getDataset()
2254                     .addSequence(sequences[i].getDatasetSequence());
2255             // TODO: avoid creation of duplicate dataset sequences with a
2256             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2257           }
2258           alignment.addSequence(sequences[i]); // merges dataset
2259         }
2260         if (newDs != null)
2261         {
2262           newDs.clear(); // tidy up
2263         }
2264         if (alignment.getAlignmentAnnotation() != null)
2265         {
2266           for (AlignmentAnnotation alan : alignment
2267                   .getAlignmentAnnotation())
2268           {
2269             if (alan.graphGroup > fgroup)
2270             {
2271               fgroup = alan.graphGroup;
2272             }
2273           }
2274         }
2275         if (pastedal.getAlignmentAnnotation() != null)
2276         {
2277           // Add any annotation attached to alignment.
2278           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2279           for (int i = 0; i < alann.length; i++)
2280           {
2281             annotationAdded = true;
2282             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2283             {
2284               AlignmentAnnotation newann = new AlignmentAnnotation(
2285                       alann[i]);
2286               if (newann.graphGroup > -1)
2287               {
2288                 if (newGraphGroups.size() <= newann.graphGroup
2289                         || newGraphGroups.get(newann.graphGroup) == null)
2290                 {
2291                   for (int q = newGraphGroups
2292                           .size(); q <= newann.graphGroup; q++)
2293                   {
2294                     newGraphGroups.add(q, null);
2295                   }
2296                   newGraphGroups.set(newann.graphGroup,
2297                           Integer.valueOf(++fgroup));
2298                 }
2299                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2300                         .intValue();
2301               }
2302
2303               newann.padAnnotation(alwidth);
2304               alignment.addAnnotation(newann);
2305             }
2306           }
2307         }
2308       }
2309       if (!newAlignment)
2310       {
2311         // /////
2312         // ADD HISTORY ITEM
2313         //
2314         addHistoryItem(new EditCommand(
2315                 MessageManager.getString("label.add_sequences"),
2316                 Action.PASTE, sequences, 0, alignment.getWidth(),
2317                 alignment));
2318       }
2319       // Add any annotations attached to sequences
2320       for (int i = 0; i < sequences.length; i++)
2321       {
2322         if (sequences[i].getAnnotation() != null)
2323         {
2324           AlignmentAnnotation newann;
2325           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2326           {
2327             annotationAdded = true;
2328             newann = sequences[i].getAnnotation()[a];
2329             newann.adjustForAlignment();
2330             newann.padAnnotation(alwidth);
2331             if (newann.graphGroup > -1)
2332             {
2333               if (newann.graphGroup > -1)
2334               {
2335                 if (newGraphGroups.size() <= newann.graphGroup
2336                         || newGraphGroups.get(newann.graphGroup) == null)
2337                 {
2338                   for (int q = newGraphGroups
2339                           .size(); q <= newann.graphGroup; q++)
2340                   {
2341                     newGraphGroups.add(q, null);
2342                   }
2343                   newGraphGroups.set(newann.graphGroup,
2344                           Integer.valueOf(++fgroup));
2345                 }
2346                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2347                         .intValue();
2348               }
2349             }
2350             // annotation was duplicated earlier
2351             alignment.addAnnotation(sequences[i].getAnnotation()[a]);
2352             // take care of contact matrix too
2353             ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]);
2354             if (cm!=null)
2355             {
2356               alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
2357             }
2358
2359             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2360                     a);
2361           }
2362         }
2363       }
2364       if (!newAlignment)
2365       {
2366
2367         // propagate alignment changed.
2368         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2369         if (annotationAdded)
2370         {
2371           // Duplicate sequence annotation in all views.
2372           AlignmentI[] alview = this.getViewAlignments();
2373           for (int i = 0; i < sequences.length; i++)
2374           {
2375             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2376             if (sann == null)
2377             {
2378               continue;
2379             }
2380             for (int avnum = 0; avnum < alview.length; avnum++)
2381             {
2382               if (alview[avnum] != alignment)
2383               {
2384                 // duplicate in a view other than the one with input focus
2385                 int avwidth = alview[avnum].getWidth() + 1;
2386                 // this relies on sann being preserved after we
2387                 // modify the sequence's annotation array for each duplication
2388                 for (int a = 0; a < sann.length; a++)
2389                 {
2390                   AlignmentAnnotation newann = new AlignmentAnnotation(
2391                           sann[a]);
2392                   sequences[i].addAlignmentAnnotation(newann);
2393                   newann.padAnnotation(avwidth);
2394                   alview[avnum].addAnnotation(newann); // annotation was
2395                   // duplicated earlier
2396                   // TODO JAL-1145 graphGroups are not updated for sequence
2397                   // annotation added to several views. This may cause
2398                   // strangeness
2399                   alview[avnum].setAnnotationIndex(newann, a);
2400                 }
2401               }
2402             }
2403           }
2404           buildSortByAnnotationScoresMenu();
2405         }
2406         viewport.firePropertyChange("alignment", null,
2407                 alignment.getSequences());
2408         if (alignPanels != null)
2409         {
2410           for (AlignmentPanel ap : alignPanels)
2411           {
2412             ap.validateAnnotationDimensions(false);
2413           }
2414         }
2415         else
2416         {
2417           alignPanel.validateAnnotationDimensions(false);
2418         }
2419
2420       }
2421       else
2422       {
2423         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2424                 DEFAULT_HEIGHT);
2425         String newtitle = new String("Copied sequences");
2426
2427         if (Desktop.jalviewClipboard != null
2428                 && Desktop.jalviewClipboard[2] != null)
2429         {
2430           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2431           af.viewport.setHiddenColumns(hc);
2432         }
2433
2434         // >>>This is a fix for the moment, until a better solution is
2435         // found!!<<<
2436         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2437                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2438                         .getFeatureRenderer());
2439
2440         // TODO: maintain provenance of an alignment, rather than just make the
2441         // title a concatenation of operations.
2442         if (!externalPaste)
2443         {
2444           if (title.startsWith("Copied sequences"))
2445           {
2446             newtitle = title;
2447           }
2448           else
2449           {
2450             newtitle = newtitle.concat("- from " + title);
2451           }
2452         }
2453         else
2454         {
2455           newtitle = new String("Pasted sequences");
2456         }
2457
2458         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2459                 DEFAULT_HEIGHT);
2460
2461       }
2462
2463     } catch (Exception ex)
2464     {
2465       ex.printStackTrace();
2466       System.out.println("Exception whilst pasting: " + ex);
2467       // could be anything being pasted in here
2468     }
2469
2470   }
2471
2472   @Override
2473   protected void expand_newalign(ActionEvent e)
2474   {
2475     try
2476     {
2477       AlignmentI alignment = AlignmentUtils
2478               .expandContext(getViewport().getAlignment(), -1);
2479       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2480               DEFAULT_HEIGHT);
2481       String newtitle = new String("Flanking alignment");
2482
2483       if (Desktop.jalviewClipboard != null
2484               && Desktop.jalviewClipboard[2] != null)
2485       {
2486         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2487         af.viewport.setHiddenColumns(hc);
2488       }
2489
2490       // >>>This is a fix for the moment, until a better solution is
2491       // found!!<<<
2492       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2493               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2494                       .getFeatureRenderer());
2495
2496       // TODO: maintain provenance of an alignment, rather than just make the
2497       // title a concatenation of operations.
2498       {
2499         if (title.startsWith("Copied sequences"))
2500         {
2501           newtitle = title;
2502         }
2503         else
2504         {
2505           newtitle = newtitle.concat("- from " + title);
2506         }
2507       }
2508
2509       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2510
2511     } catch (Exception ex)
2512     {
2513       ex.printStackTrace();
2514       System.out.println("Exception whilst pasting: " + ex);
2515       // could be anything being pasted in here
2516     } catch (OutOfMemoryError oom)
2517     {
2518       new OOMWarning("Viewing flanking region of alignment", oom);
2519     }
2520   }
2521
2522   /**
2523    * Action Cut (delete and copy) the selected region
2524    */
2525   @Override
2526   protected void cut_actionPerformed()
2527   {
2528     copy_actionPerformed();
2529     delete_actionPerformed();
2530   }
2531
2532   /**
2533    * Performs menu option to Delete the currently selected region
2534    */
2535   @Override
2536   protected void delete_actionPerformed()
2537   {
2538
2539     SequenceGroup sg = viewport.getSelectionGroup();
2540     if (sg == null)
2541     {
2542       return;
2543     }
2544
2545     Runnable okAction = () -> {
2546       SequenceI[] cut = sg.getSequences()
2547               .toArray(new SequenceI[sg.getSize()]);
2548
2549       addHistoryItem(new EditCommand(
2550               MessageManager.getString("label.cut_sequences"), Action.CUT,
2551               cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2552               viewport.getAlignment()));
2553
2554       viewport.setSelectionGroup(null);
2555       viewport.sendSelection();
2556       viewport.getAlignment().deleteGroup(sg);
2557
2558       viewport.firePropertyChange("alignment", null,
2559               viewport.getAlignment().getSequences());
2560       if (viewport.getAlignment().getHeight() < 1)
2561       {
2562         try
2563         {
2564           AlignFrame.this.setClosed(true);
2565         } catch (Exception ex)
2566         {
2567         }
2568       }
2569     };
2570
2571     /*
2572      * If the cut affects all sequences, prompt for confirmation
2573      */
2574     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2575             .getHeight();
2576     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2577             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2578     if (wholeHeight && wholeWidth)
2579     {
2580       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2581       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2582       Object[] options = new Object[] {
2583           MessageManager.getString("action.ok"),
2584           MessageManager.getString("action.cancel") };
2585       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2586               MessageManager.getString("label.delete_all"),
2587               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2588               options, options[0]);
2589     }
2590     else
2591     {
2592       try
2593       {
2594         okAction.run();
2595       } catch (Exception e)
2596       {
2597         e.printStackTrace();
2598       }
2599     }
2600   }
2601
2602   /**
2603    * DOCUMENT ME!
2604    *
2605    * @param e
2606    *          DOCUMENT ME!
2607    */
2608   @Override
2609   protected void deleteGroups_actionPerformed(ActionEvent e)
2610   {
2611     if (avc.deleteGroups())
2612     {
2613       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2614       alignPanel.updateAnnotation();
2615       alignPanel.paintAlignment(true, true);
2616     }
2617   }
2618
2619   /**
2620    * DOCUMENT ME!
2621    *
2622    * @param e
2623    *          DOCUMENT ME!
2624    */
2625   @Override
2626   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2627   {
2628     SequenceGroup sg = new SequenceGroup(
2629             viewport.getAlignment().getSequences());
2630
2631     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2632     viewport.setSelectionGroup(sg);
2633     viewport.isSelectionGroupChanged(true);
2634     viewport.sendSelection();
2635     // JAL-2034 - should delegate to
2636     // alignPanel to decide if overview needs
2637     // updating.
2638     alignPanel.paintAlignment(false, false);
2639     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2640   }
2641
2642   /**
2643    * DOCUMENT ME!
2644    *
2645    * @param e
2646    *          DOCUMENT ME!
2647    */
2648   @Override
2649   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2650   {
2651     if (viewport.cursorMode)
2652     {
2653       alignPanel.getSeqPanel().keyboardNo1 = null;
2654       alignPanel.getSeqPanel().keyboardNo2 = null;
2655     }
2656     viewport.setSelectionGroup(null);
2657     viewport.getColumnSelection().clear();
2658     viewport.setSearchResults(null);
2659     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2660     // JAL-2034 - should delegate to
2661     // alignPanel to decide if overview needs
2662     // updating.
2663     alignPanel.paintAlignment(false, false);
2664     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2665     viewport.sendSelection();
2666   }
2667
2668   /**
2669    * DOCUMENT ME!
2670    *
2671    * @param e
2672    *          DOCUMENT ME!
2673    */
2674   @Override
2675   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2676   {
2677     SequenceGroup sg = viewport.getSelectionGroup();
2678
2679     if (sg == null)
2680     {
2681       selectAllSequenceMenuItem_actionPerformed(null);
2682
2683       return;
2684     }
2685
2686     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2687     {
2688       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2689     }
2690     // JAL-2034 - should delegate to
2691     // alignPanel to decide if overview needs
2692     // updating.
2693
2694     alignPanel.paintAlignment(true, false);
2695     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2696     viewport.sendSelection();
2697   }
2698
2699   @Override
2700   public void invertColSel_actionPerformed(ActionEvent e)
2701   {
2702     viewport.invertColumnSelection();
2703     alignPanel.paintAlignment(true, false);
2704     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2705     viewport.sendSelection();
2706   }
2707
2708   /**
2709    * DOCUMENT ME!
2710    *
2711    * @param e
2712    *          DOCUMENT ME!
2713    */
2714   @Override
2715   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2716   {
2717     trimAlignment(true);
2718   }
2719
2720   /**
2721    * DOCUMENT ME!
2722    *
2723    * @param e
2724    *          DOCUMENT ME!
2725    */
2726   @Override
2727   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2728   {
2729     trimAlignment(false);
2730   }
2731
2732   void trimAlignment(boolean trimLeft)
2733   {
2734     ColumnSelection colSel = viewport.getColumnSelection();
2735     int column;
2736
2737     if (!colSel.isEmpty())
2738     {
2739       if (trimLeft)
2740       {
2741         column = colSel.getMin();
2742       }
2743       else
2744       {
2745         column = colSel.getMax();
2746       }
2747
2748       SequenceI[] seqs;
2749       if (viewport.getSelectionGroup() != null)
2750       {
2751         seqs = viewport.getSelectionGroup()
2752                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2753       }
2754       else
2755       {
2756         seqs = viewport.getAlignment().getSequencesArray();
2757       }
2758
2759       TrimRegionCommand trimRegion;
2760       if (trimLeft)
2761       {
2762         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2763                 column, viewport.getAlignment());
2764         viewport.getRanges().setStartRes(0);
2765       }
2766       else
2767       {
2768         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2769                 column, viewport.getAlignment());
2770       }
2771
2772       setStatus(MessageManager.formatMessage("label.removed_columns",
2773               new String[]
2774               { Integer.valueOf(trimRegion.getSize()).toString() }));
2775
2776       addHistoryItem(trimRegion);
2777
2778       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2779       {
2780         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2781                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2782         {
2783           viewport.getAlignment().deleteGroup(sg);
2784         }
2785       }
2786
2787       viewport.firePropertyChange("alignment", null,
2788               viewport.getAlignment().getSequences());
2789     }
2790   }
2791
2792   /**
2793    * DOCUMENT ME!
2794    *
2795    * @param e
2796    *          DOCUMENT ME!
2797    */
2798   @Override
2799   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2800   {
2801     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2802
2803     SequenceI[] seqs;
2804     if (viewport.getSelectionGroup() != null)
2805     {
2806       seqs = viewport.getSelectionGroup()
2807               .getSequencesAsArray(viewport.getHiddenRepSequences());
2808       start = viewport.getSelectionGroup().getStartRes();
2809       end = viewport.getSelectionGroup().getEndRes();
2810     }
2811     else
2812     {
2813       seqs = viewport.getAlignment().getSequencesArray();
2814     }
2815
2816     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2817             "Remove Gapped Columns", seqs, start, end,
2818             viewport.getAlignment());
2819
2820     addHistoryItem(removeGapCols);
2821
2822     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2823             new Object[]
2824             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2825
2826     // This is to maintain viewport position on first residue
2827     // of first sequence
2828     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2829     ViewportRanges ranges = viewport.getRanges();
2830     int startRes = seq.findPosition(ranges.getStartRes());
2831     // ShiftList shifts;
2832     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2833     // edit.alColumnChanges=shifts.getInverse();
2834     // if (viewport.hasHiddenColumns)
2835     // viewport.getColumnSelection().compensateForEdits(shifts);
2836     ranges.setStartRes(seq.findIndex(startRes) - 1);
2837     viewport.firePropertyChange("alignment", null,
2838             viewport.getAlignment().getSequences());
2839
2840   }
2841
2842   /**
2843    * DOCUMENT ME!
2844    *
2845    * @param e
2846    *          DOCUMENT ME!
2847    */
2848   @Override
2849   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2850   {
2851     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2852
2853     SequenceI[] seqs;
2854     if (viewport.getSelectionGroup() != null)
2855     {
2856       seqs = viewport.getSelectionGroup()
2857               .getSequencesAsArray(viewport.getHiddenRepSequences());
2858       start = viewport.getSelectionGroup().getStartRes();
2859       end = viewport.getSelectionGroup().getEndRes();
2860     }
2861     else
2862     {
2863       seqs = viewport.getAlignment().getSequencesArray();
2864     }
2865
2866     // This is to maintain viewport position on first residue
2867     // of first sequence
2868     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2869     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2870
2871     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2872             viewport.getAlignment()));
2873
2874     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2875
2876     viewport.firePropertyChange("alignment", null,
2877             viewport.getAlignment().getSequences());
2878
2879   }
2880
2881   /**
2882    * DOCUMENT ME!
2883    *
2884    * @param e
2885    *          DOCUMENT ME!
2886    */
2887   @Override
2888   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2889   {
2890     viewport.setPadGaps(padGapsMenuitem.isSelected());
2891     viewport.firePropertyChange("alignment", null,
2892             viewport.getAlignment().getSequences());
2893   }
2894
2895   /**
2896    * Opens a Finder dialog
2897    *
2898    * @param e
2899    */
2900   @Override
2901   public void findMenuItem_actionPerformed(ActionEvent e)
2902   {
2903     new Finder(alignPanel, false, null);
2904   }
2905
2906   /**
2907    * Create a new view of the current alignment.
2908    */
2909   @Override
2910   public void newView_actionPerformed(ActionEvent e)
2911   {
2912     newView(null, true);
2913   }
2914
2915   /**
2916    * Creates and shows a new view of the current alignment.
2917    *
2918    * @param viewTitle
2919    *          title of newly created view; if null, one will be generated
2920    * @param copyAnnotation
2921    *          if true then duplicate all annnotation, groups and settings
2922    * @return new alignment panel, already displayed.
2923    */
2924   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2925   {
2926     /*
2927      * Create a new AlignmentPanel (with its own, new Viewport)
2928      */
2929     AlignmentPanel newap = new jalview.project.Jalview2XML()
2930             .copyAlignPanel(alignPanel);
2931     if (!copyAnnotation)
2932     {
2933       /*
2934        * remove all groups and annotation except for the automatic stuff
2935        */
2936       newap.av.getAlignment().deleteAllGroups();
2937       newap.av.getAlignment().deleteAllAnnotations(false);
2938     }
2939
2940     newap.av.setGatherViewsHere(false);
2941
2942     if (viewport.getViewName() == null)
2943     {
2944       viewport.setViewName(
2945               MessageManager.getString("label.view_name_original"));
2946     }
2947
2948     /*
2949      * Views share the same edits undo and redo stacks
2950      */
2951     newap.av.setHistoryList(viewport.getHistoryList());
2952     newap.av.setRedoList(viewport.getRedoList());
2953
2954     /*
2955      * copy any visualisation settings that are not saved in the project
2956      */
2957     newap.av.setColourAppliesToAllGroups(
2958             viewport.getColourAppliesToAllGroups());
2959
2960     /*
2961      * Views share the same mappings; need to deregister any new mappings
2962      * created by copyAlignPanel, and register the new reference to the shared
2963      * mappings
2964      */
2965     newap.av.replaceMappings(viewport.getAlignment());
2966
2967     /*
2968      * start up cDNA consensus (if applicable) now mappings are in place
2969      */
2970     if (newap.av.initComplementConsensus())
2971     {
2972       newap.refresh(true); // adjust layout of annotations
2973     }
2974
2975     newap.av.setViewName(getNewViewName(viewTitle));
2976
2977     addAlignmentPanel(newap, true);
2978     newap.alignmentChanged();
2979
2980     if (alignPanels.size() == 2)
2981     {
2982       viewport.setGatherViewsHere(true);
2983     }
2984     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2985
2986     return newap;
2987   }
2988
2989   /**
2990    * Make a new name for the view, ensuring it is unique within the current
2991    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2992    * these now use viewId. Unique view names are still desirable for usability.)
2993    *
2994    * @param viewTitle
2995    * @return
2996    */
2997   protected String getNewViewName(String viewTitle)
2998   {
2999     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3000     boolean addFirstIndex = false;
3001     if (viewTitle == null || viewTitle.trim().length() == 0)
3002     {
3003       viewTitle = MessageManager.getString("action.view");
3004       addFirstIndex = true;
3005     }
3006     else
3007     {
3008       index = 1;// we count from 1 if given a specific name
3009     }
3010     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3011
3012     List<Component> comps = PaintRefresher.components
3013             .get(viewport.getSequenceSetId());
3014
3015     List<String> existingNames = getExistingViewNames(comps);
3016
3017     while (existingNames.contains(newViewName))
3018     {
3019       newViewName = viewTitle + " " + (++index);
3020     }
3021     return newViewName;
3022   }
3023
3024   /**
3025    * Returns a list of distinct view names found in the given list of
3026    * components. View names are held on the viewport of an AlignmentPanel.
3027    *
3028    * @param comps
3029    * @return
3030    */
3031   protected List<String> getExistingViewNames(List<Component> comps)
3032   {
3033     List<String> existingNames = new ArrayList<>();
3034     for (Component comp : comps)
3035     {
3036       if (comp instanceof AlignmentPanel)
3037       {
3038         AlignmentPanel ap = (AlignmentPanel) comp;
3039         if (!existingNames.contains(ap.av.getViewName()))
3040         {
3041           existingNames.add(ap.av.getViewName());
3042         }
3043       }
3044     }
3045     return existingNames;
3046   }
3047
3048   /**
3049    * Explode tabbed views into separate windows.
3050    */
3051   @Override
3052   public void expandViews_actionPerformed(ActionEvent e)
3053   {
3054     Desktop.explodeViews(this);
3055   }
3056
3057   /**
3058    * Gather views in separate windows back into a tabbed presentation.
3059    */
3060   @Override
3061   public void gatherViews_actionPerformed(ActionEvent e)
3062   {
3063     Desktop.instance.gatherViews(this);
3064   }
3065
3066   /**
3067    * DOCUMENT ME!
3068    *
3069    * @param e
3070    *          DOCUMENT ME!
3071    */
3072   @Override
3073   public void font_actionPerformed(ActionEvent e)
3074   {
3075     new FontChooser(alignPanel);
3076   }
3077
3078   /**
3079    * DOCUMENT ME!
3080    *
3081    * @param e
3082    *          DOCUMENT ME!
3083    */
3084   @Override
3085   protected void seqLimit_actionPerformed(ActionEvent e)
3086   {
3087     viewport.setShowJVSuffix(seqLimits.isSelected());
3088
3089     alignPanel.getIdPanel().getIdCanvas()
3090             .setPreferredSize(alignPanel.calculateIdWidth());
3091     alignPanel.paintAlignment(true, false);
3092   }
3093
3094   @Override
3095   public void idRightAlign_actionPerformed(ActionEvent e)
3096   {
3097     viewport.setRightAlignIds(idRightAlign.isSelected());
3098     alignPanel.paintAlignment(false, false);
3099   }
3100
3101   @Override
3102   public void centreColumnLabels_actionPerformed(ActionEvent e)
3103   {
3104     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3105     alignPanel.paintAlignment(false, false);
3106   }
3107
3108   /*
3109    * (non-Javadoc)
3110    *
3111    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3112    */
3113   @Override
3114   protected void followHighlight_actionPerformed()
3115   {
3116     /*
3117      * Set the 'follow' flag on the Viewport (and scroll to position if now
3118      * true).
3119      */
3120     final boolean state = this.followHighlightMenuItem.getState();
3121     viewport.setFollowHighlight(state);
3122     if (state)
3123     {
3124       alignPanel.scrollToPosition(viewport.getSearchResults());
3125     }
3126   }
3127
3128   /**
3129    * DOCUMENT ME!
3130    *
3131    * @param e
3132    *          DOCUMENT ME!
3133    */
3134   @Override
3135   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3136   {
3137     viewport.setColourText(colourTextMenuItem.isSelected());
3138     alignPanel.paintAlignment(false, false);
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   public void wrapMenuItem_actionPerformed(ActionEvent e)
3149   {
3150     scaleAbove.setVisible(wrapMenuItem.isSelected());
3151     scaleLeft.setVisible(wrapMenuItem.isSelected());
3152     scaleRight.setVisible(wrapMenuItem.isSelected());
3153     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3154     alignPanel.updateLayout();
3155   }
3156
3157   @Override
3158   public void showAllSeqs_actionPerformed(ActionEvent e)
3159   {
3160     viewport.showAllHiddenSeqs();
3161   }
3162
3163   @Override
3164   public void showAllColumns_actionPerformed(ActionEvent e)
3165   {
3166     viewport.showAllHiddenColumns();
3167     alignPanel.paintAlignment(true, true);
3168     viewport.sendSelection();
3169   }
3170
3171   @Override
3172   public void hideSelSequences_actionPerformed(ActionEvent e)
3173   {
3174     viewport.hideAllSelectedSeqs();
3175   }
3176
3177   /**
3178    * called by key handler and the hide all/show all menu items
3179    *
3180    * @param toggleSeqs
3181    * @param toggleCols
3182    */
3183   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3184   {
3185
3186     boolean hide = false;
3187     SequenceGroup sg = viewport.getSelectionGroup();
3188     if (!toggleSeqs && !toggleCols)
3189     {
3190       // Hide everything by the current selection - this is a hack - we do the
3191       // invert and then hide
3192       // first check that there will be visible columns after the invert.
3193       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3194               && sg.getStartRes() <= sg.getEndRes()))
3195       {
3196         // now invert the sequence set, if required - empty selection implies
3197         // that no hiding is required.
3198         if (sg != null)
3199         {
3200           invertSequenceMenuItem_actionPerformed(null);
3201           sg = viewport.getSelectionGroup();
3202           toggleSeqs = true;
3203
3204         }
3205         viewport.expandColSelection(sg, true);
3206         // finally invert the column selection and get the new sequence
3207         // selection.
3208         invertColSel_actionPerformed(null);
3209         toggleCols = true;
3210       }
3211     }
3212
3213     if (toggleSeqs)
3214     {
3215       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3216       {
3217         hideSelSequences_actionPerformed(null);
3218         hide = true;
3219       }
3220       else if (!(toggleCols && viewport.hasSelectedColumns()))
3221       {
3222         showAllSeqs_actionPerformed(null);
3223       }
3224     }
3225
3226     if (toggleCols)
3227     {
3228       if (viewport.hasSelectedColumns())
3229       {
3230         hideSelColumns_actionPerformed(null);
3231         if (!toggleSeqs)
3232         {
3233           viewport.setSelectionGroup(sg);
3234         }
3235       }
3236       else if (!hide)
3237       {
3238         showAllColumns_actionPerformed(null);
3239       }
3240     }
3241   }
3242
3243   /*
3244    * (non-Javadoc)
3245    *
3246    * @see
3247    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3248    * event.ActionEvent)
3249    */
3250   @Override
3251   public void hideAllButSelection_actionPerformed(ActionEvent e)
3252   {
3253     toggleHiddenRegions(false, false);
3254     viewport.sendSelection();
3255   }
3256
3257   /*
3258    * (non-Javadoc)
3259    *
3260    * @see
3261    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3262    * .ActionEvent)
3263    */
3264   @Override
3265   public void hideAllSelection_actionPerformed(ActionEvent e)
3266   {
3267     SequenceGroup sg = viewport.getSelectionGroup();
3268     viewport.expandColSelection(sg, false);
3269     viewport.hideAllSelectedSeqs();
3270     viewport.hideSelectedColumns();
3271     alignPanel.updateLayout();
3272     alignPanel.paintAlignment(true, true);
3273     viewport.sendSelection();
3274   }
3275
3276   /*
3277    * (non-Javadoc)
3278    *
3279    * @see
3280    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3281    * ActionEvent)
3282    */
3283   @Override
3284   public void showAllhidden_actionPerformed(ActionEvent e)
3285   {
3286     viewport.showAllHiddenColumns();
3287     viewport.showAllHiddenSeqs();
3288     alignPanel.paintAlignment(true, true);
3289     viewport.sendSelection();
3290   }
3291
3292   @Override
3293   public void hideSelColumns_actionPerformed(ActionEvent e)
3294   {
3295     viewport.hideSelectedColumns();
3296     alignPanel.updateLayout();
3297     alignPanel.paintAlignment(true, true);
3298     viewport.sendSelection();
3299   }
3300
3301   @Override
3302   public void hiddenMarkers_actionPerformed(ActionEvent e)
3303   {
3304     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3305     repaint();
3306   }
3307
3308   /**
3309    * DOCUMENT ME!
3310    *
3311    * @param e
3312    *          DOCUMENT ME!
3313    */
3314   @Override
3315   protected void scaleAbove_actionPerformed(ActionEvent e)
3316   {
3317     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3318     alignPanel.updateLayout();
3319     alignPanel.paintAlignment(true, false);
3320   }
3321
3322   /**
3323    * DOCUMENT ME!
3324    *
3325    * @param e
3326    *          DOCUMENT ME!
3327    */
3328   @Override
3329   protected void scaleLeft_actionPerformed(ActionEvent e)
3330   {
3331     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3332     alignPanel.updateLayout();
3333     alignPanel.paintAlignment(true, false);
3334   }
3335
3336   /**
3337    * DOCUMENT ME!
3338    *
3339    * @param e
3340    *          DOCUMENT ME!
3341    */
3342   @Override
3343   protected void scaleRight_actionPerformed(ActionEvent e)
3344   {
3345     viewport.setScaleRightWrapped(scaleRight.isSelected());
3346     alignPanel.updateLayout();
3347     alignPanel.paintAlignment(true, false);
3348   }
3349
3350   /**
3351    * DOCUMENT ME!
3352    *
3353    * @param e
3354    *          DOCUMENT ME!
3355    */
3356   @Override
3357   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3358   {
3359     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3360     alignPanel.paintAlignment(false, false);
3361   }
3362
3363   /**
3364    * DOCUMENT ME!
3365    *
3366    * @param e
3367    *          DOCUMENT ME!
3368    */
3369   @Override
3370   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3371   {
3372     viewport.setShowText(viewTextMenuItem.isSelected());
3373     alignPanel.paintAlignment(false, false);
3374   }
3375
3376   /**
3377    * DOCUMENT ME!
3378    *
3379    * @param e
3380    *          DOCUMENT ME!
3381    */
3382   @Override
3383   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3384   {
3385     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3386     alignPanel.paintAlignment(false, false);
3387   }
3388
3389   public FeatureSettings featureSettings;
3390
3391   @Override
3392   public FeatureSettingsControllerI getFeatureSettingsUI()
3393   {
3394     return featureSettings;
3395   }
3396
3397   @Override
3398   public void featureSettings_actionPerformed(ActionEvent e)
3399   {
3400     showFeatureSettingsUI();
3401   }
3402
3403   @Override
3404   public FeatureSettingsControllerI showFeatureSettingsUI()
3405   {
3406     if (featureSettings != null)
3407     {
3408       featureSettings.closeOldSettings();
3409       featureSettings = null;
3410     }
3411     if (!showSeqFeatures.isSelected())
3412     {
3413       // make sure features are actually displayed
3414       showSeqFeatures.setSelected(true);
3415       showSeqFeatures_actionPerformed(null);
3416     }
3417     featureSettings = new FeatureSettings(this);
3418     return featureSettings;
3419   }
3420
3421   /**
3422    * Set or clear 'Show Sequence Features'
3423    *
3424    * @param evt
3425    *          DOCUMENT ME!
3426    */
3427   @Override
3428   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3429   {
3430     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3431     alignPanel.paintAlignment(true, true);
3432   }
3433
3434   /**
3435    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3436    * the annotations panel as a whole.
3437    *
3438    * The options to show/hide all annotations should be enabled when the panel
3439    * is shown, and disabled when the panel is hidden.
3440    *
3441    * @param e
3442    */
3443   @Override
3444   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3445   {
3446     final boolean setVisible = annotationPanelMenuItem.isSelected();
3447     viewport.setShowAnnotation(setVisible);
3448     this.showAllSeqAnnotations.setEnabled(setVisible);
3449     this.hideAllSeqAnnotations.setEnabled(setVisible);
3450     this.showAllAlAnnotations.setEnabled(setVisible);
3451     this.hideAllAlAnnotations.setEnabled(setVisible);
3452     alignPanel.updateLayout();
3453   }
3454
3455   @Override
3456   public void alignmentProperties()
3457   {
3458     JComponent pane;
3459     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3460
3461             .formatAsHtml();
3462     String content = MessageManager.formatMessage("label.html_content",
3463             new Object[]
3464             { contents.toString() });
3465     contents = null;
3466
3467     if (Platform.isJS())
3468     {
3469       JLabel textLabel = new JLabel();
3470       textLabel.setText(content);
3471       textLabel.setBackground(Color.WHITE);
3472
3473       pane = new JPanel(new BorderLayout());
3474       ((JPanel) pane).setOpaque(true);
3475       pane.setBackground(Color.WHITE);
3476       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3477     }
3478     else
3479     /**
3480      * Java only
3481      *
3482      * @j2sIgnore
3483      */
3484     {
3485       JEditorPane editPane = new JEditorPane("text/html", "");
3486       editPane.setEditable(false);
3487       editPane.setText(content);
3488       pane = editPane;
3489     }
3490
3491     JInternalFrame frame = new JInternalFrame();
3492
3493     frame.getContentPane().add(new JScrollPane(pane));
3494
3495     Desktop.addInternalFrame(frame, MessageManager
3496             .formatMessage("label.alignment_properties", new Object[]
3497             { getTitle() }), 500, 400);
3498   }
3499
3500   /**
3501    * Opens an Overview panel for the alignment, unless one is open already
3502    *
3503    * @param e
3504    */
3505   @Override
3506   public void overviewMenuItem_actionPerformed(ActionEvent e)
3507   {
3508     boolean showHiddenRegions = Cache
3509             .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
3510     openOverviewPanel(showHiddenRegions);
3511   }
3512
3513   public OverviewPanel openOverviewPanel(boolean showHidden)
3514   {
3515     if (alignPanel.overviewPanel != null)
3516     {
3517       return alignPanel.overviewPanel;
3518     }
3519     JInternalFrame frame = new JInternalFrame();
3520     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
3521             showHidden);
3522     frame.setContentPane(overview);
3523     Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
3524             frame.getHeight(), true, true);
3525     frame.setFrameIcon(null);
3526     frame.pack();
3527     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3528     final AlignmentPanel thePanel = this.alignPanel;
3529     frame.addInternalFrameListener(
3530             new javax.swing.event.InternalFrameAdapter()
3531             {
3532               @Override
3533               public void internalFrameClosed(
3534                       javax.swing.event.InternalFrameEvent evt)
3535               {
3536                 overview.dispose();
3537                 thePanel.setOverviewPanel(null);
3538               }
3539             });
3540     if (getKeyListeners().length > 0)
3541     {
3542       frame.addKeyListener(getKeyListeners()[0]);
3543     }
3544
3545     alignPanel.setOverviewPanel(overview);
3546     alignPanel.setOverviewTitle(this);
3547
3548     return overview;
3549   }
3550
3551   @Override
3552   public void textColour_actionPerformed()
3553   {
3554     new TextColourChooser().chooseColour(alignPanel, null);
3555   }
3556
3557   /*
3558    * public void covariationColour_actionPerformed() {
3559    * changeColour(new
3560    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3561    * ()[0])); }
3562    */
3563   @Override
3564   public void annotationColour_actionPerformed()
3565   {
3566     new AnnotationColourChooser(viewport, alignPanel);
3567   }
3568
3569   @Override
3570   public void annotationColumn_actionPerformed(ActionEvent e)
3571   {
3572     new AnnotationColumnChooser(viewport, alignPanel);
3573   }
3574
3575   /**
3576    * Action on the user checking or unchecking the option to apply the selected
3577    * colour scheme to all groups. If unchecked, groups may have their own
3578    * independent colour schemes.
3579    *
3580    * @param selected
3581    */
3582   @Override
3583   public void applyToAllGroups_actionPerformed(boolean selected)
3584   {
3585     viewport.setColourAppliesToAllGroups(selected);
3586   }
3587
3588   /**
3589    * Action on user selecting a colour from the colour menu
3590    *
3591    * @param name
3592    *          the name (not the menu item label!) of the colour scheme
3593    */
3594   @Override
3595   public void changeColour_actionPerformed(String name)
3596   {
3597     /*
3598      * 'User Defined' opens a panel to configure or load a
3599      * user-defined colour scheme
3600      */
3601     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3602     {
3603       new UserDefinedColours(alignPanel);
3604       return;
3605     }
3606
3607     /*
3608      * otherwise set the chosen colour scheme (or null for 'None')
3609      */
3610     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3611             viewport, viewport.getAlignment(),
3612             viewport.getHiddenRepSequences());
3613     changeColour(cs);
3614   }
3615
3616   /**
3617    * Actions on setting or changing the alignment colour scheme
3618    *
3619    * @param cs
3620    */
3621   @Override
3622   public void changeColour(ColourSchemeI cs)
3623   {
3624     // TODO: pull up to controller method
3625     ColourMenuHelper.setColourSelected(colourMenu, cs);
3626
3627     viewport.setGlobalColourScheme(cs);
3628
3629     alignPanel.paintAlignment(true, true);
3630   }
3631
3632   /**
3633    * Show the PID threshold slider panel
3634    */
3635   @Override
3636   protected void modifyPID_actionPerformed()
3637   {
3638     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3639             alignPanel.getViewName());
3640     SliderPanel.showPIDSlider();
3641   }
3642
3643   /**
3644    * Show the Conservation slider panel
3645    */
3646   @Override
3647   protected void modifyConservation_actionPerformed()
3648   {
3649     SliderPanel.setConservationSlider(alignPanel,
3650             viewport.getResidueShading(), alignPanel.getViewName());
3651     SliderPanel.showConservationSlider();
3652   }
3653
3654   /**
3655    * Action on selecting or deselecting (Colour) By Conservation
3656    */
3657   @Override
3658   public void conservationMenuItem_actionPerformed(boolean selected)
3659   {
3660     modifyConservation.setEnabled(selected);
3661     viewport.setConservationSelected(selected);
3662     viewport.getResidueShading().setConservationApplied(selected);
3663
3664     changeColour(viewport.getGlobalColourScheme());
3665     if (selected)
3666     {
3667       modifyConservation_actionPerformed();
3668     }
3669     else
3670     {
3671       SliderPanel.hideConservationSlider();
3672     }
3673   }
3674
3675   /**
3676    * Action on selecting or deselecting (Colour) Above PID Threshold
3677    */
3678   @Override
3679   public void abovePIDThreshold_actionPerformed(boolean selected)
3680   {
3681     modifyPID.setEnabled(selected);
3682     viewport.setAbovePIDThreshold(selected);
3683     if (!selected)
3684     {
3685       viewport.getResidueShading().setThreshold(0,
3686               viewport.isIgnoreGapsConsensus());
3687     }
3688
3689     changeColour(viewport.getGlobalColourScheme());
3690     if (selected)
3691     {
3692       modifyPID_actionPerformed();
3693     }
3694     else
3695     {
3696       SliderPanel.hidePIDSlider();
3697     }
3698   }
3699
3700   /**
3701    * DOCUMENT ME!
3702    *
3703    * @param e
3704    *          DOCUMENT ME!
3705    */
3706   @Override
3707   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3708   {
3709     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3710     AlignmentSorter.sortByPID(viewport.getAlignment(),
3711             viewport.getAlignment().getSequenceAt(0));
3712     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3713             viewport.getAlignment()));
3714     alignPanel.paintAlignment(true, false);
3715   }
3716
3717   /**
3718    * DOCUMENT ME!
3719    *
3720    * @param e
3721    *          DOCUMENT ME!
3722    */
3723   @Override
3724   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3725   {
3726     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3727     AlignmentSorter.sortByID(viewport.getAlignment());
3728     addHistoryItem(
3729             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3730     alignPanel.paintAlignment(true, false);
3731   }
3732
3733   /**
3734    * DOCUMENT ME!
3735    *
3736    * @param e
3737    *          DOCUMENT ME!
3738    */
3739   @Override
3740   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3741   {
3742     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3743     AlignmentSorter.sortByLength(viewport.getAlignment());
3744     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3745             viewport.getAlignment()));
3746     alignPanel.paintAlignment(true, false);
3747   }
3748
3749   /**
3750    * DOCUMENT ME!
3751    *
3752    * @param e
3753    *          DOCUMENT ME!
3754    */
3755   @Override
3756   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3757   {
3758     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3759     AlignmentSorter.sortByGroup(viewport.getAlignment());
3760     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3761             viewport.getAlignment()));
3762
3763     alignPanel.paintAlignment(true, false);
3764   }
3765
3766   /**
3767    * DOCUMENT ME!
3768    *
3769    * @param e
3770    *          DOCUMENT ME!
3771    */
3772   @Override
3773   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3774   {
3775     new RedundancyPanel(alignPanel, this);
3776   }
3777
3778   /**
3779    * DOCUMENT ME!
3780    *
3781    * @param e
3782    *          DOCUMENT ME!
3783    */
3784   @Override
3785   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3786   {
3787     if ((viewport.getSelectionGroup() == null)
3788             || (viewport.getSelectionGroup().getSize() < 2))
3789     {
3790       JvOptionPane.showInternalMessageDialog(this,
3791               MessageManager.getString(
3792                       "label.you_must_select_least_two_sequences"),
3793               MessageManager.getString("label.invalid_selection"),
3794               JvOptionPane.WARNING_MESSAGE);
3795     }
3796     else
3797     {
3798       JInternalFrame frame = new JInternalFrame();
3799       frame.setContentPane(new PairwiseAlignPanel(viewport));
3800       Desktop.addInternalFrame(frame,
3801               MessageManager.getString("action.pairwise_alignment"), 600,
3802               500);
3803     }
3804   }
3805
3806   @Override
3807   public void autoCalculate_actionPerformed(ActionEvent e)
3808   {
3809     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3810     if (viewport.autoCalculateConsensus)
3811     {
3812       viewport.firePropertyChange("alignment", null,
3813               viewport.getAlignment().getSequences());
3814     }
3815   }
3816
3817   @Override
3818   public void sortByTreeOption_actionPerformed(ActionEvent e)
3819   {
3820     viewport.sortByTree = sortByTree.isSelected();
3821   }
3822
3823   @Override
3824   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3825   {
3826     viewport.followSelection = listenToViewSelections.isSelected();
3827   }
3828
3829   /**
3830    * Constructs a tree panel and adds it to the desktop
3831    *
3832    * @param type
3833    *          tree type (NJ or AV)
3834    * @param modelName
3835    *          name of score model used to compute the tree
3836    * @param options
3837    *          parameters for the distance or similarity calculation
3838    */
3839   void newTreePanel(String type, String modelName,
3840           SimilarityParamsI options)
3841   {
3842     String frameTitle = "";
3843     TreePanel tp;
3844
3845     boolean onSelection = false;
3846     if (viewport.getSelectionGroup() != null
3847             && viewport.getSelectionGroup().getSize() > 0)
3848     {
3849       SequenceGroup sg = viewport.getSelectionGroup();
3850
3851       /* Decide if the selection is a column region */
3852       for (SequenceI _s : sg.getSequences())
3853       {
3854         if (_s.getLength() < sg.getEndRes())
3855         {
3856           JvOptionPane.showMessageDialog(Desktop.desktop,
3857                   MessageManager.getString(
3858                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3859                   MessageManager.getString(
3860                           "label.sequences_selection_not_aligned"),
3861                   JvOptionPane.WARNING_MESSAGE);
3862
3863           return;
3864         }
3865       }
3866       onSelection = true;
3867     }
3868     else
3869     {
3870       if (viewport.getAlignment().getHeight() < 2)
3871       {
3872         return;
3873       }
3874     }
3875
3876     tp = new TreePanel(alignPanel, type, modelName, options);
3877     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3878
3879     frameTitle += " from ";
3880
3881     if (viewport.getViewName() != null)
3882     {
3883       frameTitle += viewport.getViewName() + " of ";
3884     }
3885
3886     frameTitle += this.title;
3887
3888     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3889   }
3890
3891   /**
3892    * DOCUMENT ME!
3893    *
3894    * @param title
3895    *          DOCUMENT ME!
3896    * @param order
3897    *          DOCUMENT ME!
3898    */
3899   public void addSortByOrderMenuItem(String title,
3900           final AlignmentOrder order)
3901   {
3902     final JMenuItem item = new JMenuItem(MessageManager
3903             .formatMessage("action.by_title_param", new Object[]
3904             { title }));
3905     sort.add(item);
3906     item.addActionListener(new java.awt.event.ActionListener()
3907     {
3908       @Override
3909       public void actionPerformed(ActionEvent e)
3910       {
3911         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3912
3913         // TODO: JBPNote - have to map order entries to curent SequenceI
3914         // pointers
3915         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3916
3917         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3918                 viewport.getAlignment()));
3919
3920         alignPanel.paintAlignment(true, false);
3921       }
3922     });
3923   }
3924
3925   /**
3926    * Add a new sort by annotation score menu item
3927    *
3928    * @param sort
3929    *          the menu to add the option to
3930    * @param scoreLabel
3931    *          the label used to retrieve scores for each sequence on the
3932    *          alignment
3933    */
3934   public void addSortByAnnotScoreMenuItem(JMenu sort,
3935           final String scoreLabel)
3936   {
3937     final JMenuItem item = new JMenuItem(scoreLabel);
3938     sort.add(item);
3939     item.addActionListener(new java.awt.event.ActionListener()
3940     {
3941       @Override
3942       public void actionPerformed(ActionEvent e)
3943       {
3944         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3945         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3946                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3947         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3948                 viewport.getAlignment()));
3949         alignPanel.paintAlignment(true, false);
3950       }
3951     });
3952   }
3953
3954   /**
3955    * last hash for alignment's annotation array - used to minimise cost of
3956    * rebuild.
3957    */
3958   protected int _annotationScoreVectorHash;
3959
3960   /**
3961    * search the alignment and rebuild the sort by annotation score submenu the
3962    * last alignment annotation vector hash is stored to minimize cost of
3963    * rebuilding in subsequence calls.
3964    *
3965    */
3966   @Override
3967   public void buildSortByAnnotationScoresMenu()
3968   {
3969     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3970     {
3971       return;
3972     }
3973
3974     if (viewport.getAlignment().getAlignmentAnnotation()
3975             .hashCode() != _annotationScoreVectorHash)
3976     {
3977       sortByAnnotScore.removeAll();
3978       // almost certainly a quicker way to do this - but we keep it simple
3979       Hashtable<String, String> scoreSorts = new Hashtable<>();
3980       AlignmentAnnotation aann[];
3981       for (SequenceI sqa : viewport.getAlignment().getSequences())
3982       {
3983         aann = sqa.getAnnotation();
3984         for (int i = 0; aann != null && i < aann.length; i++)
3985         {
3986           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3987           {
3988             scoreSorts.put(aann[i].label, aann[i].label);
3989           }
3990         }
3991       }
3992       Enumeration<String> labels = scoreSorts.keys();
3993       while (labels.hasMoreElements())
3994       {
3995         addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
3996       }
3997       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3998       scoreSorts.clear();
3999
4000       _annotationScoreVectorHash = viewport.getAlignment()
4001               .getAlignmentAnnotation().hashCode();
4002     }
4003   }
4004
4005   /**
4006    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4007    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4008    * call. Listeners are added to remove the menu item when the treePanel is
4009    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4010    * modified.
4011    */
4012   @Override
4013   public void buildTreeSortMenu()
4014   {
4015     sortByTreeMenu.removeAll();
4016
4017     List<Component> comps = PaintRefresher.components
4018             .get(viewport.getSequenceSetId());
4019     List<TreePanel> treePanels = new ArrayList<>();
4020     for (Component comp : comps)
4021     {
4022       if (comp instanceof TreePanel)
4023       {
4024         treePanels.add((TreePanel) comp);
4025       }
4026     }
4027
4028     if (treePanels.size() < 1)
4029     {
4030       sortByTreeMenu.setVisible(false);
4031       return;
4032     }
4033
4034     sortByTreeMenu.setVisible(true);
4035
4036     for (final TreePanel tp : treePanels)
4037     {
4038       final JMenuItem item = new JMenuItem(tp.getTitle());
4039       item.addActionListener(new java.awt.event.ActionListener()
4040       {
4041         @Override
4042         public void actionPerformed(ActionEvent e)
4043         {
4044           tp.sortByTree_actionPerformed();
4045           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4046
4047         }
4048       });
4049
4050       sortByTreeMenu.add(item);
4051     }
4052   }
4053
4054   public boolean sortBy(AlignmentOrder alorder, String undoname)
4055   {
4056     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4057     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4058     if (undoname != null)
4059     {
4060       addHistoryItem(new OrderCommand(undoname, oldOrder,
4061               viewport.getAlignment()));
4062     }
4063     alignPanel.paintAlignment(true, false);
4064     return true;
4065   }
4066
4067   /**
4068    * Work out whether the whole set of sequences or just the selected set will
4069    * be submitted for multiple alignment.
4070    *
4071    */
4072   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4073   {
4074     // Now, check we have enough sequences
4075     AlignmentView msa = null;
4076
4077     if ((viewport.getSelectionGroup() != null)
4078             && (viewport.getSelectionGroup().getSize() > 1))
4079     {
4080       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4081       // some common interface!
4082       /*
4083        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4084        * SequenceI[sz = seqs.getSize(false)];
4085        *
4086        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4087        * seqs.getSequenceAt(i); }
4088        */
4089       msa = viewport.getAlignmentView(true);
4090     }
4091     else if (viewport.getSelectionGroup() != null
4092             && viewport.getSelectionGroup().getSize() == 1)
4093     {
4094       int option = JvOptionPane.showConfirmDialog(this,
4095               MessageManager.getString("warn.oneseq_msainput_selection"),
4096               MessageManager.getString("label.invalid_selection"),
4097               JvOptionPane.OK_CANCEL_OPTION);
4098       if (option == JvOptionPane.OK_OPTION)
4099       {
4100         msa = viewport.getAlignmentView(false);
4101       }
4102     }
4103     else
4104     {
4105       msa = viewport.getAlignmentView(false);
4106     }
4107     return msa;
4108   }
4109
4110   /**
4111    * Decides what is submitted to a secondary structure prediction service: the
4112    * first sequence in the alignment, or in the current selection, or, if the
4113    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4114    * region or the whole alignment. (where the first sequence in the set is the
4115    * one that the prediction will be for).
4116    */
4117   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4118   {
4119     AlignmentView seqs = null;
4120
4121     if ((viewport.getSelectionGroup() != null)
4122             && (viewport.getSelectionGroup().getSize() > 0))
4123     {
4124       seqs = viewport.getAlignmentView(true);
4125     }
4126     else
4127     {
4128       seqs = viewport.getAlignmentView(false);
4129     }
4130     // limit sequences - JBPNote in future - could spawn multiple prediction
4131     // jobs
4132     // TODO: viewport.getAlignment().isAligned is a global state - the local
4133     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4134     if (!viewport.getAlignment().isAligned(false))
4135     {
4136       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4137       // TODO: if seqs.getSequences().length>1 then should really have warned
4138       // user!
4139
4140     }
4141     return seqs;
4142   }
4143
4144   /**
4145    * DOCUMENT ME!
4146    *
4147    * @param e
4148    *          DOCUMENT ME!
4149    */
4150   @Override
4151   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4152   {
4153     // Pick the tree file
4154     JalviewFileChooser chooser = new JalviewFileChooser(
4155             Cache.getProperty("LAST_DIRECTORY"));
4156     chooser.setFileView(new JalviewFileView());
4157     chooser.setDialogTitle(
4158             MessageManager.getString("label.select_newick_like_tree_file"));
4159     chooser.setToolTipText(
4160             MessageManager.getString("label.load_tree_file"));
4161
4162     chooser.setResponseHandler(0, () -> {
4163       String filePath = chooser.getSelectedFile().getPath();
4164       Cache.setProperty("LAST_DIRECTORY", filePath);
4165       NewickFile fin = null;
4166       try
4167       {
4168         fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4169                 DataSourceType.FILE));
4170         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4171       } catch (Exception ex)
4172       {
4173         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4174                 MessageManager.getString("label.problem_reading_tree_file"),
4175                 JvOptionPane.WARNING_MESSAGE);
4176         ex.printStackTrace();
4177       }
4178       if (fin != null && fin.hasWarningMessage())
4179       {
4180         JvOptionPane.showMessageDialog(Desktop.desktop,
4181                 fin.getWarningMessage(),
4182                 MessageManager
4183                         .getString("label.possible_problem_with_tree_file"),
4184                 JvOptionPane.WARNING_MESSAGE);
4185       }
4186     });
4187     chooser.showOpenDialog(this);
4188   }
4189
4190   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4191   {
4192     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4193   }
4194
4195   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4196           int h, int x, int y)
4197   {
4198     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4199   }
4200
4201   /**
4202    * Add a treeviewer for the tree extracted from a Newick file object to the
4203    * current alignment view
4204    *
4205    * @param nf
4206    *          the tree
4207    * @param title
4208    *          tree viewer title
4209    * @param input
4210    *          Associated alignment input data (or null)
4211    * @param w
4212    *          width
4213    * @param h
4214    *          height
4215    * @param x
4216    *          position
4217    * @param y
4218    *          position
4219    * @return TreePanel handle
4220    */
4221   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4222           AlignmentView input, int w, int h, int x, int y)
4223   {
4224     TreePanel tp = null;
4225
4226     try
4227     {
4228       nf.parse();
4229
4230       if (nf.getTree() != null)
4231       {
4232         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4233
4234         tp.setSize(w, h);
4235
4236         if (x > 0 && y > 0)
4237         {
4238           tp.setLocation(x, y);
4239         }
4240
4241         Desktop.addInternalFrame(tp, treeTitle, w, h);
4242       }
4243     } catch (Exception ex)
4244     {
4245       ex.printStackTrace();
4246     }
4247
4248     return tp;
4249   }
4250
4251   public void showContactMapTree(AlignmentAnnotation aa,
4252           ContactMatrixI cm)
4253   {
4254     int x = 4, y = 5;
4255     int w = 400, h = 500;
4256
4257     try
4258     {
4259       NewickFile fin = new NewickFile(
4260               new FileParse(cm.getNewick(), DataSourceType.PASTE));
4261       String title = aa.label + " "
4262               + cm.getTreeMethod() + " tree" + (aa.sequenceRef != null
4263                       ? (" for " + aa.sequenceRef.getDisplayId(false))
4264                       : "");
4265
4266       showColumnWiseTree(fin, aa, title, w, h, x, y);
4267     } catch (Throwable xx)
4268     {
4269       Console.error("Unexpected exception showing tree for contact matrix",
4270               xx);
4271     }
4272   }
4273
4274   public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
4275           String treeTitle, int w, int h, int x, int y)
4276   {
4277     try
4278     {
4279       nf.parse();
4280       if (nf.getTree() == null)
4281       {
4282         return null;
4283       }
4284       TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle);
4285
4286       tp.setSize(w, h);
4287
4288       if (x > 0 && y > 0)
4289       {
4290         tp.setLocation(x, y);
4291       }
4292
4293       Desktop.addInternalFrame(tp, treeTitle, w, h);
4294       return tp;
4295     } catch (Throwable xx)
4296     {
4297       Console.error("Unexpected exception showing tree for contact matrix",
4298               xx);
4299     }
4300     return null;
4301   }
4302
4303   private boolean buildingMenu = false;
4304
4305   /**
4306    * Generates menu items and listener event actions for web service clients
4307    *
4308    */
4309   public void BuildWebServiceMenu()
4310   {
4311     while (buildingMenu)
4312     {
4313       try
4314       {
4315         System.err.println("Waiting for building menu to finish.");
4316         Thread.sleep(10);
4317       } catch (Exception e)
4318       {
4319       }
4320     }
4321     final AlignFrame me = this;
4322     buildingMenu = true;
4323     new Thread(new Runnable()
4324     {
4325       @Override
4326       public void run()
4327       {
4328         final List<JMenuItem> legacyItems = new ArrayList<>();
4329         try
4330         {
4331           // System.err.println("Building ws menu again "
4332           // + Thread.currentThread());
4333           // TODO: add support for context dependent disabling of services based
4334           // on
4335           // alignment and current selection
4336           // TODO: add additional serviceHandle parameter to specify abstract
4337           // handler
4338           // class independently of AbstractName
4339           // TODO: add in rediscovery GUI function to restart discoverer
4340           // TODO: group services by location as well as function and/or
4341           // introduce
4342           // object broker mechanism.
4343           final Vector<JMenu> wsmenu = new Vector<>();
4344           final IProgressIndicator af = me;
4345
4346           /*
4347            * do not i18n these strings - they are hard-coded in class
4348            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4349            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4350            */
4351           final JMenu msawsmenu = new JMenu("Alignment");
4352           final JMenu secstrmenu = new JMenu(
4353                   "Secondary Structure Prediction");
4354           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4355           final JMenu analymenu = new JMenu("Analysis");
4356           final JMenu dismenu = new JMenu("Protein Disorder");
4357           // JAL-940 - only show secondary structure prediction services from
4358           // the legacy server
4359           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4360               // &&
4361           Discoverer.services != null && (Discoverer.services.size() > 0))
4362           {
4363             // TODO: refactor to allow list of AbstractName/Handler bindings to
4364             // be
4365             // stored or retrieved from elsewhere
4366             // No MSAWS used any more:
4367             // Vector msaws = null; // (Vector)
4368             // Discoverer.services.get("MsaWS");
4369             Vector<ServiceHandle> secstrpr = Discoverer.services
4370                     .get("SecStrPred");
4371             if (secstrpr != null)
4372             {
4373               // Add any secondary structure prediction services
4374               for (int i = 0, j = secstrpr.size(); i < j; i++)
4375               {
4376                 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4377                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4378                         .getServiceClient(sh);
4379                 int p = secstrmenu.getItemCount();
4380                 impl.attachWSMenuEntry(secstrmenu, me);
4381                 int q = secstrmenu.getItemCount();
4382                 for (int litm = p; litm < q; litm++)
4383                 {
4384                   legacyItems.add(secstrmenu.getItem(litm));
4385                 }
4386               }
4387             }
4388           }
4389
4390           // Add all submenus in the order they should appear on the web
4391           // services menu
4392           wsmenu.add(msawsmenu);
4393           wsmenu.add(secstrmenu);
4394           wsmenu.add(dismenu);
4395           wsmenu.add(analymenu);
4396           // No search services yet
4397           // wsmenu.add(seqsrchmenu);
4398
4399           javax.swing.SwingUtilities.invokeLater(new Runnable()
4400           {
4401             @Override
4402             public void run()
4403             {
4404               try
4405               {
4406                 webService.removeAll();
4407                 // first, add discovered services onto the webservices menu
4408                 if (wsmenu.size() > 0)
4409                 {
4410                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4411                   {
4412                     webService.add(wsmenu.get(i));
4413                   }
4414                 }
4415                 else
4416                 {
4417                   webService.add(me.webServiceNoServices);
4418                 }
4419                 // TODO: move into separate menu builder class.
4420                 {
4421                   // logic for 2.11.1.4 is
4422                   // always look to see if there is a discover. if there isn't
4423                   // we can't show any Jws2 services
4424                   // if there are services available, show them - regardless of
4425                   // the 'show JWS2 preference'
4426                   // if the discoverer is running then say so
4427                   // otherwise offer to trigger discovery if 'show JWS2' is not
4428                   // enabled
4429                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4430                   if (jws2servs != null)
4431                   {
4432                     if (jws2servs.hasServices())
4433                     {
4434                       jws2servs.attachWSMenuEntry(webService, me);
4435                       for (Jws2Instance sv : jws2servs.getServices())
4436                       {
4437                         if (sv.description.toLowerCase(Locale.ROOT)
4438                                 .contains("jpred"))
4439                         {
4440                           for (JMenuItem jmi : legacyItems)
4441                           {
4442                             jmi.setVisible(false);
4443                           }
4444                         }
4445                       }
4446                     }
4447
4448                     if (jws2servs.isRunning())
4449                     {
4450                       JMenuItem tm = new JMenuItem(
4451                               "Still discovering JABA Services");
4452                       tm.setEnabled(false);
4453                       webService.add(tm);
4454                     }
4455                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4456                     {
4457                       JMenuItem enableJws2 = new JMenuItem(
4458                               "Discover Web Services");
4459                       enableJws2.setToolTipText(
4460                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4461                       enableJws2.setEnabled(true);
4462                       enableJws2.addActionListener(new ActionListener()
4463                       {
4464
4465                         @Override
4466                         public void actionPerformed(ActionEvent e)
4467                         {
4468                           // start service discoverer, but ignore preference
4469                           Desktop.instance.startServiceDiscovery(false,
4470                                   true);
4471                         }
4472                       });
4473                       webService.add(enableJws2);
4474                     }
4475                   }
4476                 }
4477                 build_urlServiceMenu(me.webService);
4478                 build_fetchdbmenu(webService);
4479                 for (JMenu item : wsmenu)
4480                 {
4481                   if (item.getItemCount() == 0)
4482                   {
4483                     item.setEnabled(false);
4484                   }
4485                   else
4486                   {
4487                     item.setEnabled(true);
4488                   }
4489                 }
4490               } catch (Exception e)
4491               {
4492                 Console.debug(
4493                         "Exception during web service menu building process.",
4494                         e);
4495               }
4496             }
4497           });
4498         } catch (Exception e)
4499         {
4500         }
4501         buildingMenu = false;
4502       }
4503     }).start();
4504
4505   }
4506
4507   /**
4508    * construct any groupURL type service menu entries.
4509    *
4510    * @param webService
4511    */
4512   protected void build_urlServiceMenu(JMenu webService)
4513   {
4514     // TODO: remove this code when 2.7 is released
4515     // DEBUG - alignmentView
4516     /*
4517      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4518      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4519      *
4520      * @Override public void actionPerformed(ActionEvent e) {
4521      * jalview.datamodel.AlignmentView
4522      * .testSelectionViews(af.viewport.getAlignment(),
4523      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4524      *
4525      * }); webService.add(testAlView);
4526      */
4527     // TODO: refactor to RestClient discoverer and merge menu entries for
4528     // rest-style services with other types of analysis/calculation service
4529     // SHmmr test client - still being implemented.
4530     // DEBUG - alignmentView
4531
4532     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4533             .getRestClients())
4534     {
4535       client.attachWSMenuEntry(
4536               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4537               this);
4538     }
4539   }
4540
4541   /**
4542    * Searches the alignment sequences for xRefs and builds the Show
4543    * Cross-References menu (formerly called Show Products), with database
4544    * sources for which cross-references are found (protein sources for a
4545    * nucleotide alignment and vice versa)
4546    *
4547    * @return true if Show Cross-references menu should be enabled
4548    */
4549   public boolean canShowProducts()
4550   {
4551     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4552     AlignmentI dataset = viewport.getAlignment().getDataset();
4553
4554     showProducts.removeAll();
4555     final boolean dna = viewport.getAlignment().isNucleotide();
4556
4557     if (seqs == null || seqs.length == 0)
4558     {
4559       // nothing to see here.
4560       return false;
4561     }
4562
4563     boolean showp = false;
4564     try
4565     {
4566       List<String> ptypes = new CrossRef(seqs, dataset)
4567               .findXrefSourcesForSequences(dna);
4568
4569       for (final String source : ptypes)
4570       {
4571         showp = true;
4572         final AlignFrame af = this;
4573         JMenuItem xtype = new JMenuItem(source);
4574         xtype.addActionListener(new ActionListener()
4575         {
4576           @Override
4577           public void actionPerformed(ActionEvent e)
4578           {
4579             showProductsFor(af.viewport.getSequenceSelection(), dna,
4580                     source);
4581           }
4582         });
4583         showProducts.add(xtype);
4584       }
4585       showProducts.setVisible(showp);
4586       showProducts.setEnabled(showp);
4587     } catch (Exception e)
4588     {
4589       Console.warn(
4590               "canShowProducts threw an exception - please report to help@jalview.org",
4591               e);
4592       return false;
4593     }
4594     return showp;
4595   }
4596
4597   /**
4598    * Finds and displays cross-references for the selected sequences (protein
4599    * products for nucleotide sequences, dna coding sequences for peptides).
4600    *
4601    * @param sel
4602    *          the sequences to show cross-references for
4603    * @param dna
4604    *          true if from a nucleotide alignment (so showing proteins)
4605    * @param source
4606    *          the database to show cross-references for
4607    */
4608   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4609           final String source)
4610   {
4611     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4612             .start();
4613   }
4614
4615   /**
4616    * Construct and display a new frame containing the translation of this
4617    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4618    */
4619   @Override
4620   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4621   {
4622     AlignmentI al = null;
4623     try
4624     {
4625       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4626
4627       al = dna.translateCdna(codeTable);
4628     } catch (Exception ex)
4629     {
4630       Console.error("Exception during translation. Please report this !",
4631               ex);
4632       final String msg = MessageManager.getString(
4633               "label.error_when_translating_sequences_submit_bug_report");
4634       final String errorTitle = MessageManager
4635               .getString("label.implementation_error")
4636               + MessageManager.getString("label.translation_failed");
4637       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4638               JvOptionPane.ERROR_MESSAGE);
4639       return;
4640     }
4641     if (al == null || al.getHeight() == 0)
4642     {
4643       final String msg = MessageManager.getString(
4644               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4645       final String errorTitle = MessageManager
4646               .getString("label.translation_failed");
4647       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4648               JvOptionPane.WARNING_MESSAGE);
4649     }
4650     else
4651     {
4652       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4653       af.setFileFormat(this.currentFileFormat);
4654       final String newTitle = MessageManager
4655               .formatMessage("label.translation_of_params", new Object[]
4656               { this.getTitle(), codeTable.getId() });
4657       af.setTitle(newTitle);
4658       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4659       {
4660         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4661         viewport.openSplitFrame(af, new Alignment(seqs));
4662       }
4663       else
4664       {
4665         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4666                 DEFAULT_HEIGHT);
4667       }
4668     }
4669   }
4670
4671   /**
4672    * Set the file format
4673    *
4674    * @param format
4675    */
4676   public void setFileFormat(FileFormatI format)
4677   {
4678     this.currentFileFormat = format;
4679   }
4680
4681   /**
4682    * Try to load a features file onto the alignment.
4683    *
4684    * @param file
4685    *          contents or path to retrieve file or a File object
4686    * @param sourceType
4687    *          access mode of file (see jalview.io.AlignFile)
4688    * @return true if features file was parsed correctly.
4689    */
4690   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4691   {
4692     // BH 2018
4693     return avc.parseFeaturesFile(file, sourceType,
4694             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4695
4696   }
4697
4698   @Override
4699   public void refreshFeatureUI(boolean enableIfNecessary)
4700   {
4701     // note - currently this is only still here rather than in the controller
4702     // because of the featureSettings hard reference that is yet to be
4703     // abstracted
4704     if (enableIfNecessary)
4705     {
4706       viewport.setShowSequenceFeatures(true);
4707       showSeqFeatures.setSelected(true);
4708     }
4709
4710   }
4711
4712   @Override
4713   public void dragEnter(DropTargetDragEvent evt)
4714   {
4715   }
4716
4717   @Override
4718   public void dragExit(DropTargetEvent evt)
4719   {
4720   }
4721
4722   @Override
4723   public void dragOver(DropTargetDragEvent evt)
4724   {
4725   }
4726
4727   @Override
4728   public void dropActionChanged(DropTargetDragEvent evt)
4729   {
4730   }
4731
4732   @Override
4733   public void drop(DropTargetDropEvent evt)
4734   {
4735     // JAL-1552 - acceptDrop required before getTransferable call for
4736     // Java's Transferable for native dnd
4737     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4738     Transferable t = evt.getTransferable();
4739
4740     final AlignFrame thisaf = this;
4741     final List<Object> files = new ArrayList<>();
4742     List<DataSourceType> protocols = new ArrayList<>();
4743
4744     try
4745     {
4746       Desktop.transferFromDropTarget(files, protocols, evt, t);
4747     } catch (Exception e)
4748     {
4749       e.printStackTrace();
4750     }
4751     if (files != null)
4752     {
4753       new Thread(new Runnable()
4754       {
4755         @Override
4756         public void run()
4757         {
4758           try
4759           {
4760             // check to see if any of these files have names matching sequences
4761             // in
4762             // the alignment
4763             SequenceIdMatcher idm = new SequenceIdMatcher(
4764                     viewport.getAlignment().getSequencesArray());
4765             /**
4766              * Object[] { String,SequenceI}
4767              */
4768             ArrayList<Object[]> filesmatched = new ArrayList<>();
4769             ArrayList<Object> filesnotmatched = new ArrayList<>();
4770             for (int i = 0; i < files.size(); i++)
4771             {
4772               // BH 2018
4773               Object file = files.get(i);
4774               String fileName = file.toString();
4775               String pdbfn = "";
4776               DataSourceType protocol = (file instanceof File
4777                       ? DataSourceType.FILE
4778                       : FormatAdapter.checkProtocol(fileName));
4779               if (protocol == DataSourceType.FILE)
4780               {
4781                 File fl;
4782                 if (file instanceof File)
4783                 {
4784                   fl = (File) file;
4785                   Platform.cacheFileData(fl);
4786                 }
4787                 else
4788                 {
4789                   fl = new File(fileName);
4790                 }
4791                 pdbfn = fl.getName();
4792               }
4793               else if (protocol == DataSourceType.URL)
4794               {
4795                 URL url = new URL(fileName);
4796                 pdbfn = url.getFile();
4797               }
4798               if (pdbfn.length() > 0)
4799               {
4800                 // attempt to find a match in the alignment
4801                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4802                 int l = 0, c = pdbfn.indexOf(".");
4803                 while (mtch == null && c != -1)
4804                 {
4805                   do
4806                   {
4807                     l = c;
4808                   } while ((c = pdbfn.indexOf(".", l)) > l);
4809                   if (l > -1)
4810                   {
4811                     pdbfn = pdbfn.substring(0, l);
4812                   }
4813                   mtch = idm.findAllIdMatches(pdbfn);
4814                 }
4815                 if (mtch != null)
4816                 {
4817                   FileFormatI type;
4818                   try
4819                   {
4820                     type = new IdentifyFile().identify(file, protocol);
4821                   } catch (Exception ex)
4822                   {
4823                     type = null;
4824                   }
4825                   if (type != null && type.isStructureFile())
4826                   {
4827                     filesmatched.add(new Object[] { file, protocol, mtch });
4828                     continue;
4829                   }
4830                 }
4831                 // File wasn't named like one of the sequences or wasn't a PDB
4832                 // file.
4833                 filesnotmatched.add(file);
4834               }
4835             }
4836             int assocfiles = 0;
4837             if (filesmatched.size() > 0)
4838             {
4839               boolean autoAssociate = Cache
4840                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4841               if (!autoAssociate)
4842               {
4843                 String msg = MessageManager.formatMessage(
4844                         "label.automatically_associate_structure_files_with_sequences_same_name",
4845                         new Object[]
4846                         { Integer.valueOf(filesmatched.size())
4847                                 .toString() });
4848                 String ttl = MessageManager.getString(
4849                         "label.automatically_associate_structure_files_by_name");
4850                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4851                         ttl, JvOptionPane.YES_NO_OPTION);
4852                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4853               }
4854               if (autoAssociate)
4855               {
4856                 for (Object[] fm : filesmatched)
4857                 {
4858                   // try and associate
4859                   // TODO: may want to set a standard ID naming formalism for
4860                   // associating PDB files which have no IDs.
4861                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4862                   {
4863                     PDBEntry pe = new AssociatePdbFileWithSeq()
4864                             .associatePdbWithSeq(fm[0].toString(),
4865                                     (DataSourceType) fm[1], toassoc, false,
4866                                     Desktop.instance);
4867                     if (pe != null)
4868                     {
4869                       System.err.println("Associated file : "
4870                               + (fm[0].toString()) + " with "
4871                               + toassoc.getDisplayId(true));
4872                       assocfiles++;
4873                     }
4874                   }
4875                   // TODO: do we need to update overview ? only if features are
4876                   // shown I guess
4877                   alignPanel.paintAlignment(true, false);
4878                 }
4879               }
4880               else
4881               {
4882                 /*
4883                  * add declined structures as sequences
4884                  */
4885                 for (Object[] o : filesmatched)
4886                 {
4887                   filesnotmatched.add(o[0]);
4888                 }
4889               }
4890             }
4891             if (filesnotmatched.size() > 0)
4892             {
4893               if (assocfiles > 0 && (Cache.getDefault(
4894                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4895                       || JvOptionPane.showConfirmDialog(thisaf,
4896                               "<html>" + MessageManager.formatMessage(
4897                                       "label.ignore_unmatched_dropped_files_info",
4898                                       new Object[]
4899                                       { Integer.valueOf(
4900                                               filesnotmatched.size())
4901                                               .toString() })
4902                                       + "</html>",
4903                               MessageManager.getString(
4904                                       "label.ignore_unmatched_dropped_files"),
4905                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4906               {
4907                 return;
4908               }
4909               for (Object fn : filesnotmatched)
4910               {
4911                 loadJalviewDataFile(fn, null, null, null);
4912               }
4913
4914             }
4915           } catch (Exception ex)
4916           {
4917             ex.printStackTrace();
4918           }
4919         }
4920       }).start();
4921     }
4922   }
4923
4924   /**
4925    * Attempt to load a "dropped" file or URL string, by testing in turn for
4926    * <ul>
4927    * <li>an Annotation file</li>
4928    * <li>a JNet file</li>
4929    * <li>a features file</li>
4930    * <li>else try to interpret as an alignment file</li>
4931    * </ul>
4932    *
4933    * @param file
4934    *          either a filename or a URL string.
4935    */
4936   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4937           FileFormatI format, SequenceI assocSeq)
4938   {
4939     // BH 2018 was String file
4940     try
4941     {
4942       if (sourceType == null)
4943       {
4944         sourceType = FormatAdapter.checkProtocol(file);
4945       }
4946       // if the file isn't identified, or not positively identified as some
4947       // other filetype (PFAM is default unidentified alignment file type) then
4948       // try to parse as annotation.
4949       boolean isAnnotation = (format == null
4950               || FileFormat.Pfam.equals(format))
4951                       ? new AnnotationFile().annotateAlignmentView(viewport,
4952                               file, sourceType)
4953                       : false;
4954
4955       if (!isAnnotation)
4956       {
4957         // first see if its a T-COFFEE score file
4958         TCoffeeScoreFile tcf = null;
4959         try
4960         {
4961           tcf = new TCoffeeScoreFile(file, sourceType);
4962           if (tcf.isValid())
4963           {
4964             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4965             {
4966               buildColourMenu();
4967               changeColour(
4968                       new TCoffeeColourScheme(viewport.getAlignment()));
4969               isAnnotation = true;
4970               setStatus(MessageManager.getString(
4971                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4972             }
4973             else
4974             {
4975               // some problem - if no warning its probable that the ID matching
4976               // process didn't work
4977               JvOptionPane.showMessageDialog(Desktop.desktop,
4978                       tcf.getWarningMessage() == null
4979                               ? MessageManager.getString(
4980                                       "label.check_file_matches_sequence_ids_alignment")
4981                               : tcf.getWarningMessage(),
4982                       MessageManager.getString(
4983                               "label.problem_reading_tcoffee_score_file"),
4984                       JvOptionPane.WARNING_MESSAGE);
4985             }
4986           }
4987           else
4988           {
4989             tcf = null;
4990           }
4991         } catch (Exception x)
4992         {
4993           Console.debug(
4994                   "Exception when processing data source as T-COFFEE score file",
4995                   x);
4996           tcf = null;
4997         }
4998         if (tcf == null)
4999         {
5000           // try to see if its a JNet 'concise' style annotation file *before*
5001           // we
5002           // try to parse it as a features file
5003           if (format == null)
5004           {
5005             format = new IdentifyFile().identify(file, sourceType);
5006           }
5007           if (FileFormat.ScoreMatrix == format)
5008           {
5009             ScoreMatrixFile sm = new ScoreMatrixFile(
5010                     new FileParse(file, sourceType));
5011             sm.parse();
5012             // todo: i18n this message
5013             setStatus(MessageManager.formatMessage(
5014                     "label.successfully_loaded_matrix",
5015                     sm.getMatrixName()));
5016           }
5017           else if (FileFormat.Jnet.equals(format))
5018           {
5019             JPredFile predictions = new JPredFile(file, sourceType);
5020             new JnetAnnotationMaker();
5021             JnetAnnotationMaker.add_annotation(predictions,
5022                     viewport.getAlignment(), 0, false);
5023             viewport.getAlignment().setupJPredAlignment();
5024             isAnnotation = true;
5025           }
5026           // else if (IdentifyFile.FeaturesFile.equals(format))
5027           else if (FileFormat.Features.equals(format))
5028           {
5029             if (parseFeaturesFile(file, sourceType))
5030             {
5031               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
5032               if (splitFrame != null)
5033               {
5034                 splitFrame.repaint();
5035               }
5036               else
5037               {
5038                 alignPanel.paintAlignment(true, true);
5039               }
5040             }
5041           }
5042           else
5043           {
5044             new FileLoader().LoadFile(viewport, file, sourceType, format);
5045           }
5046         }
5047       }
5048       if (isAnnotation)
5049       {
5050
5051         alignPanel.adjustAnnotationHeight();
5052         viewport.updateSequenceIdColours();
5053         buildSortByAnnotationScoresMenu();
5054         alignPanel.paintAlignment(true, true);
5055       }
5056     } catch (Exception ex)
5057     {
5058       ex.printStackTrace();
5059     } catch (OutOfMemoryError oom)
5060     {
5061       try
5062       {
5063         System.gc();
5064       } catch (Exception x)
5065       {
5066       }
5067       new OOMWarning(
5068               "loading data "
5069                       + (sourceType != null
5070                               ? (sourceType == DataSourceType.PASTE
5071                                       ? "from clipboard."
5072                                       : "using " + sourceType + " from "
5073                                               + file)
5074                               : ".")
5075                       + (format != null
5076                               ? "(parsing as '" + format + "' file)"
5077                               : ""),
5078               oom, Desktop.desktop);
5079     }
5080   }
5081
5082   /**
5083    * Method invoked by the ChangeListener on the tabbed pane, in other words
5084    * when a different tabbed pane is selected by the user or programmatically.
5085    */
5086   @Override
5087   public void tabSelectionChanged(int index)
5088   {
5089     if (index > -1)
5090     {
5091       /*
5092        * update current Overview window title (if there is one)
5093        * to add view name "Original" if necessary
5094        */
5095       alignPanel.setOverviewTitle(this);
5096
5097       /*
5098        * switch panels and set Overview title (if there is one
5099        * because it was opened automatically)
5100        */
5101       alignPanel = alignPanels.get(index);
5102       alignPanel.setOverviewTitle(this);
5103
5104       viewport = alignPanel.av;
5105       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5106       setMenusFromViewport(viewport);
5107       if (featureSettings != null && featureSettings.isOpen()
5108               && featureSettings.fr.getViewport() != viewport)
5109       {
5110         if (viewport.isShowSequenceFeatures())
5111         {
5112           // refresh the featureSettings to reflect UI change
5113           showFeatureSettingsUI();
5114         }
5115         else
5116         {
5117           // close feature settings for this view.
5118           featureSettings.close();
5119         }
5120       }
5121
5122     }
5123
5124     /*
5125      * 'focus' any colour slider that is open to the selected viewport
5126      */
5127     if (viewport.getConservationSelected())
5128     {
5129       SliderPanel.setConservationSlider(alignPanel,
5130               viewport.getResidueShading(), alignPanel.getViewName());
5131     }
5132     else
5133     {
5134       SliderPanel.hideConservationSlider();
5135     }
5136     if (viewport.getAbovePIDThreshold())
5137     {
5138       SliderPanel.setPIDSliderSource(alignPanel,
5139               viewport.getResidueShading(), alignPanel.getViewName());
5140     }
5141     else
5142     {
5143       SliderPanel.hidePIDSlider();
5144     }
5145
5146     /*
5147      * If there is a frame linked to this one in a SplitPane, switch it to the
5148      * same view tab index. No infinite recursion of calls should happen, since
5149      * tabSelectionChanged() should not get invoked on setting the selected
5150      * index to an unchanged value. Guard against setting an invalid index
5151      * before the new view peer tab has been created.
5152      */
5153     final AlignViewportI peer = viewport.getCodingComplement();
5154     if (peer != null)
5155     {
5156       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5157               .getAlignPanel().alignFrame;
5158       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5159       {
5160         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5161       }
5162     }
5163   }
5164
5165   /**
5166    * On right mouse click on view tab, prompt for and set new view name.
5167    */
5168   @Override
5169   public void tabbedPane_mousePressed(MouseEvent e)
5170   {
5171     if (e.isPopupTrigger())
5172     {
5173       String msg = MessageManager.getString("label.enter_view_name");
5174       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5175       String reply = JvOptionPane.showInputDialog(msg, ttl);
5176
5177       if (reply != null)
5178       {
5179         viewport.setViewName(reply);
5180         // TODO warn if reply is in getExistingViewNames()?
5181         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5182       }
5183     }
5184   }
5185
5186   public AlignViewport getCurrentView()
5187   {
5188     return viewport;
5189   }
5190
5191   /**
5192    * Open the dialog for regex description parsing.
5193    */
5194   @Override
5195   protected void extractScores_actionPerformed(ActionEvent e)
5196   {
5197     ParseProperties pp = new jalview.analysis.ParseProperties(
5198             viewport.getAlignment());
5199     // TODO: verify regex and introduce GUI dialog for version 2.5
5200     // if (pp.getScoresFromDescription("col", "score column ",
5201     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5202     // true)>0)
5203     if (pp.getScoresFromDescription("description column",
5204             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5205     {
5206       buildSortByAnnotationScoresMenu();
5207     }
5208   }
5209
5210   /*
5211    * (non-Javadoc)
5212    *
5213    * @see
5214    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5215    * )
5216    */
5217   @Override
5218   protected void showDbRefs_actionPerformed(ActionEvent e)
5219   {
5220     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5221   }
5222
5223   /*
5224    * (non-Javadoc)
5225    *
5226    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5227    * ActionEvent)
5228    */
5229   @Override
5230   protected void showNpFeats_actionPerformed(ActionEvent e)
5231   {
5232     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5233   }
5234
5235   /**
5236    * find the viewport amongst the tabs in this alignment frame and close that
5237    * tab
5238    *
5239    * @param av
5240    */
5241   public boolean closeView(AlignViewportI av)
5242   {
5243     if (viewport == av)
5244     {
5245       this.closeMenuItem_actionPerformed(false);
5246       return true;
5247     }
5248     Component[] comp = tabbedPane.getComponents();
5249     for (int i = 0; comp != null && i < comp.length; i++)
5250     {
5251       if (comp[i] instanceof AlignmentPanel)
5252       {
5253         if (((AlignmentPanel) comp[i]).av == av)
5254         {
5255           // close the view.
5256           closeView((AlignmentPanel) comp[i]);
5257           return true;
5258         }
5259       }
5260     }
5261     return false;
5262   }
5263
5264   protected void build_fetchdbmenu(JMenu webService)
5265   {
5266     // Temporary hack - DBRef Fetcher always top level ws entry.
5267     // TODO We probably want to store a sequence database checklist in
5268     // preferences and have checkboxes.. rather than individual sources selected
5269     // here
5270     final JMenu rfetch = new JMenu(
5271             MessageManager.getString("action.fetch_db_references"));
5272     rfetch.setToolTipText(MessageManager.getString(
5273             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5274     webService.add(rfetch);
5275
5276     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5277             MessageManager.getString("option.trim_retrieved_seqs"));
5278     trimrs.setToolTipText(
5279             MessageManager.getString("label.trim_retrieved_sequences"));
5280     trimrs.setSelected(
5281             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5282     trimrs.addActionListener(new ActionListener()
5283     {
5284       @Override
5285       public void actionPerformed(ActionEvent e)
5286       {
5287         trimrs.setSelected(trimrs.isSelected());
5288         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5289                 Boolean.valueOf(trimrs.isSelected()).toString());
5290       }
5291     });
5292     rfetch.add(trimrs);
5293     JMenuItem fetchr = new JMenuItem(
5294             MessageManager.getString("label.standard_databases"));
5295     fetchr.setToolTipText(
5296             MessageManager.getString("label.fetch_embl_uniprot"));
5297     fetchr.addActionListener(new ActionListener()
5298     {
5299
5300       @Override
5301       public void actionPerformed(ActionEvent e)
5302       {
5303         new Thread(new Runnable()
5304         {
5305           @Override
5306           public void run()
5307           {
5308             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5309                     .getAlignment().isNucleotide();
5310             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5311                     alignPanel.av.getSequenceSelection(),
5312                     alignPanel.alignFrame, null,
5313                     alignPanel.alignFrame.featureSettings, isNucleotide);
5314             dbRefFetcher.addListener(new FetchFinishedListenerI()
5315             {
5316               @Override
5317               public void finished()
5318               {
5319
5320                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5321                         .getFeatureSettingsModels())
5322                 {
5323
5324                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5325                 }
5326                 AlignFrame.this.setMenusForViewport();
5327               }
5328             });
5329             dbRefFetcher.fetchDBRefs(false);
5330           }
5331         }).start();
5332
5333       }
5334
5335     });
5336     rfetch.add(fetchr);
5337     new Thread(new Runnable()
5338     {
5339       @Override
5340       public void run()
5341       {
5342         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5343                 .getSequenceFetcherSingleton();
5344         javax.swing.SwingUtilities.invokeLater(new Runnable()
5345         {
5346           @Override
5347           public void run()
5348           {
5349             String[] dbclasses = sf.getNonAlignmentSources();
5350             List<DbSourceProxy> otherdb;
5351             JMenu dfetch = new JMenu();
5352             JMenu ifetch = new JMenu();
5353             JMenuItem fetchr = null;
5354             int comp = 0, icomp = 0, mcomp = 15;
5355             String mname = null;
5356             int dbi = 0;
5357             for (String dbclass : dbclasses)
5358             {
5359               otherdb = sf.getSourceProxy(dbclass);
5360               // add a single entry for this class, or submenu allowing 'fetch
5361               // all' or pick one
5362               if (otherdb == null || otherdb.size() < 1)
5363               {
5364                 continue;
5365               }
5366               if (mname == null)
5367               {
5368                 mname = "From " + dbclass;
5369               }
5370               if (otherdb.size() == 1)
5371               {
5372                 final DbSourceProxy[] dassource = otherdb
5373                         .toArray(new DbSourceProxy[0]);
5374                 DbSourceProxy src = otherdb.get(0);
5375                 fetchr = new JMenuItem(src.getDbSource());
5376                 fetchr.addActionListener(new ActionListener()
5377                 {
5378
5379                   @Override
5380                   public void actionPerformed(ActionEvent e)
5381                   {
5382                     new Thread(new Runnable()
5383                     {
5384
5385                       @Override
5386                       public void run()
5387                       {
5388                         boolean isNucleotide = alignPanel.alignFrame
5389                                 .getViewport().getAlignment()
5390                                 .isNucleotide();
5391                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5392                                 alignPanel.av.getSequenceSelection(),
5393                                 alignPanel.alignFrame, dassource,
5394                                 alignPanel.alignFrame.featureSettings,
5395                                 isNucleotide);
5396                         dbRefFetcher
5397                                 .addListener(new FetchFinishedListenerI()
5398                                 {
5399                                   @Override
5400                                   public void finished()
5401                                   {
5402                                     FeatureSettingsModelI srcSettings = dassource[0]
5403                                             .getFeatureColourScheme();
5404                                     alignPanel.av.mergeFeaturesStyle(
5405                                             srcSettings);
5406                                     AlignFrame.this.setMenusForViewport();
5407                                   }
5408                                 });
5409                         dbRefFetcher.fetchDBRefs(false);
5410                       }
5411                     }).start();
5412                   }
5413
5414                 });
5415                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5416                         MessageManager.formatMessage(
5417                                 "label.fetch_retrieve_from", new Object[]
5418                                 { src.getDbName() })));
5419                 dfetch.add(fetchr);
5420                 comp++;
5421               }
5422               else
5423               {
5424                 final DbSourceProxy[] dassource = otherdb
5425                         .toArray(new DbSourceProxy[0]);
5426                 // fetch all entry
5427                 DbSourceProxy src = otherdb.get(0);
5428                 fetchr = new JMenuItem(MessageManager
5429                         .formatMessage("label.fetch_all_param", new Object[]
5430                         { src.getDbSource() }));
5431                 fetchr.addActionListener(new ActionListener()
5432                 {
5433                   @Override
5434                   public void actionPerformed(ActionEvent e)
5435                   {
5436                     new Thread(new Runnable()
5437                     {
5438
5439                       @Override
5440                       public void run()
5441                       {
5442                         boolean isNucleotide = alignPanel.alignFrame
5443                                 .getViewport().getAlignment()
5444                                 .isNucleotide();
5445                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5446                                 alignPanel.av.getSequenceSelection(),
5447                                 alignPanel.alignFrame, dassource,
5448                                 alignPanel.alignFrame.featureSettings,
5449                                 isNucleotide);
5450                         dbRefFetcher
5451                                 .addListener(new FetchFinishedListenerI()
5452                                 {
5453                                   @Override
5454                                   public void finished()
5455                                   {
5456                                     AlignFrame.this.setMenusForViewport();
5457                                   }
5458                                 });
5459                         dbRefFetcher.fetchDBRefs(false);
5460                       }
5461                     }).start();
5462                   }
5463                 });
5464
5465                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5466                         MessageManager.formatMessage(
5467                                 "label.fetch_retrieve_from_all_sources",
5468                                 new Object[]
5469                                 { Integer.valueOf(otherdb.size())
5470                                         .toString(),
5471                                     src.getDbSource(), src.getDbName() })));
5472                 dfetch.add(fetchr);
5473                 comp++;
5474                 // and then build the rest of the individual menus
5475                 ifetch = new JMenu(MessageManager.formatMessage(
5476                         "label.source_from_db_source", new Object[]
5477                         { src.getDbSource() }));
5478                 icomp = 0;
5479                 String imname = null;
5480                 int i = 0;
5481                 for (DbSourceProxy sproxy : otherdb)
5482                 {
5483                   String dbname = sproxy.getDbName();
5484                   String sname = dbname.length() > 5
5485                           ? dbname.substring(0, 5) + "..."
5486                           : dbname;
5487                   String msname = dbname.length() > 10
5488                           ? dbname.substring(0, 10) + "..."
5489                           : dbname;
5490                   if (imname == null)
5491                   {
5492                     imname = MessageManager
5493                             .formatMessage("label.from_msname", new Object[]
5494                             { sname });
5495                   }
5496                   fetchr = new JMenuItem(msname);
5497                   final DbSourceProxy[] dassrc = { sproxy };
5498                   fetchr.addActionListener(new ActionListener()
5499                   {
5500
5501                     @Override
5502                     public void actionPerformed(ActionEvent e)
5503                     {
5504                       new Thread(new Runnable()
5505                       {
5506
5507                         @Override
5508                         public void run()
5509                         {
5510                           boolean isNucleotide = alignPanel.alignFrame
5511                                   .getViewport().getAlignment()
5512                                   .isNucleotide();
5513                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5514                                   alignPanel.av.getSequenceSelection(),
5515                                   alignPanel.alignFrame, dassrc,
5516                                   alignPanel.alignFrame.featureSettings,
5517                                   isNucleotide);
5518                           dbRefFetcher
5519                                   .addListener(new FetchFinishedListenerI()
5520                                   {
5521                                     @Override
5522                                     public void finished()
5523                                     {
5524                                       AlignFrame.this.setMenusForViewport();
5525                                     }
5526                                   });
5527                           dbRefFetcher.fetchDBRefs(false);
5528                         }
5529                       }).start();
5530                     }
5531
5532                   });
5533                   fetchr.setToolTipText(
5534                           "<html>" + MessageManager.formatMessage(
5535                                   "label.fetch_retrieve_from", new Object[]
5536                                   { dbname }));
5537                   ifetch.add(fetchr);
5538                   ++i;
5539                   if (++icomp >= mcomp || i == (otherdb.size()))
5540                   {
5541                     ifetch.setText(MessageManager.formatMessage(
5542                             "label.source_to_target", imname, sname));
5543                     dfetch.add(ifetch);
5544                     ifetch = new JMenu();
5545                     imname = null;
5546                     icomp = 0;
5547                     comp++;
5548                   }
5549                 }
5550               }
5551               ++dbi;
5552               if (comp >= mcomp || dbi >= (dbclasses.length))
5553               {
5554                 dfetch.setText(MessageManager.formatMessage(
5555                         "label.source_to_target", mname, dbclass));
5556                 rfetch.add(dfetch);
5557                 dfetch = new JMenu();
5558                 mname = null;
5559                 comp = 0;
5560               }
5561             }
5562           }
5563         });
5564       }
5565     }).start();
5566
5567   }
5568
5569   /**
5570    * Left justify the whole alignment.
5571    */
5572   @Override
5573   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5574   {
5575     AlignmentI al = viewport.getAlignment();
5576     al.justify(false);
5577     viewport.firePropertyChange("alignment", null, al);
5578   }
5579
5580   /**
5581    * Right justify the whole alignment.
5582    */
5583   @Override
5584   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5585   {
5586     AlignmentI al = viewport.getAlignment();
5587     al.justify(true);
5588     viewport.firePropertyChange("alignment", null, al);
5589   }
5590
5591   @Override
5592   public void setShowSeqFeatures(boolean b)
5593   {
5594     showSeqFeatures.setSelected(b);
5595     viewport.setShowSequenceFeatures(b);
5596   }
5597
5598   /*
5599    * (non-Javadoc)
5600    *
5601    * @see
5602    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5603    * awt.event.ActionEvent)
5604    */
5605   @Override
5606   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5607   {
5608     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5609     alignPanel.paintAlignment(false, false);
5610   }
5611
5612   /*
5613    * (non-Javadoc)
5614    *
5615    * @see
5616    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5617    * .ActionEvent)
5618    */
5619   @Override
5620   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5621   {
5622     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5623     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5624
5625   }
5626
5627   /*
5628    * (non-Javadoc)
5629    *
5630    * @see
5631    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5632    * .event.ActionEvent)
5633    */
5634   @Override
5635   protected void showGroupConservation_actionPerformed(ActionEvent e)
5636   {
5637     viewport.setShowGroupConservation(showGroupConservation.getState());
5638     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5639   }
5640
5641   /*
5642    * (non-Javadoc)
5643    *
5644    * @see
5645    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5646    * .event.ActionEvent)
5647    */
5648   @Override
5649   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5650   {
5651     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5652     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5653   }
5654
5655   /*
5656    * (non-Javadoc)
5657    *
5658    * @see
5659    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5660    * .event.ActionEvent)
5661    */
5662   @Override
5663   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5664   {
5665     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5666     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5667   }
5668
5669   @Override
5670   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5671   {
5672     showSequenceLogo.setState(true);
5673     viewport.setShowSequenceLogo(true);
5674     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5675     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5676   }
5677
5678   @Override
5679   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5680   {
5681     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5682   }
5683
5684   /*
5685    * (non-Javadoc)
5686    *
5687    * @see
5688    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5689    * .event.ActionEvent)
5690    */
5691   @Override
5692   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5693   {
5694     if (avc.makeGroupsFromSelection())
5695     {
5696       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5697       alignPanel.updateAnnotation();
5698       alignPanel.paintAlignment(true,
5699               viewport.needToUpdateStructureViews());
5700     }
5701   }
5702
5703   public void clearAlignmentSeqRep()
5704   {
5705     // TODO refactor alignmentseqrep to controller
5706     if (viewport.getAlignment().hasSeqrep())
5707     {
5708       viewport.getAlignment().setSeqrep(null);
5709       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5710       alignPanel.updateAnnotation();
5711       alignPanel.paintAlignment(true, true);
5712     }
5713   }
5714
5715   @Override
5716   protected void createGroup_actionPerformed(ActionEvent e)
5717   {
5718     if (avc.createGroup())
5719     {
5720       if (applyAutoAnnotationSettings.isSelected())
5721       {
5722         alignPanel.updateAnnotation(true, false);
5723       }
5724       alignPanel.alignmentChanged();
5725     }
5726   }
5727
5728   @Override
5729   protected void unGroup_actionPerformed(ActionEvent e)
5730   {
5731     if (avc.unGroup())
5732     {
5733       alignPanel.alignmentChanged();
5734     }
5735   }
5736
5737   /**
5738    * make the given alignmentPanel the currently selected tab
5739    *
5740    * @param alignmentPanel
5741    */
5742   public void setDisplayedView(AlignmentPanel alignmentPanel)
5743   {
5744     if (!viewport.getSequenceSetId()
5745             .equals(alignmentPanel.av.getSequenceSetId()))
5746     {
5747       throw new Error(MessageManager.getString(
5748               "error.implementation_error_cannot_show_view_alignment_frame"));
5749     }
5750     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5751             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5752     {
5753       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5754     }
5755   }
5756
5757   /**
5758    * Action on selection of menu options to Show or Hide annotations.
5759    *
5760    * @param visible
5761    * @param forSequences
5762    *          update sequence-related annotations
5763    * @param forAlignment
5764    *          update non-sequence-related annotations
5765    */
5766   @Override
5767   public void setAnnotationsVisibility(boolean visible,
5768           boolean forSequences, boolean forAlignment)
5769   {
5770     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5771             .getAlignmentAnnotation();
5772     if (anns == null)
5773     {
5774       return;
5775     }
5776     for (AlignmentAnnotation aa : anns)
5777     {
5778       /*
5779        * don't display non-positional annotations on an alignment
5780        */
5781       if (aa.annotations == null)
5782       {
5783         continue;
5784       }
5785       boolean apply = (aa.sequenceRef == null && forAlignment)
5786               || (aa.sequenceRef != null && forSequences);
5787       if (apply)
5788       {
5789         aa.visible = visible;
5790       }
5791     }
5792     alignPanel.validateAnnotationDimensions(true);
5793     alignPanel.alignmentChanged();
5794   }
5795
5796   /**
5797    * Store selected annotation sort order for the view and repaint.
5798    */
5799   @Override
5800   protected void sortAnnotations_actionPerformed()
5801   {
5802     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5803     this.alignPanel.av
5804             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5805     alignPanel.paintAlignment(false, false);
5806   }
5807
5808   /**
5809    *
5810    * @return alignment panels in this alignment frame
5811    */
5812   public List<? extends AlignmentViewPanel> getAlignPanels()
5813   {
5814     // alignPanels is never null
5815     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5816     return alignPanels;
5817   }
5818
5819   /**
5820    * Open a new alignment window, with the cDNA associated with this (protein)
5821    * alignment, aligned as is the protein.
5822    */
5823   protected void viewAsCdna_actionPerformed()
5824   {
5825     // TODO no longer a menu action - refactor as required
5826     final AlignmentI alignment = getViewport().getAlignment();
5827     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5828     if (mappings == null)
5829     {
5830       return;
5831     }
5832     List<SequenceI> cdnaSeqs = new ArrayList<>();
5833     for (SequenceI aaSeq : alignment.getSequences())
5834     {
5835       for (AlignedCodonFrame acf : mappings)
5836       {
5837         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5838         if (dnaSeq != null)
5839         {
5840           /*
5841            * There is a cDNA mapping for this protein sequence - add to new
5842            * alignment. It will share the same dataset sequence as other mapped
5843            * cDNA (no new mappings need to be created).
5844            */
5845           final Sequence newSeq = new Sequence(dnaSeq);
5846           newSeq.setDatasetSequence(dnaSeq);
5847           cdnaSeqs.add(newSeq);
5848         }
5849       }
5850     }
5851     if (cdnaSeqs.size() == 0)
5852     {
5853       // show a warning dialog no mapped cDNA
5854       return;
5855     }
5856     AlignmentI cdna = new Alignment(
5857             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5858     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5859             AlignFrame.DEFAULT_HEIGHT);
5860     cdna.alignAs(alignment);
5861     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5862             + this.title;
5863     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5864             AlignFrame.DEFAULT_HEIGHT);
5865   }
5866
5867   /**
5868    * Set visibility of dna/protein complement view (available when shown in a
5869    * split frame).
5870    *
5871    * @param show
5872    */
5873   @Override
5874   protected void showComplement_actionPerformed(boolean show)
5875   {
5876     SplitContainerI sf = getSplitViewContainer();
5877     if (sf != null)
5878     {
5879       sf.setComplementVisible(this, show);
5880     }
5881   }
5882
5883   /**
5884    * Generate the reverse (optionally complemented) of the selected sequences,
5885    * and add them to the alignment
5886    */
5887   @Override
5888   protected void showReverse_actionPerformed(boolean complement)
5889   {
5890     AlignmentI al = null;
5891     try
5892     {
5893       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5894       al = dna.reverseCdna(complement);
5895       viewport.addAlignment(al, "");
5896       addHistoryItem(new EditCommand(
5897               MessageManager.getString("label.add_sequences"), Action.PASTE,
5898               al.getSequencesArray(), 0, al.getWidth(),
5899               viewport.getAlignment()));
5900     } catch (Exception ex)
5901     {
5902       System.err.println(ex.getMessage());
5903       return;
5904     }
5905   }
5906
5907   /**
5908    * Try to run a script in the Groovy console, having first ensured that this
5909    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5910    * be targeted at this alignment.
5911    */
5912   @Override
5913   protected void runGroovy_actionPerformed()
5914   {
5915     Jalview.setCurrentAlignFrame(this);
5916     groovy.ui.Console console = Desktop.getGroovyConsole();
5917     if (console != null)
5918     {
5919       try
5920       {
5921         console.runScript();
5922       } catch (Exception ex)
5923       {
5924         System.err.println((ex.toString()));
5925         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5926                 MessageManager.getString("label.couldnt_run_groovy_script"),
5927                 MessageManager.getString("label.groovy_support_failed"),
5928                 JvOptionPane.ERROR_MESSAGE);
5929       }
5930     }
5931     else
5932     {
5933       System.err.println("Can't run Groovy script as console not found");
5934     }
5935   }
5936
5937   /**
5938    * Hides columns containing (or not containing) a specified feature, provided
5939    * that would not leave all columns hidden
5940    *
5941    * @param featureType
5942    * @param columnsContaining
5943    * @return
5944    */
5945   public boolean hideFeatureColumns(String featureType,
5946           boolean columnsContaining)
5947   {
5948     boolean notForHiding = avc.markColumnsContainingFeatures(
5949             columnsContaining, false, false, featureType);
5950     if (notForHiding)
5951     {
5952       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5953               false, featureType))
5954       {
5955         getViewport().hideSelectedColumns();
5956         return true;
5957       }
5958     }
5959     return false;
5960   }
5961
5962   @Override
5963   protected void selectHighlightedColumns_actionPerformed(
5964           ActionEvent actionEvent)
5965   {
5966     // include key modifier check in case user selects from menu
5967     avc.markHighlightedColumns(
5968             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5969             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5970                     | ActionEvent.CTRL_MASK)) != 0);
5971   }
5972
5973   @Override
5974   protected void copyHighlightedColumns_actionPerformed(
5975           ActionEvent actionEvent)
5976   {
5977     avc.copyHighlightedRegionsToClipboard();
5978   }
5979
5980   /**
5981    * Rebuilds the Colour menu, including any user-defined colours which have
5982    * been loaded either on startup or during the session
5983    */
5984   public void buildColourMenu()
5985   {
5986     colourMenu.removeAll();
5987
5988     colourMenu.add(applyToAllGroups);
5989     colourMenu.add(textColour);
5990     colourMenu.addSeparator();
5991
5992     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5993             viewport.getAlignment(), false);
5994
5995     colourMenu.add(annotationColour);
5996     bg.add(annotationColour);
5997     colourMenu.addSeparator();
5998     colourMenu.add(conservationMenuItem);
5999     colourMenu.add(modifyConservation);
6000     colourMenu.add(abovePIDThreshold);
6001     colourMenu.add(modifyPID);
6002
6003     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
6004     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
6005   }
6006
6007   /**
6008    * Open a dialog (if not already open) that allows the user to select and
6009    * calculate PCA or Tree analysis
6010    */
6011   protected void openTreePcaDialog()
6012   {
6013     if (alignPanel.getCalculationDialog() == null)
6014     {
6015       new CalculationChooser(AlignFrame.this);
6016     }
6017   }
6018
6019   @Override
6020   protected void loadVcf_actionPerformed()
6021   {
6022     JalviewFileChooser chooser = new JalviewFileChooser(
6023             Cache.getProperty("LAST_DIRECTORY"));
6024     chooser.setFileView(new JalviewFileView());
6025     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
6026     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
6027     final AlignFrame us = this;
6028     chooser.setResponseHandler(0, () -> {
6029       String choice = chooser.getSelectedFile().getPath();
6030       Cache.setProperty("LAST_DIRECTORY", choice);
6031       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
6032       new VCFLoader(choice).loadVCF(seqs, us);
6033     });
6034     chooser.showOpenDialog(null);
6035
6036   }
6037
6038   private Rectangle lastFeatureSettingsBounds = null;
6039
6040   @Override
6041   public void setFeatureSettingsGeometry(Rectangle bounds)
6042   {
6043     lastFeatureSettingsBounds = bounds;
6044   }
6045
6046   @Override
6047   public Rectangle getFeatureSettingsGeometry()
6048   {
6049     return lastFeatureSettingsBounds;
6050   }
6051
6052 }
6053
6054 class PrintThread extends Thread
6055 {
6056   AlignmentPanel ap;
6057
6058   public PrintThread(AlignmentPanel ap)
6059   {
6060     this.ap = ap;
6061   }
6062
6063   static PageFormat pf;
6064
6065   @Override
6066   public void run()
6067   {
6068     PrinterJob printJob = PrinterJob.getPrinterJob();
6069
6070     if (pf != null)
6071     {
6072       printJob.setPrintable(ap, pf);
6073     }
6074     else
6075     {
6076       printJob.setPrintable(ap);
6077     }
6078
6079     if (printJob.printDialog())
6080     {
6081       try
6082       {
6083         printJob.print();
6084       } catch (Exception PrintException)
6085       {
6086         PrintException.printStackTrace();
6087       }
6088     }
6089   }
6090 }