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.OutputStreamWriter;
  53 import java.io.PrintWriter;
  54 import java.net.URL;
  55 import java.util.ArrayList;
  56 import java.util.Arrays;
  57 import java.util.Deque;
  58 import java.util.Enumeration;
  59 import java.util.Hashtable;
  60 import java.util.List;
  61 import java.util.Locale;
  62 import java.util.Vector;
  63
  64 import javax.swing.ButtonGroup;
  65 import javax.swing.JCheckBoxMenuItem;
  66 import javax.swing.JComponent;
  67 import javax.swing.JEditorPane;
  68 import javax.swing.JInternalFrame;
  69 import javax.swing.JLabel;
  70 import javax.swing.JLayeredPane;
  71 import javax.swing.JMenu;
  72 import javax.swing.JMenuItem;
  73 import javax.swing.JPanel;
  74 import javax.swing.JScrollPane;
  75 import javax.swing.SwingUtilities;
  76
  77 import ext.vamsas.ServiceHandle;
  78 import jalview.analysis.AlignmentSorter;
  79 import jalview.analysis.AlignmentUtils;
  80 import jalview.analysis.CrossRef;
  81 import jalview.analysis.Dna;
  82 import jalview.analysis.GeneticCodeI;
  83 import jalview.analysis.ParseProperties;
  84 import jalview.analysis.SequenceIdMatcher;
  85 import jalview.api.AlignExportSettingsI;
  86 import jalview.api.AlignViewControllerGuiI;
  87 import jalview.api.AlignViewControllerI;
  88 import jalview.api.AlignViewportI;
  89 import jalview.api.AlignmentViewPanel;
  90 import jalview.api.FeatureSettingsControllerI;
  91 import jalview.api.FeatureSettingsModelI;
  92 import jalview.api.SplitContainerI;
  93 import jalview.api.ViewStyleI;
  94 import jalview.api.analysis.SimilarityParamsI;
  95 import jalview.bin.Cache;
  96 import jalview.bin.Console;
  97 import jalview.bin.Jalview;
  98 import jalview.commands.CommandI;
  99 import jalview.commands.EditCommand;
 100 import jalview.commands.EditCommand.Action;
 101 import jalview.commands.OrderCommand;
 102 import jalview.commands.RemoveGapColCommand;
 103 import jalview.commands.RemoveGapsCommand;
 104 import jalview.commands.SlideSequencesCommand;
 105 import jalview.commands.TrimRegionCommand;
 106 import jalview.datamodel.AlignExportSettingsAdapter;
 107 import jalview.datamodel.AlignedCodonFrame;
 108 import jalview.datamodel.Alignment;
 109 import jalview.datamodel.AlignmentAnnotation;
 110 import jalview.datamodel.AlignmentExportData;
 111 import jalview.datamodel.AlignmentI;
 112 import jalview.datamodel.AlignmentOrder;
 113 import jalview.datamodel.AlignmentView;
 114 import jalview.datamodel.ColumnSelection;
 115 import jalview.datamodel.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.jws1.Discoverer;
 162 import jalview.ws.jws2.Jws2Discoverer;
 163 import jalview.ws.jws2.jabaws2.Jws2Instance;
 164 import jalview.ws.seqfetcher.DbSourceProxy;
 165
 166 /**
 167  * DOCUMENT ME!
 168  *
 169  * @author $author$
 170  * @version $Revision$
 171  */
 172 @SuppressWarnings("serial")
 173 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 174         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 175 {
 176
 177   public static final int DEFAULT_WIDTH = 700;
 178
 179   public static final int DEFAULT_HEIGHT = 500;
 180
 181   /*
 182    * The currently displayed panel (selected tabbed view if more than one)
 183    */
 184   public AlignmentPanel alignPanel;
 185
 186   AlignViewport viewport;
 187
 188   public AlignViewControllerI avc;
 189
 190   List<AlignmentPanel> alignPanels = new ArrayList<>();
 191
 192   /**
 193    * Last format used to load or save alignments in this window
 194    */
 195   FileFormatI currentFileFormat = null;
 196
 197   /**
 198    * Current filename for this alignment
 199    */
 200   String fileName = null;
 201
 202   File fileObject;
 203
 204   /**
 205    * Creates a new AlignFrame object with specific width and height.
 206    *
 207    * @param al
 208    * @param width
 209    * @param height
 210    */
 211   public AlignFrame(AlignmentI al, int width, int height)
 212   {
 213     this(al, null, width, height);
 214   }
 215
 216   /**
 217    * Creates a new AlignFrame object with specific width, height and
 218    * sequenceSetId
 219    *
 220    * @param al
 221    * @param width
 222    * @param height
 223    * @param sequenceSetId
 224    */
 225   public AlignFrame(AlignmentI al, int width, int height,
 226           String sequenceSetId)
 227   {
 228     this(al, null, width, height, sequenceSetId);
 229   }
 230
 231   /**
 232    * Creates a new AlignFrame object with specific width, height and
 233    * sequenceSetId
 234    *
 235    * @param al
 236    * @param width
 237    * @param height
 238    * @param sequenceSetId
 239    * @param viewId
 240    */
 241   public AlignFrame(AlignmentI al, int width, int height,
 242           String sequenceSetId, String viewId)
 243   {
 244     this(al, null, width, height, sequenceSetId, viewId);
 245   }
 246
 247   /**
 248    * new alignment window with hidden columns
 249    *
 250    * @param al
 251    *          AlignmentI
 252    * @param hiddenColumns
 253    *          ColumnSelection or null
 254    * @param width
 255    *          Width of alignment frame
 256    * @param height
 257    *          height of frame.
 258    */
 259   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 260           int height)
 261   {
 262     this(al, hiddenColumns, width, height, null);
 263   }
 264
 265   /**
 266    * Create alignment frame for al with hiddenColumns, a specific width and
 267    * height, and specific sequenceId
 268    *
 269    * @param al
 270    * @param hiddenColumns
 271    * @param width
 272    * @param height
 273    * @param sequenceSetId
 274    *          (may be null)
 275    */
 276   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 277           int height, String sequenceSetId)
 278   {
 279     this(al, hiddenColumns, width, height, sequenceSetId, null);
 280   }
 281
 282   /**
 283    * Create alignment frame for al with hiddenColumns, a specific width and
 284    * height, and specific sequenceId
 285    *
 286    * @param al
 287    * @param hiddenColumns
 288    * @param width
 289    * @param height
 290    * @param sequenceSetId
 291    *          (may be null)
 292    * @param viewId
 293    *          (may be null)
 294    */
 295   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 296           int height, String sequenceSetId, String viewId)
 297   {
 298     setSize(width, height);
 299
 300     if (al.getDataset() == null)
 301     {
 302       al.setDataset(null);
 303     }
 304
 305     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 306
 307     alignPanel = new AlignmentPanel(this, viewport);
 308
 309     addAlignmentPanel(alignPanel, true);
 310     init();
 311   }
 312
 313   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 314           HiddenColumns hiddenColumns, int width, int height)
 315   {
 316     setSize(width, height);
 317
 318     if (al.getDataset() == null)
 319     {
 320       al.setDataset(null);
 321     }
 322
 323     viewport = new AlignViewport(al, hiddenColumns);
 324
 325     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 326     {
 327       viewport.hideSequence(hiddenSeqs);
 328     }
 329     alignPanel = new AlignmentPanel(this, viewport);
 330     addAlignmentPanel(alignPanel, true);
 331     init();
 332   }
 333
 334   /**
 335    * Make a new AlignFrame from existing alignmentPanels
 336    *
 337    * @param ap
 338    *          AlignmentPanel
 339    * @param av
 340    *          AlignViewport
 341    */
 342   public AlignFrame(AlignmentPanel ap)
 343   {
 344     viewport = ap.av;
 345     alignPanel = ap;
 346     addAlignmentPanel(ap, false);
 347     init();
 348   }
 349
 350   /**
 351    * initalise the alignframe from the underlying viewport data and the
 352    * configurations
 353    */
 354   void init()
 355   {
 356     setFrameIcon(null);
 357
 358     // setBackground(Color.white); // BH 2019
 359
 360     if (!Jalview.isHeadlessMode())
 361     {
 362       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 363     }
 364
 365     avc = new jalview.controller.AlignViewController(this, viewport,
 366             alignPanel);
 367     if (viewport.getAlignmentConservationAnnotation() == null)
 368     {
 369       // BLOSUM62Colour.setEnabled(false);
 370       conservationMenuItem.setEnabled(false);
 371       modifyConservation.setEnabled(false);
 372       // PIDColour.setEnabled(false);
 373       // abovePIDThreshold.setEnabled(false);
 374       // modifyPID.setEnabled(false);
 375     }
 376
 377     String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 378
 379     if (sortby.equals("Id"))
 380     {
 381       sortIDMenuItem_actionPerformed(null);
 382     }
 383     else if (sortby.equals("Pairwise Identity"))
 384     {
 385       sortPairwiseMenuItem_actionPerformed(null);
 386     }
 387
 388     this.alignPanel.av
 389             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 390
 391     setMenusFromViewport(viewport);
 392     buildSortByAnnotationScoresMenu();
 393     calculateTree.addActionListener(new ActionListener()
 394     {
 395
 396       @Override
 397       public void actionPerformed(ActionEvent e)
 398       {
 399         openTreePcaDialog();
 400       }
 401     });
 402     buildColourMenu();
 403
 404     if (Desktop.desktop != null)
 405     {
 406       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 407       if (!Platform.isJS())
 408       {
 409         addServiceListeners();
 410       }
 411       setGUINucleotide();
 412     }
 413
 414     if (viewport.getWrapAlignment())
 415     {
 416       wrapMenuItem_actionPerformed(null);
 417     }
 418
 419     if (Cache.getDefault("SHOW_OVERVIEW", false))
 420     {
 421       this.overviewMenuItem_actionPerformed(null);
 422     }
 423
 424     addKeyListener();
 425
 426     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 427     final List<AlignmentPanel> origview = new ArrayList<>();
 428     final String menuLabel = MessageManager
 429             .getString("label.copy_format_from");
 430     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 431             new ViewSetProvider()
 432             {
 433
 434               @Override
 435               public AlignmentPanel[] getAllAlignmentPanels()
 436               {
 437                 origview.clear();
 438                 origview.add(alignPanel);
 439                 // make an array of all alignment panels except for this one
 440                 List<AlignmentPanel> aps = new ArrayList<>(
 441                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 442                 aps.remove(AlignFrame.this.alignPanel);
 443                 return aps.toArray(new AlignmentPanel[aps.size()]);
 444               }
 445             }, selviews, new ItemListener()
 446             {
 447
 448               @Override
 449               public void itemStateChanged(ItemEvent e)
 450               {
 451                 if (origview.size() > 0)
 452                 {
 453                   final AlignmentPanel ap = origview.get(0);
 454
 455                   /*
 456                    * Copy the ViewStyle of the selected panel to 'this one'.
 457                    * Don't change value of 'scaleProteinAsCdna' unless copying
 458                    * from a SplitFrame.
 459                    */
 460                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 461                           .getViewStyle();
 462                   boolean fromSplitFrame = selviews.get(0)
 463                           .getAlignViewport().getCodingComplement() != null;
 464                   if (!fromSplitFrame)
 465                   {
 466                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 467                             .getViewStyle().isScaleProteinAsCdna());
 468                   }
 469                   ap.getAlignViewport().setViewStyle(vs);
 470
 471                   /*
 472                    * Also rescale ViewStyle of SplitFrame complement if there is
 473                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 474                    * the whole ViewStyle (allow cDNA protein to have different
 475                    * fonts)
 476                    */
 477                   AlignViewportI complement = ap.getAlignViewport()
 478                           .getCodingComplement();
 479                   if (complement != null && vs.isScaleProteinAsCdna())
 480                   {
 481                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 482                     ((SplitFrame) af.getSplitViewContainer())
 483                             .adjustLayout();
 484                     af.setMenusForViewport();
 485                   }
 486
 487                   ap.updateLayout();
 488                   ap.setSelected(true);
 489                   ap.alignFrame.setMenusForViewport();
 490
 491                 }
 492               }
 493             });
 494     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
 495             .indexOf("devel") > -1
 496             || Cache.getDefault("VERSION", "DEVELOPMENT")
 497                     .toLowerCase(Locale.ROOT).indexOf("test") > -1)
 498     {
 499       formatMenu.add(vsel);
 500     }
 501     addFocusListener(new FocusAdapter()
 502     {
 503       @Override
 504       public void focusGained(FocusEvent e)
 505       {
 506         Jalview.setCurrentAlignFrame(AlignFrame.this);
 507       }
 508     });
 509
 510   }
 511
 512   /**
 513    * Change the filename and format for the alignment, and enable the 'reload'
 514    * button functionality.
 515    *
 516    * @param file
 517    *          valid filename
 518    * @param format
 519    *          format of file
 520    */
 521   public void setFileName(String file, FileFormatI format)
 522   {
 523     fileName = file;
 524     setFileFormat(format);
 525     reload.setEnabled(true);
 526   }
 527
 528   /**
 529    * JavaScript will have this, maybe others. More dependable than a file name
 530    * and maintains a reference to the actual bytes loaded.
 531    *
 532    * @param file
 533    */
 534   public void setFileObject(File file)
 535   {
 536     this.fileObject = file;
 537   }
 538
 539   /**
 540    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 541    * events
 542    */
 543   void addKeyListener()
 544   {
 545     addKeyListener(new KeyAdapter()
 546     {
 547       @Override
 548       public void keyPressed(KeyEvent evt)
 549       {
 550         if (viewport.cursorMode
 551                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 552                         && evt.getKeyCode() <= KeyEvent.VK_9)
 553                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 554                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 555                 && Character.isDigit(evt.getKeyChar()))
 556         {
 557           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 558         }
 559
 560         switch (evt.getKeyCode())
 561         {
 562
 563         case 27: // escape key
 564           deselectAllSequenceMenuItem_actionPerformed(null);
 565
 566           break;
 567
 568         case KeyEvent.VK_DOWN:
 569           if (evt.isAltDown() || !viewport.cursorMode)
 570           {
 571             moveSelectedSequences(false);
 572           }
 573           if (viewport.cursorMode)
 574           {
 575             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 576           }
 577           break;
 578
 579         case KeyEvent.VK_UP:
 580           if (evt.isAltDown() || !viewport.cursorMode)
 581           {
 582             moveSelectedSequences(true);
 583           }
 584           if (viewport.cursorMode)
 585           {
 586             alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
 587           }
 588
 589           break;
 590
 591         case KeyEvent.VK_LEFT:
 592           if (evt.isAltDown() || !viewport.cursorMode)
 593           {
 594             slideSequences(false,
 595                     alignPanel.getSeqPanel().getKeyboardNo1());
 596           }
 597           else
 598           {
 599             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 600           }
 601
 602           break;
 603
 604         case KeyEvent.VK_RIGHT:
 605           if (evt.isAltDown() || !viewport.cursorMode)
 606           {
 607             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 608           }
 609           else
 610           {
 611             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 612           }
 613           break;
 614
 615         case KeyEvent.VK_SPACE:
 616           if (viewport.cursorMode)
 617           {
 618             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 619                     || evt.isShiftDown() || evt.isAltDown());
 620           }
 621           break;
 622
 623         // case KeyEvent.VK_A:
 624         // if (viewport.cursorMode)
 625         // {
 626         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 627         // //jalview.bin.Console.outPrintln("A");
 628         // }
 629         // break;
 630         /*
 631          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 632          * jalview.bin.Console.outPrintln("closing bracket"); } break;
 633          */
 634         case KeyEvent.VK_DELETE:
 635         case KeyEvent.VK_BACK_SPACE:
 636           if (!viewport.cursorMode)
 637           {
 638             cut_actionPerformed();
 639           }
 640           else
 641           {
 642             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 643                     || evt.isShiftDown() || evt.isAltDown());
 644           }
 645
 646           break;
 647
 648         case KeyEvent.VK_S:
 649           if (viewport.cursorMode)
 650           {
 651             alignPanel.getSeqPanel().setCursorRow();
 652           }
 653           break;
 654         case KeyEvent.VK_C:
 655           if (viewport.cursorMode && !evt.isControlDown())
 656           {
 657             alignPanel.getSeqPanel().setCursorColumn();
 658           }
 659           break;
 660         case KeyEvent.VK_P:
 661           if (viewport.cursorMode)
 662           {
 663             alignPanel.getSeqPanel().setCursorPosition();
 664           }
 665           break;
 666
 667         case KeyEvent.VK_ENTER:
 668         case KeyEvent.VK_COMMA:
 669           if (viewport.cursorMode)
 670           {
 671             alignPanel.getSeqPanel().setCursorRowAndColumn();
 672           }
 673           break;
 674
 675         case KeyEvent.VK_Q:
 676           if (viewport.cursorMode)
 677           {
 678             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 679           }
 680           break;
 681         case KeyEvent.VK_M:
 682           if (viewport.cursorMode)
 683           {
 684             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 685           }
 686           break;
 687
 688         case KeyEvent.VK_F2:
 689           viewport.cursorMode = !viewport.cursorMode;
 690           setStatus(MessageManager
 691                   .formatMessage("label.keyboard_editing_mode", new String[]
 692                   { (viewport.cursorMode ? "on" : "off") }));
 693           if (viewport.cursorMode)
 694           {
 695             ViewportRanges ranges = viewport.getRanges();
 696             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 697                     .getStartRes();
 698             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 699                     .getStartSeq();
 700           }
 701           alignPanel.getSeqPanel().seqCanvas.repaint();
 702           break;
 703
 704         case KeyEvent.VK_F1:
 705           try
 706           {
 707             Help.showHelpWindow();
 708           } catch (Exception ex)
 709           {
 710             ex.printStackTrace();
 711           }
 712           break;
 713         case KeyEvent.VK_H:
 714         {
 715           boolean toggleSeqs = !evt.isControlDown();
 716           boolean toggleCols = !evt.isShiftDown();
 717           toggleHiddenRegions(toggleSeqs, toggleCols);
 718           break;
 719         }
 720         case KeyEvent.VK_B:
 721         {
 722           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 723           boolean modifyExisting = true; // always modify, don't clear
 724                                          // evt.isShiftDown();
 725           boolean invertHighlighted = evt.isAltDown();
 726           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 727                   toggleSel);
 728           break;
 729         }
 730         case KeyEvent.VK_PAGE_UP:
 731           viewport.getRanges().pageUp();
 732           break;
 733         case KeyEvent.VK_PAGE_DOWN:
 734           viewport.getRanges().pageDown();
 735           break;
 736         }
 737       }
 738
 739       @Override
 740       public void keyReleased(KeyEvent evt)
 741       {
 742         switch (evt.getKeyCode())
 743         {
 744         case KeyEvent.VK_LEFT:
 745           if (evt.isAltDown() || !viewport.cursorMode)
 746           {
 747             viewport.firePropertyChange("alignment", null,
 748                     viewport.getAlignment().getSequences());
 749           }
 750           break;
 751
 752         case KeyEvent.VK_RIGHT:
 753           if (evt.isAltDown() || !viewport.cursorMode)
 754           {
 755             viewport.firePropertyChange("alignment", null,
 756                     viewport.getAlignment().getSequences());
 757           }
 758           break;
 759         }
 760       }
 761     });
 762   }
 763
 764   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 765   {
 766     ap.alignFrame = this;
 767     avc = new jalview.controller.AlignViewController(this, viewport,
 768             alignPanel);
 769
 770     alignPanels.add(ap);
 771
 772     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 773
 774     int aSize = alignPanels.size();
 775
 776     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 777
 778     if (aSize == 1 && ap.av.getViewName() == null)
 779     {
 780       this.getContentPane().add(ap, BorderLayout.CENTER);
 781     }
 782     else
 783     {
 784       if (aSize == 2)
 785       {
 786         setInitialTabVisible();
 787       }
 788
 789       expandViews.setEnabled(true);
 790       gatherViews.setEnabled(true);
 791       tabbedPane.addTab(ap.av.getViewName(), ap);
 792
 793       ap.setVisible(false);
 794     }
 795
 796     if (newPanel)
 797     {
 798       if (ap.av.isPadGaps())
 799       {
 800         ap.av.getAlignment().padGaps();
 801       }
 802       ap.av.updateConservation(ap);
 803       ap.av.updateConsensus(ap);
 804       ap.av.updateStrucConsensus(ap);
 805     }
 806   }
 807
 808   public void setInitialTabVisible()
 809   {
 810     expandViews.setEnabled(true);
 811     gatherViews.setEnabled(true);
 812     tabbedPane.setVisible(true);
 813     AlignmentPanel first = alignPanels.get(0);
 814     tabbedPane.addTab(first.av.getViewName(), first);
 815     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 816   }
 817
 818   public AlignViewport getViewport()
 819   {
 820     return viewport;
 821   }
 822
 823   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 824   private void addServiceListeners()
 825   {
 826     final java.beans.PropertyChangeListener thisListener;
 827     Desktop.instance.addJalviewPropertyChangeListener("services",
 828             thisListener = new java.beans.PropertyChangeListener()
 829             {
 830               @Override
 831               public void propertyChange(PropertyChangeEvent evt)
 832               {
 833                 // // jalview.bin.Console.outPrintln("Discoverer property
 834                 // change.");
 835                 // if (evt.getPropertyName().equals("services"))
 836                 {
 837                   SwingUtilities.invokeLater(new Runnable()
 838                   {
 839
 840                     @Override
 841                     public void run()
 842                     {
 843                       jalview.bin.Console.errPrintln(
 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         // jalview.bin.Console.outPrintln("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 void registerHandler(final long id,
 993           final IProgressIndicatorHandler handler)
 994   {
 995     if (progressBar != null)
 996       progressBar.registerHandler(id, handler);
 997   }
 998
 999   /**
1000    *
1001    * @return true if any progress bars are still active
1002    */
1003   @Override
1004   public boolean operationInProgress()
1005   {
1006     return progressBar == null ? false : progressBar.operationInProgress();
1007   }
1008
1009   /**
1010    * Sets the text of the status bar. Note that setting a null or empty value
1011    * will cause the status bar to be hidden, with possibly undesirable flicker
1012    * of the screen layout.
1013    */
1014   @Override
1015   public void setStatus(String text)
1016   {
1017     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1018   }
1019
1020   /*
1021    * Added so Castor Mapping file can obtain Jalview Version
1022    */
1023   public String getVersion()
1024   {
1025     return Cache.getProperty("VERSION");
1026   }
1027
1028   public FeatureRenderer getFeatureRenderer()
1029   {
1030     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1031   }
1032
1033   @Override
1034   public void fetchSequence_actionPerformed()
1035   {
1036     new SequenceFetcher(this);
1037   }
1038
1039   @Override
1040   public void addFromFile_actionPerformed(ActionEvent e)
1041   {
1042     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1043   }
1044
1045   @Override
1046   public void reload_actionPerformed(ActionEvent e)
1047   {
1048     if (fileName != null)
1049     {
1050       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1051       // originating file's format
1052       // TODO: work out how to recover feature settings for correct view(s) when
1053       // file is reloaded.
1054       if (FileFormat.Jalview.equals(currentFileFormat))
1055       {
1056         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1057         for (int i = 0; i < frames.length; i++)
1058         {
1059           if (frames[i] instanceof AlignFrame && frames[i] != this
1060                   && ((AlignFrame) frames[i]).fileName != null
1061                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1062           {
1063             try
1064             {
1065               frames[i].setSelected(true);
1066               Desktop.instance.closeAssociatedWindows();
1067             } catch (java.beans.PropertyVetoException ex)
1068             {
1069             }
1070           }
1071
1072         }
1073         Desktop.instance.closeAssociatedWindows();
1074
1075         FileLoader loader = new FileLoader();
1076         DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1077                 ? DataSourceType.URL
1078                 : DataSourceType.FILE;
1079         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1080       }
1081       else
1082       {
1083         Rectangle bounds = this.getBounds();
1084
1085         FileLoader loader = new FileLoader();
1086
1087         AlignFrame newframe = null;
1088
1089         if (fileObject == null)
1090         {
1091
1092           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1093                   fileName) ? DataSourceType.URL : DataSourceType.FILE;
1094           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1095                   currentFileFormat);
1096         }
1097         else
1098         {
1099           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1100                   DataSourceType.FILE, currentFileFormat);
1101         }
1102
1103         newframe.setBounds(bounds);
1104         if (featureSettings != null && featureSettings.isShowing())
1105         {
1106           final Rectangle fspos = featureSettings.frame.getBounds();
1107           // TODO: need a 'show feature settings' function that takes bounds -
1108           // need to refactor Desktop.addFrame
1109           newframe.featureSettings_actionPerformed(null);
1110           final FeatureSettings nfs = newframe.featureSettings;
1111           SwingUtilities.invokeLater(new Runnable()
1112           {
1113             @Override
1114             public void run()
1115             {
1116               nfs.frame.setBounds(fspos);
1117             }
1118           });
1119           this.featureSettings.close();
1120           this.featureSettings = null;
1121         }
1122         this.closeMenuItem_actionPerformed(true);
1123       }
1124     }
1125   }
1126
1127   @Override
1128   public void addFromText_actionPerformed(ActionEvent e)
1129   {
1130     Desktop.instance
1131             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1132   }
1133
1134   @Override
1135   public void addFromURL_actionPerformed(ActionEvent e)
1136   {
1137     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1138   }
1139
1140   @Override
1141   public void save_actionPerformed(ActionEvent e)
1142   {
1143     if (fileName == null || (currentFileFormat == null)
1144             || HttpUtils.startsWithHttpOrHttps(fileName))
1145     {
1146       saveAs_actionPerformed();
1147     }
1148     else
1149     {
1150       saveAlignment(fileName, currentFileFormat);
1151     }
1152   }
1153
1154   /**
1155    * Saves the alignment to a file with a name chosen by the user, if necessary
1156    * warning if a file would be overwritten
1157    */
1158   @Override
1159   public void saveAs_actionPerformed()
1160   {
1161     String format = currentFileFormat == null ? null
1162             : currentFileFormat.getName();
1163     JalviewFileChooser chooser = JalviewFileChooser
1164             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1165
1166     chooser.setFileView(new JalviewFileView());
1167     chooser.setDialogTitle(
1168             MessageManager.getString("label.save_alignment_to_file"));
1169     chooser.setToolTipText(MessageManager.getString("action.save"));
1170
1171     int value = chooser.showSaveDialog(this);
1172
1173     if (value != JalviewFileChooser.APPROVE_OPTION)
1174     {
1175       return;
1176     }
1177     currentFileFormat = chooser.getSelectedFormat();
1178     // todo is this (2005) test now obsolete - value is never null?
1179     while (currentFileFormat == null)
1180     {
1181       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1182               MessageManager
1183                       .getString("label.select_file_format_before_saving"),
1184               MessageManager.getString("label.file_format_not_specified"),
1185               JvOptionPane.WARNING_MESSAGE);
1186       currentFileFormat = chooser.getSelectedFormat();
1187       value = chooser.showSaveDialog(this);
1188       if (value != JalviewFileChooser.APPROVE_OPTION)
1189       {
1190         return;
1191       }
1192     }
1193
1194     fileName = chooser.getSelectedFile().getPath();
1195
1196     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1197     Cache.setProperty("LAST_DIRECTORY", fileName);
1198     saveAlignment(fileName, currentFileFormat);
1199   }
1200
1201   boolean lastSaveSuccessful = false;
1202
1203   FileFormatI lastFormatSaved;
1204
1205   String lastFilenameSaved;
1206
1207   /**
1208    * Raise a dialog or status message for the last call to saveAlignment.
1209    *
1210    * @return true if last call to saveAlignment(file, format) was successful.
1211    */
1212   public boolean isSaveAlignmentSuccessful()
1213   {
1214
1215     if (!lastSaveSuccessful)
1216     {
1217       if (!Platform.isHeadless())
1218       {
1219         JvOptionPane.showInternalMessageDialog(this, MessageManager
1220                 .formatMessage("label.couldnt_save_file", new Object[]
1221                 { lastFilenameSaved }),
1222                 MessageManager.getString("label.error_saving_file"),
1223                 JvOptionPane.WARNING_MESSAGE);
1224       }
1225       else
1226       {
1227         Console.error(MessageManager
1228                 .formatMessage("label.couldnt_save_file", new Object[]
1229                 { lastFilenameSaved }));
1230       }
1231     }
1232     else
1233     {
1234
1235       setStatus(MessageManager.formatMessage(
1236               "label.successfully_saved_to_file_in_format", new Object[]
1237               { lastFilenameSaved, lastFormatSaved }));
1238
1239     }
1240     return lastSaveSuccessful;
1241   }
1242
1243   /**
1244    * Saves the alignment to the specified file path, in the specified format,
1245    * which may be an alignment format, or Jalview project format. If the
1246    * alignment has hidden regions, or the format is one capable of including
1247    * non-sequence data (features, annotations, groups), then the user may be
1248    * prompted to specify what to include in the output.
1249    *
1250    * @param file
1251    * @param format
1252    */
1253   public void saveAlignment(String file, FileFormatI format)
1254   {
1255     saveAlignment(file, format, false);
1256   }
1257
1258   public void saveAlignment(String file, FileFormatI format, boolean stdout)
1259   {
1260     lastSaveSuccessful = true;
1261     if (!stdout)
1262     {
1263       lastFilenameSaved = file;
1264     }
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       // TODO deal with stdout=true
1276       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1277               shortName);
1278
1279       Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1280       if (lastSaveSuccessful)
1281       {
1282         this.getViewport().setSavedUpToDate(true);
1283       }
1284
1285       statusBar.setText(MessageManager.formatMessage(
1286               "label.successfully_saved_to_file_in_format", new Object[]
1287               { file, format }));
1288
1289       return;
1290     }
1291
1292     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1293     Runnable cancelAction = () -> {
1294       lastSaveSuccessful = false;
1295     };
1296     Runnable outputAction = () -> {
1297       // todo defer this to inside formatSequences (or later)
1298       AlignmentExportData exportData = viewport.getAlignExportData(options);
1299       String output = new FormatAdapter(alignPanel, options)
1300               .formatSequences(format, exportData.getAlignment(),
1301                       exportData.getOmitHidden(),
1302                       exportData.getStartEndPostions(),
1303                       viewport.getAlignment().getHiddenColumns());
1304       if (output == null)
1305       {
1306         lastSaveSuccessful = false;
1307       }
1308       else
1309       {
1310         // create backupfiles object and get new temp filename destination
1311         boolean doBackup = BackupFiles.getEnabled() && !stdout;
1312         BackupFiles backupfiles = null;
1313         if (doBackup)
1314         {
1315           Console.trace("ALIGNFRAME making backupfiles object for " + file);
1316           backupfiles = new BackupFiles(file);
1317         }
1318         try
1319         {
1320           String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1321                   : file;
1322           Console.trace("ALIGNFRAME setting PrintWriter");
1323           PrintWriter out = stdout
1324                   ? new PrintWriter(new OutputStreamWriter(System.out))
1325                   : new PrintWriter(new FileWriter(tempFilePath));
1326
1327           if (backupfiles != null)
1328           {
1329             Console.trace("ALIGNFRAME about to write to temp file "
1330                     + backupfiles.getTempFilePath());
1331           }
1332
1333           out.print(output);
1334           out.flush();
1335           if (!stdout)
1336           {
1337             Console.trace("ALIGNFRAME about to close file");
1338             out.close();
1339             Console.trace("ALIGNFRAME closed file");
1340           }
1341           AlignFrame.this.setTitle(stdout ? "STDOUT" : file);
1342           if (stdout)
1343           {
1344             statusBar.setText(MessageManager.formatMessage(
1345                     "label.successfully_printed_to_stdout_in_format",
1346                     new Object[]
1347                     { format.getName() }));
1348           }
1349           else
1350           {
1351             statusBar.setText(MessageManager.formatMessage(
1352                     "label.successfully_saved_to_file_in_format",
1353                     new Object[]
1354                     { fileName, format.getName() }));
1355           }
1356           lastSaveSuccessful = true;
1357         } catch (IOException e)
1358         {
1359           lastSaveSuccessful = false;
1360           Console.error(
1361                   "ALIGNFRAME Something happened writing the temp file");
1362           Console.error(e.getMessage());
1363           Console.debug(Cache.getStackTraceString(e));
1364         } catch (Exception ex)
1365         {
1366           lastSaveSuccessful = false;
1367           Console.error(
1368                   "ALIGNFRAME Something unexpected happened writing the temp file");
1369           Console.error(ex.getMessage());
1370           Console.debug(Cache.getStackTraceString(ex));
1371         }
1372
1373         if (doBackup)
1374         {
1375           backupfiles.setWriteSuccess(lastSaveSuccessful);
1376           Console.debug("ALIGNFRAME writing temp file was "
1377                   + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1378           // do the backup file roll and rename the temp file to actual file
1379           Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1380           lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1381           Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1382                   + (lastSaveSuccessful ? "" : "un") + "successfully");
1383         }
1384
1385         Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
1386         if (lastSaveSuccessful)
1387         {
1388           AlignFrame.this.getViewport().setSavedUpToDate(true);
1389         }
1390       }
1391     };
1392
1393     /*
1394      * show dialog with export options if applicable; else just do it
1395      */
1396     if (AlignExportOptions.isNeeded(viewport, format))
1397     {
1398       AlignExportOptions choices = new AlignExportOptions(
1399               alignPanel.getAlignViewport(), format, options);
1400       choices.setResponseAction(0, outputAction);
1401       choices.setResponseAction(1, cancelAction);
1402       choices.showDialog();
1403     }
1404     else
1405     {
1406       try
1407       {
1408         outputAction.run();
1409       } catch (Exception e)
1410       {
1411         // TODO Auto-generated catch block
1412         e.printStackTrace();
1413       }
1414     }
1415   }
1416
1417   /**
1418    * Outputs the alignment to textbox in the requested format, if necessary
1419    * first prompting the user for whether to include hidden regions or
1420    * non-sequence data
1421    *
1422    * @param fileFormatName
1423    */
1424   @Override
1425   protected void outputText_actionPerformed(String fileFormatName)
1426   {
1427     FileFormatI fileFormat = FileFormats.getInstance()
1428             .forName(fileFormatName);
1429     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1430     Runnable outputAction = () -> {
1431       // todo defer this to inside formatSequences (or later)
1432       AlignmentExportData exportData = viewport.getAlignExportData(options);
1433       CutAndPasteTransfer cap = new CutAndPasteTransfer();
1434       cap.setForInput(null);
1435       try
1436       {
1437         FileFormatI format = fileFormat;
1438         cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
1439                 format, exportData.getAlignment(),
1440                 exportData.getOmitHidden(),
1441                 exportData.getStartEndPostions(),
1442                 viewport.getAlignment().getHiddenColumns()));
1443         Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1444                 "label.alignment_output_command", new Object[]
1445                 { fileFormat.getName() }), 600, 500);
1446       } catch (OutOfMemoryError oom)
1447       {
1448         new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1449                 oom);
1450         cap.dispose();
1451       }
1452     };
1453
1454     /*
1455      * show dialog with export options if applicable; else just do it
1456      */
1457     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1458     {
1459       AlignExportOptions choices = new AlignExportOptions(
1460               alignPanel.getAlignViewport(), fileFormat, options);
1461       choices.setResponseAction(0, outputAction);
1462       choices.showDialog();
1463     }
1464     else
1465     {
1466       try
1467       {
1468         outputAction.run();
1469       } catch (Exception e)
1470       {
1471         e.printStackTrace();
1472       }
1473     }
1474   }
1475
1476   /**
1477    * DOCUMENT ME!
1478    *
1479    * @param e
1480    *          DOCUMENT ME!
1481    */
1482   @Override
1483   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1484   {
1485     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1486     try
1487     {
1488       htmlSVG.exportHTML(null);
1489     } catch (ImageOutputException x)
1490     {
1491       // report problem to console and raise dialog
1492     }
1493   }
1494
1495   @Override
1496   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1497   {
1498     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1499     try
1500     {
1501       bjs.exportHTML(null);
1502     } catch (ImageOutputException x)
1503     {
1504       // report problem to console and raise dialog
1505     }
1506   }
1507
1508   public void createImageMap(File file, String image)
1509   {
1510     try
1511     {
1512       alignPanel.makePNGImageMap(file, image);
1513     } catch (ImageOutputException x)
1514     {
1515       // report problem to console and raise dialog
1516     }
1517   }
1518
1519   @Override
1520   public void createPNG_actionPerformed(ActionEvent e)
1521   {
1522     try
1523     {
1524       createPNG(null);
1525     } catch (ImageOutputException ioex)
1526     {
1527       // raise dialog, and report via console
1528     }
1529   }
1530
1531   @Override
1532   public void createEPS_actionPerformed(ActionEvent e)
1533   {
1534     try
1535     {
1536       createEPS(null);
1537     } catch (ImageOutputException ioex)
1538     {
1539       // raise dialog, and report via console
1540     }
1541
1542   }
1543
1544   @Override
1545   public void createSVG_actionPerformed(ActionEvent e)
1546   {
1547     try
1548     {
1549       createSVG(null);
1550     } catch (ImageOutputException ioex)
1551     {
1552       // raise dialog, and report via console
1553     }
1554
1555   }
1556
1557   /**
1558    * Creates a PNG image of the alignment and writes it to the given file. If
1559    * the file is null, the user is prompted to choose a file.
1560    *
1561    * @param f
1562    */
1563   public void createPNG(File f) throws ImageOutputException
1564   {
1565     createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
1566   }
1567
1568   public void createPNG(File f, String renderer, BitmapImageSizing userBis)
1569           throws ImageOutputException
1570   {
1571     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
1572   }
1573
1574   /**
1575    * Creates an EPS image of the alignment and writes it to the given file. If
1576    * the file is null, the user is prompted to choose a file.
1577    *
1578    * @param f
1579    */
1580   public void createEPS(File f) throws ImageOutputException
1581   {
1582     createEPS(f, null);
1583   }
1584
1585   public void createEPS(File f, String renderer) throws ImageOutputException
1586   {
1587     alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
1588   }
1589
1590   /**
1591    * Creates an SVG image of the alignment and writes it to the given file. If
1592    * the file is null, the user is prompted to choose a file.
1593    *
1594    * @param f
1595    */
1596   public void createSVG(File f) throws ImageOutputException
1597   {
1598     createSVG(f, null);
1599   }
1600
1601   public void createSVG(File f, String renderer) throws ImageOutputException
1602   {
1603     alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
1604   }
1605
1606   @Override
1607   public void pageSetup_actionPerformed(ActionEvent e)
1608   {
1609     PrinterJob printJob = PrinterJob.getPrinterJob();
1610     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1611   }
1612
1613   /**
1614    * DOCUMENT ME!
1615    *
1616    * @param e
1617    *          DOCUMENT ME!
1618    */
1619   @Override
1620   public void printMenuItem_actionPerformed(ActionEvent e)
1621   {
1622     // Putting in a thread avoids Swing painting problems
1623     PrintThread thread = new PrintThread(alignPanel);
1624     thread.start();
1625   }
1626
1627   @Override
1628   public void exportFeatures_actionPerformed(ActionEvent e)
1629   {
1630     new AnnotationExporter(alignPanel).exportFeatures();
1631   }
1632
1633   @Override
1634   public void exportAnnotations_actionPerformed(ActionEvent e)
1635   {
1636     new AnnotationExporter(alignPanel).exportAnnotations();
1637   }
1638
1639   @Override
1640   public void associatedData_actionPerformed(ActionEvent e)
1641   {
1642     final JalviewFileChooser chooser = new JalviewFileChooser(
1643             Cache.getProperty("LAST_DIRECTORY"));
1644     chooser.setFileView(new JalviewFileView());
1645     String tooltip = MessageManager
1646             .getString("label.load_jalview_annotations");
1647     chooser.setDialogTitle(tooltip);
1648     chooser.setToolTipText(tooltip);
1649     chooser.setResponseHandler(0, () -> {
1650       String choice = chooser.getSelectedFile().getPath();
1651       Cache.setProperty("LAST_DIRECTORY", choice);
1652       loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1653     });
1654
1655     chooser.showOpenDialog(this);
1656   }
1657
1658   /**
1659    * Close the current view or all views in the alignment frame. If the frame
1660    * only contains one view then the alignment will be removed from memory.
1661    *
1662    * @param closeAllTabs
1663    */
1664   @Override
1665   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1666   {
1667     if (alignPanels != null && alignPanels.size() < 2)
1668     {
1669       closeAllTabs = true;
1670     }
1671
1672     try
1673     {
1674       if (alignPanels != null)
1675       {
1676         if (closeAllTabs)
1677         {
1678           if (this.isClosed())
1679           {
1680             // really close all the windows - otherwise wait till
1681             // setClosed(true) is called
1682             for (int i = 0; i < alignPanels.size(); i++)
1683             {
1684               AlignmentPanel ap = alignPanels.get(i);
1685               ap.closePanel();
1686             }
1687           }
1688         }
1689         else
1690         {
1691           closeView(alignPanel);
1692         }
1693       }
1694       if (closeAllTabs)
1695       {
1696         if (featureSettings != null && featureSettings.isOpen())
1697         {
1698           featureSettings.close();
1699           featureSettings = null;
1700         }
1701         /*
1702          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1703          * be called recursively, with the frame now in 'closed' state
1704          */
1705         this.setClosed(true);
1706       }
1707     } catch (Exception ex)
1708     {
1709       ex.printStackTrace();
1710     }
1711   }
1712
1713   /**
1714    * Close the specified panel and close up tabs appropriately.
1715    *
1716    * @param panelToClose
1717    */
1718   public void closeView(AlignmentPanel panelToClose)
1719   {
1720     int index = tabbedPane.getSelectedIndex();
1721     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1722     alignPanels.remove(panelToClose);
1723     panelToClose.closePanel();
1724     panelToClose = null;
1725
1726     tabbedPane.removeTabAt(closedindex);
1727     tabbedPane.validate();
1728
1729     if (index > closedindex || index == tabbedPane.getTabCount())
1730     {
1731       // modify currently selected tab index if necessary.
1732       index--;
1733     }
1734
1735     this.tabSelectionChanged(index);
1736   }
1737
1738   /**
1739    * DOCUMENT ME!
1740    */
1741   void updateEditMenuBar()
1742   {
1743
1744     if (viewport.getHistoryList().size() > 0)
1745     {
1746       undoMenuItem.setEnabled(true);
1747       CommandI command = viewport.getHistoryList().peek();
1748       undoMenuItem.setText(MessageManager
1749               .formatMessage("label.undo_command", new Object[]
1750               { command.getDescription() }));
1751     }
1752     else
1753     {
1754       undoMenuItem.setEnabled(false);
1755       undoMenuItem.setText(MessageManager.getString("action.undo"));
1756     }
1757
1758     if (viewport.getRedoList().size() > 0)
1759     {
1760       redoMenuItem.setEnabled(true);
1761
1762       CommandI command = viewport.getRedoList().peek();
1763       redoMenuItem.setText(MessageManager
1764               .formatMessage("label.redo_command", new Object[]
1765               { command.getDescription() }));
1766     }
1767     else
1768     {
1769       redoMenuItem.setEnabled(false);
1770       redoMenuItem.setText(MessageManager.getString("action.redo"));
1771     }
1772   }
1773
1774   @Override
1775   public void addHistoryItem(CommandI command)
1776   {
1777     if (command.getSize() > 0)
1778     {
1779       viewport.addToHistoryList(command);
1780       viewport.clearRedoList();
1781       updateEditMenuBar();
1782       viewport.updateHiddenColumns();
1783       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1784       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1785       // viewport.getColumnSelection()
1786       // .getHiddenColumns().size() > 0);
1787     }
1788   }
1789
1790   /**
1791    *
1792    * @return alignment objects for all views
1793    */
1794   AlignmentI[] getViewAlignments()
1795   {
1796     if (alignPanels != null)
1797     {
1798       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1799       int i = 0;
1800       for (AlignmentPanel ap : alignPanels)
1801       {
1802         als[i++] = ap.av.getAlignment();
1803       }
1804       return als;
1805     }
1806     if (viewport != null)
1807     {
1808       return new AlignmentI[] { viewport.getAlignment() };
1809     }
1810     return null;
1811   }
1812
1813   /**
1814    * DOCUMENT ME!
1815    *
1816    * @param e
1817    *          DOCUMENT ME!
1818    */
1819   @Override
1820   protected void undoMenuItem_actionPerformed(ActionEvent e)
1821   {
1822     if (viewport.getHistoryList().isEmpty())
1823     {
1824       return;
1825     }
1826     CommandI command = viewport.getHistoryList().pop();
1827     viewport.addToRedoList(command);
1828     command.undoCommand(getViewAlignments());
1829
1830     AlignmentViewport originalSource = getOriginatingSource(command);
1831     updateEditMenuBar();
1832
1833     if (originalSource != null)
1834     {
1835       if (originalSource != viewport)
1836       {
1837         Console.warn(
1838                 "Implementation worry: mismatch of viewport origin for undo");
1839       }
1840       originalSource.updateHiddenColumns();
1841       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1842       // null
1843       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1844       // viewport.getColumnSelection()
1845       // .getHiddenColumns().size() > 0);
1846       originalSource.firePropertyChange("alignment", null,
1847               originalSource.getAlignment().getSequences());
1848     }
1849   }
1850
1851   /**
1852    * DOCUMENT ME!
1853    *
1854    * @param e
1855    *          DOCUMENT ME!
1856    */
1857   @Override
1858   protected void redoMenuItem_actionPerformed(ActionEvent e)
1859   {
1860     if (viewport.getRedoList().size() < 1)
1861     {
1862       return;
1863     }
1864
1865     CommandI command = viewport.getRedoList().pop();
1866     viewport.addToHistoryList(command);
1867     command.doCommand(getViewAlignments());
1868
1869     AlignmentViewport originalSource = getOriginatingSource(command);
1870     updateEditMenuBar();
1871
1872     if (originalSource != null)
1873     {
1874
1875       if (originalSource != viewport)
1876       {
1877         Console.warn(
1878                 "Implementation worry: mismatch of viewport origin for redo");
1879       }
1880       originalSource.updateHiddenColumns();
1881       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1882       // null
1883       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1884       // viewport.getColumnSelection()
1885       // .getHiddenColumns().size() > 0);
1886       originalSource.firePropertyChange("alignment", null,
1887               originalSource.getAlignment().getSequences());
1888     }
1889   }
1890
1891   AlignmentViewport getOriginatingSource(CommandI command)
1892   {
1893     AlignmentViewport originalSource = null;
1894     // For sequence removal and addition, we need to fire
1895     // the property change event FROM the viewport where the
1896     // original alignment was altered
1897     AlignmentI al = null;
1898     if (command instanceof EditCommand)
1899     {
1900       EditCommand editCommand = (EditCommand) command;
1901       al = editCommand.getAlignment();
1902       List<Component> comps = PaintRefresher.components
1903               .get(viewport.getSequenceSetId());
1904
1905       for (Component comp : comps)
1906       {
1907         if (comp instanceof AlignmentPanel)
1908         {
1909           if (al == ((AlignmentPanel) comp).av.getAlignment())
1910           {
1911             originalSource = ((AlignmentPanel) comp).av;
1912             break;
1913           }
1914         }
1915       }
1916     }
1917
1918     if (originalSource == null)
1919     {
1920       // The original view is closed, we must validate
1921       // the current view against the closed view first
1922       if (al != null)
1923       {
1924         PaintRefresher.validateSequences(al, viewport.getAlignment());
1925       }
1926
1927       originalSource = viewport;
1928     }
1929
1930     return originalSource;
1931   }
1932
1933   /**
1934    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1935    * or the sequence under cursor in keyboard mode
1936    *
1937    * @param up
1938    *          or down (if !up)
1939    */
1940   public void moveSelectedSequences(boolean up)
1941   {
1942     SequenceGroup sg = viewport.getSelectionGroup();
1943
1944     if (sg == null)
1945     {
1946       if (viewport.cursorMode)
1947       {
1948         sg = new SequenceGroup();
1949         sg.addSequence(viewport.getAlignment().getSequenceAt(
1950                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1951       }
1952       else
1953       {
1954         return;
1955       }
1956     }
1957
1958     if (sg.getSize() < 1)
1959     {
1960       return;
1961     }
1962
1963     // TODO: JAL-3733 - add an event to the undo buffer for this !
1964
1965     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1966             viewport.getHiddenRepSequences(), up);
1967     alignPanel.paintAlignment(true, false);
1968   }
1969
1970   synchronized void slideSequences(boolean right, int size)
1971   {
1972     List<SequenceI> sg = new ArrayList<>();
1973     if (viewport.cursorMode)
1974     {
1975       sg.add(viewport.getAlignment()
1976               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1977     }
1978     else if (viewport.getSelectionGroup() != null
1979             && viewport.getSelectionGroup().getSize() != viewport
1980                     .getAlignment().getHeight())
1981     {
1982       sg = viewport.getSelectionGroup()
1983               .getSequences(viewport.getHiddenRepSequences());
1984     }
1985
1986     if (sg.size() < 1)
1987     {
1988       return;
1989     }
1990
1991     List<SequenceI> invertGroup = new ArrayList<>();
1992
1993     for (SequenceI seq : viewport.getAlignment().getSequences())
1994     {
1995       if (!sg.contains(seq))
1996       {
1997         invertGroup.add(seq);
1998       }
1999     }
2000
2001     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
2002
2003     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
2004     for (int i = 0; i < invertGroup.size(); i++)
2005     {
2006       seqs2[i] = invertGroup.get(i);
2007     }
2008
2009     SlideSequencesCommand ssc;
2010     if (right)
2011     {
2012       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2013               viewport.getGapCharacter());
2014     }
2015     else
2016     {
2017       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2018               viewport.getGapCharacter());
2019     }
2020
2021     int groupAdjustment = 0;
2022     if (ssc.getGapsInsertedBegin() && right)
2023     {
2024       if (viewport.cursorMode)
2025       {
2026         alignPanel.getSeqPanel().moveCursor(size, 0);
2027       }
2028       else
2029       {
2030         groupAdjustment = size;
2031       }
2032     }
2033     else if (!ssc.getGapsInsertedBegin() && !right)
2034     {
2035       if (viewport.cursorMode)
2036       {
2037         alignPanel.getSeqPanel().moveCursor(-size, 0);
2038       }
2039       else
2040       {
2041         groupAdjustment = -size;
2042       }
2043     }
2044
2045     if (groupAdjustment != 0)
2046     {
2047       viewport.getSelectionGroup().setStartRes(
2048               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2049       viewport.getSelectionGroup().setEndRes(
2050               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2051     }
2052
2053     /*
2054      * just extend the last slide command if compatible; but not if in
2055      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2056      */
2057     boolean appendHistoryItem = false;
2058     Deque<CommandI> historyList = viewport.getHistoryList();
2059     boolean inSplitFrame = getSplitViewContainer() != null;
2060     if (!inSplitFrame && historyList != null && historyList.size() > 0
2061             && historyList.peek() instanceof SlideSequencesCommand)
2062     {
2063       appendHistoryItem = ssc.appendSlideCommand(
2064               (SlideSequencesCommand) historyList.peek());
2065     }
2066
2067     if (!appendHistoryItem)
2068     {
2069       addHistoryItem(ssc);
2070     }
2071
2072     repaint();
2073   }
2074
2075   /**
2076    * DOCUMENT ME!
2077    *
2078    * @param e
2079    *          DOCUMENT ME!
2080    */
2081   @Override
2082   protected void copy_actionPerformed()
2083   {
2084     if (viewport.getSelectionGroup() == null)
2085     {
2086       return;
2087     }
2088     // TODO: preserve the ordering of displayed alignment annotation in any
2089     // internal paste (particularly sequence associated annotation)
2090     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2091     String[] omitHidden = null;
2092
2093     if (viewport.hasHiddenColumns())
2094     {
2095       omitHidden = viewport.getViewAsString(true);
2096     }
2097
2098     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2099             seqs, omitHidden, null);
2100
2101     StringSelection ss = new StringSelection(output);
2102
2103     try
2104     {
2105       jalview.gui.Desktop.internalCopy = true;
2106       // Its really worth setting the clipboard contents
2107       // to empty before setting the large StringSelection!!
2108       Toolkit.getDefaultToolkit().getSystemClipboard()
2109               .setContents(new StringSelection(""), null);
2110
2111       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2112               Desktop.instance);
2113     } catch (OutOfMemoryError er)
2114     {
2115       new OOMWarning("copying region", er);
2116       return;
2117     }
2118
2119     HiddenColumns hiddenColumns = null;
2120     if (viewport.hasHiddenColumns())
2121     {
2122       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2123       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2124
2125       // create new HiddenColumns object with copy of hidden regions
2126       // between startRes and endRes, offset by startRes
2127       hiddenColumns = new HiddenColumns(
2128               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2129               hiddenCutoff, hiddenOffset);
2130     }
2131
2132     Desktop.jalviewClipboard = new Object[] { seqs,
2133         viewport.getAlignment().getDataset(), hiddenColumns };
2134     setStatus(MessageManager.formatMessage(
2135             "label.copied_sequences_to_clipboard", new Object[]
2136             { Integer.valueOf(seqs.length).toString() }));
2137   }
2138
2139   /**
2140    * DOCUMENT ME!
2141    *
2142    * @param e
2143    *          DOCUMENT ME!
2144    */
2145   @Override
2146   protected void pasteNew_actionPerformed(ActionEvent e)
2147   {
2148     paste(true);
2149   }
2150
2151   /**
2152    * DOCUMENT ME!
2153    *
2154    * @param e
2155    *          DOCUMENT ME!
2156    */
2157   @Override
2158   protected void pasteThis_actionPerformed(ActionEvent e)
2159   {
2160     paste(false);
2161   }
2162
2163   /**
2164    * Paste contents of Jalview clipboard
2165    *
2166    * @param newAlignment
2167    *          true to paste to a new alignment, otherwise add to this.
2168    */
2169   void paste(boolean newAlignment)
2170   {
2171     boolean externalPaste = true;
2172     try
2173     {
2174       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2175       Transferable contents = c.getContents(this);
2176
2177       if (contents == null)
2178       {
2179         return;
2180       }
2181
2182       String str;
2183       FileFormatI format;
2184       try
2185       {
2186         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2187         if (str.length() < 1)
2188         {
2189           return;
2190         }
2191
2192         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2193
2194       } catch (OutOfMemoryError er)
2195       {
2196         new OOMWarning("Out of memory pasting sequences!!", er);
2197         return;
2198       }
2199
2200       SequenceI[] sequences;
2201       boolean annotationAdded = false;
2202       AlignmentI alignment = null;
2203
2204       if (Desktop.jalviewClipboard != null)
2205       {
2206         // The clipboard was filled from within Jalview, we must use the
2207         // sequences
2208         // And dataset from the copied alignment
2209         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2210         // be doubly sure that we create *new* sequence objects.
2211         sequences = new SequenceI[newseq.length];
2212         for (int i = 0; i < newseq.length; i++)
2213         {
2214           sequences[i] = new Sequence(newseq[i]);
2215         }
2216         alignment = new Alignment(sequences);
2217         externalPaste = false;
2218       }
2219       else
2220       {
2221         // parse the clipboard as an alignment.
2222         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2223                 format);
2224         sequences = alignment.getSequencesArray();
2225       }
2226
2227       int alwidth = 0;
2228       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2229       int fgroup = -1;
2230
2231       if (newAlignment)
2232       {
2233
2234         if (Desktop.jalviewClipboard != null)
2235         {
2236           // dataset is inherited
2237           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2238         }
2239         else
2240         {
2241           // new dataset is constructed
2242           alignment.setDataset(null);
2243         }
2244         alwidth = alignment.getWidth() + 1;
2245       }
2246       else
2247       {
2248         AlignmentI pastedal = alignment; // preserve pasted alignment object
2249         // Add pasted sequences and dataset into existing alignment.
2250         alignment = viewport.getAlignment();
2251         alwidth = alignment.getWidth() + 1;
2252         // decide if we need to import sequences from an existing dataset
2253         boolean importDs = Desktop.jalviewClipboard != null
2254                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2255         // importDs==true instructs us to copy over new dataset sequences from
2256         // an existing alignment
2257         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2258                                                                       // create
2259         // minimum dataset set
2260
2261         for (int i = 0; i < sequences.length; i++)
2262         {
2263           if (importDs)
2264           {
2265             newDs.addElement(null);
2266           }
2267           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2268           // paste
2269           if (importDs && ds != null)
2270           {
2271             if (!newDs.contains(ds))
2272             {
2273               newDs.setElementAt(ds, i);
2274               ds = new Sequence(ds);
2275               // update with new dataset sequence
2276               sequences[i].setDatasetSequence(ds);
2277             }
2278             else
2279             {
2280               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2281             }
2282           }
2283           else
2284           {
2285             // copy and derive new dataset sequence
2286             sequences[i] = sequences[i].deriveSequence();
2287             alignment.getDataset()
2288                     .addSequence(sequences[i].getDatasetSequence());
2289             // TODO: avoid creation of duplicate dataset sequences with a
2290             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2291           }
2292           alignment.addSequence(sequences[i]); // merges dataset
2293         }
2294         if (newDs != null)
2295         {
2296           newDs.clear(); // tidy up
2297         }
2298         if (alignment.getAlignmentAnnotation() != null)
2299         {
2300           for (AlignmentAnnotation alan : alignment
2301                   .getAlignmentAnnotation())
2302           {
2303             if (alan.graphGroup > fgroup)
2304             {
2305               fgroup = alan.graphGroup;
2306             }
2307           }
2308         }
2309         if (pastedal.getAlignmentAnnotation() != null)
2310         {
2311           // Add any annotation attached to alignment.
2312           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2313           for (int i = 0; i < alann.length; i++)
2314           {
2315             annotationAdded = true;
2316             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2317             {
2318               AlignmentAnnotation newann = new AlignmentAnnotation(
2319                       alann[i]);
2320               if (newann.graphGroup > -1)
2321               {
2322                 if (newGraphGroups.size() <= newann.graphGroup
2323                         || newGraphGroups.get(newann.graphGroup) == null)
2324                 {
2325                   for (int q = newGraphGroups
2326                           .size(); q <= newann.graphGroup; q++)
2327                   {
2328                     newGraphGroups.add(q, null);
2329                   }
2330                   newGraphGroups.set(newann.graphGroup,
2331                           Integer.valueOf(++fgroup));
2332                 }
2333                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2334                         .intValue();
2335               }
2336
2337               newann.padAnnotation(alwidth);
2338               alignment.addAnnotation(newann);
2339             }
2340           }
2341         }
2342       }
2343       if (!newAlignment)
2344       {
2345         // /////
2346         // ADD HISTORY ITEM
2347         //
2348         addHistoryItem(new EditCommand(
2349                 MessageManager.getString("label.add_sequences"),
2350                 Action.PASTE, sequences, 0, alignment.getWidth(),
2351                 alignment));
2352       }
2353       // Add any annotations attached to sequences
2354       for (int i = 0; i < sequences.length; i++)
2355       {
2356         if (sequences[i].getAnnotation() != null)
2357         {
2358           AlignmentAnnotation newann;
2359           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2360           {
2361             annotationAdded = true;
2362             newann = sequences[i].getAnnotation()[a];
2363             newann.adjustForAlignment();
2364             newann.padAnnotation(alwidth);
2365             if (newann.graphGroup > -1)
2366             {
2367               if (newann.graphGroup > -1)
2368               {
2369                 if (newGraphGroups.size() <= newann.graphGroup
2370                         || newGraphGroups.get(newann.graphGroup) == null)
2371                 {
2372                   for (int q = newGraphGroups
2373                           .size(); q <= newann.graphGroup; q++)
2374                   {
2375                     newGraphGroups.add(q, null);
2376                   }
2377                   newGraphGroups.set(newann.graphGroup,
2378                           Integer.valueOf(++fgroup));
2379                 }
2380                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2381                         .intValue();
2382               }
2383             }
2384             // annotation was duplicated earlier
2385             alignment.addAnnotation(sequences[i].getAnnotation()[a]);
2386             // take care of contact matrix too
2387             ContactMatrixI cm = sequences[i]
2388                     .getContactMatrixFor(sequences[i].getAnnotation()[a]);
2389             if (cm != null)
2390             {
2391               alignment.addContactListFor(sequences[i].getAnnotation()[a],
2392                       cm);
2393             }
2394
2395             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2396                     a);
2397           }
2398         }
2399       }
2400       if (!newAlignment)
2401       {
2402
2403         // propagate alignment changed.
2404         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2405         if (annotationAdded)
2406         {
2407           // Duplicate sequence annotation in all views.
2408           AlignmentI[] alview = this.getViewAlignments();
2409           for (int i = 0; i < sequences.length; i++)
2410           {
2411             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2412             if (sann == null)
2413             {
2414               continue;
2415             }
2416             for (int avnum = 0; avnum < alview.length; avnum++)
2417             {
2418               if (alview[avnum] != alignment)
2419               {
2420                 // duplicate in a view other than the one with input focus
2421                 int avwidth = alview[avnum].getWidth() + 1;
2422                 // this relies on sann being preserved after we
2423                 // modify the sequence's annotation array for each duplication
2424                 for (int a = 0; a < sann.length; a++)
2425                 {
2426                   AlignmentAnnotation newann = new AlignmentAnnotation(
2427                           sann[a]);
2428                   sequences[i].addAlignmentAnnotation(newann);
2429                   newann.padAnnotation(avwidth);
2430                   alview[avnum].addAnnotation(newann); // annotation was
2431                   // duplicated earlier
2432                   // TODO JAL-1145 graphGroups are not updated for sequence
2433                   // annotation added to several views. This may cause
2434                   // strangeness
2435                   alview[avnum].setAnnotationIndex(newann, a);
2436                 }
2437               }
2438             }
2439           }
2440           buildSortByAnnotationScoresMenu();
2441         }
2442         viewport.firePropertyChange("alignment", null,
2443                 alignment.getSequences());
2444         if (alignPanels != null)
2445         {
2446           for (AlignmentPanel ap : alignPanels)
2447           {
2448             ap.validateAnnotationDimensions(false);
2449           }
2450         }
2451         else
2452         {
2453           alignPanel.validateAnnotationDimensions(false);
2454         }
2455
2456       }
2457       else
2458       {
2459         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2460                 DEFAULT_HEIGHT);
2461         String newtitle = new String("Copied sequences");
2462
2463         if (Desktop.jalviewClipboard != null
2464                 && Desktop.jalviewClipboard[2] != null)
2465         {
2466           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2467           af.viewport.setHiddenColumns(hc);
2468         }
2469
2470         // >>>This is a fix for the moment, until a better solution is
2471         // found!!<<<
2472         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2473                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2474                         .getFeatureRenderer());
2475
2476         // TODO: maintain provenance of an alignment, rather than just make the
2477         // title a concatenation of operations.
2478         if (!externalPaste)
2479         {
2480           if (title.startsWith("Copied sequences"))
2481           {
2482             newtitle = title;
2483           }
2484           else
2485           {
2486             newtitle = newtitle.concat("- from " + title);
2487           }
2488         }
2489         else
2490         {
2491           newtitle = new String("Pasted sequences");
2492         }
2493
2494         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2495                 DEFAULT_HEIGHT);
2496
2497       }
2498
2499     } catch (Exception ex)
2500     {
2501       ex.printStackTrace();
2502       jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
2503       // could be anything being pasted in here
2504     }
2505
2506   }
2507
2508   @Override
2509   protected void expand_newalign(ActionEvent e)
2510   {
2511     try
2512     {
2513       AlignmentI alignment = AlignmentUtils
2514               .expandContext(getViewport().getAlignment(), -1);
2515       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2516               DEFAULT_HEIGHT);
2517       String newtitle = new String("Flanking alignment");
2518
2519       if (Desktop.jalviewClipboard != null
2520               && Desktop.jalviewClipboard[2] != null)
2521       {
2522         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2523         af.viewport.setHiddenColumns(hc);
2524       }
2525
2526       // >>>This is a fix for the moment, until a better solution is
2527       // found!!<<<
2528       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2529               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2530                       .getFeatureRenderer());
2531
2532       // TODO: maintain provenance of an alignment, rather than just make the
2533       // title a concatenation of operations.
2534       {
2535         if (title.startsWith("Copied sequences"))
2536         {
2537           newtitle = title;
2538         }
2539         else
2540         {
2541           newtitle = newtitle.concat("- from " + title);
2542         }
2543       }
2544
2545       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2546
2547     } catch (Exception ex)
2548     {
2549       ex.printStackTrace();
2550       jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
2551       // could be anything being pasted in here
2552     } catch (OutOfMemoryError oom)
2553     {
2554       new OOMWarning("Viewing flanking region of alignment", oom);
2555     }
2556   }
2557
2558   /**
2559    * Action Cut (delete and copy) the selected region
2560    */
2561   @Override
2562   protected void cut_actionPerformed()
2563   {
2564     copy_actionPerformed();
2565     delete_actionPerformed();
2566   }
2567
2568   /**
2569    * Performs menu option to Delete the currently selected region
2570    */
2571   @Override
2572   protected void delete_actionPerformed()
2573   {
2574
2575     SequenceGroup sg = viewport.getSelectionGroup();
2576     if (sg == null)
2577     {
2578       return;
2579     }
2580
2581     Runnable okAction = () -> {
2582       SequenceI[] cut = sg.getSequences()
2583               .toArray(new SequenceI[sg.getSize()]);
2584
2585       addHistoryItem(new EditCommand(
2586               MessageManager.getString("label.cut_sequences"), Action.CUT,
2587               cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2588               viewport.getAlignment()));
2589
2590       viewport.setSelectionGroup(null);
2591       viewport.sendSelection();
2592       viewport.getAlignment().deleteGroup(sg);
2593
2594       viewport.firePropertyChange("alignment", null,
2595               viewport.getAlignment().getSequences());
2596       if (viewport.getAlignment().getHeight() < 1)
2597       {
2598         try
2599         {
2600           AlignFrame.this.setClosed(true);
2601         } catch (Exception ex)
2602         {
2603         }
2604       }
2605     };
2606
2607     /*
2608      * If the cut affects all sequences, prompt for confirmation
2609      */
2610     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2611             .getHeight();
2612     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2613             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2614     if (wholeHeight && wholeWidth)
2615     {
2616       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2617       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2618       Object[] options = new Object[] {
2619           MessageManager.getString("action.ok"),
2620           MessageManager.getString("action.cancel") };
2621       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2622               MessageManager.getString("label.delete_all"),
2623               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2624               options, options[0]);
2625     }
2626     else
2627     {
2628       try
2629       {
2630         okAction.run();
2631       } catch (Exception e)
2632       {
2633         e.printStackTrace();
2634       }
2635     }
2636   }
2637
2638   /**
2639    * DOCUMENT ME!
2640    *
2641    * @param e
2642    *          DOCUMENT ME!
2643    */
2644   @Override
2645   protected void deleteGroups_actionPerformed(ActionEvent e)
2646   {
2647     if (avc.deleteGroups())
2648     {
2649       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2650       alignPanel.updateAnnotation();
2651       alignPanel.paintAlignment(true, true);
2652     }
2653   }
2654
2655   /**
2656    * DOCUMENT ME!
2657    *
2658    * @param e
2659    *          DOCUMENT ME!
2660    */
2661   @Override
2662   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2663   {
2664     SequenceGroup sg = new SequenceGroup(
2665             viewport.getAlignment().getSequences());
2666
2667     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2668     viewport.setSelectionGroup(sg);
2669     viewport.isSelectionGroupChanged(true);
2670     viewport.sendSelection();
2671     // JAL-2034 - should delegate to
2672     // alignPanel to decide if overview needs
2673     // updating.
2674     alignPanel.paintAlignment(false, false);
2675     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2676   }
2677
2678   /**
2679    * DOCUMENT ME!
2680    *
2681    * @param e
2682    *          DOCUMENT ME!
2683    */
2684   @Override
2685   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2686   {
2687     if (viewport.cursorMode)
2688     {
2689       alignPanel.getSeqPanel().keyboardNo1 = null;
2690       alignPanel.getSeqPanel().keyboardNo2 = null;
2691     }
2692     viewport.setSelectionGroup(null);
2693     viewport.getColumnSelection().clear();
2694     viewport.setSearchResults(null);
2695     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2696     // JAL-2034 - should delegate to
2697     // alignPanel to decide if overview needs
2698     // updating.
2699     alignPanel.paintAlignment(false, false);
2700     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2701     viewport.sendSelection();
2702   }
2703
2704   /**
2705    * DOCUMENT ME!
2706    *
2707    * @param e
2708    *          DOCUMENT ME!
2709    */
2710   @Override
2711   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2712   {
2713     SequenceGroup sg = viewport.getSelectionGroup();
2714
2715     if (sg == null)
2716     {
2717       selectAllSequenceMenuItem_actionPerformed(null);
2718
2719       return;
2720     }
2721
2722     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2723     {
2724       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2725     }
2726     // JAL-2034 - should delegate to
2727     // alignPanel to decide if overview needs
2728     // updating.
2729
2730     alignPanel.paintAlignment(true, false);
2731     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2732     viewport.sendSelection();
2733   }
2734
2735   @Override
2736   public void invertColSel_actionPerformed(ActionEvent e)
2737   {
2738     viewport.invertColumnSelection();
2739     alignPanel.paintAlignment(true, false);
2740     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2741     viewport.sendSelection();
2742   }
2743
2744   /**
2745    * DOCUMENT ME!
2746    *
2747    * @param e
2748    *          DOCUMENT ME!
2749    */
2750   @Override
2751   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2752   {
2753     trimAlignment(true);
2754   }
2755
2756   /**
2757    * DOCUMENT ME!
2758    *
2759    * @param e
2760    *          DOCUMENT ME!
2761    */
2762   @Override
2763   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2764   {
2765     trimAlignment(false);
2766   }
2767
2768   void trimAlignment(boolean trimLeft)
2769   {
2770     ColumnSelection colSel = viewport.getColumnSelection();
2771     int column;
2772
2773     if (!colSel.isEmpty())
2774     {
2775       if (trimLeft)
2776       {
2777         column = colSel.getMin();
2778       }
2779       else
2780       {
2781         column = colSel.getMax();
2782       }
2783
2784       SequenceI[] seqs;
2785       if (viewport.getSelectionGroup() != null)
2786       {
2787         seqs = viewport.getSelectionGroup()
2788                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2789       }
2790       else
2791       {
2792         seqs = viewport.getAlignment().getSequencesArray();
2793       }
2794
2795       TrimRegionCommand trimRegion;
2796       if (trimLeft)
2797       {
2798         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2799                 column, viewport.getAlignment());
2800         viewport.getRanges().setStartRes(0);
2801       }
2802       else
2803       {
2804         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2805                 column, viewport.getAlignment());
2806       }
2807
2808       setStatus(MessageManager.formatMessage("label.removed_columns",
2809               new String[]
2810               { Integer.valueOf(trimRegion.getSize()).toString() }));
2811
2812       addHistoryItem(trimRegion);
2813
2814       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2815       {
2816         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2817                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2818         {
2819           viewport.getAlignment().deleteGroup(sg);
2820         }
2821       }
2822
2823       viewport.firePropertyChange("alignment", null,
2824               viewport.getAlignment().getSequences());
2825     }
2826   }
2827
2828   /**
2829    * DOCUMENT ME!
2830    *
2831    * @param e
2832    *          DOCUMENT ME!
2833    */
2834   @Override
2835   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2836   {
2837     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2838
2839     SequenceI[] seqs;
2840     if (viewport.getSelectionGroup() != null)
2841     {
2842       seqs = viewport.getSelectionGroup()
2843               .getSequencesAsArray(viewport.getHiddenRepSequences());
2844       start = viewport.getSelectionGroup().getStartRes();
2845       end = viewport.getSelectionGroup().getEndRes();
2846     }
2847     else
2848     {
2849       seqs = viewport.getAlignment().getSequencesArray();
2850     }
2851
2852     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2853             "Remove Gapped Columns", seqs, start, end,
2854             viewport.getAlignment());
2855
2856     addHistoryItem(removeGapCols);
2857
2858     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2859             new Object[]
2860             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2861
2862     // This is to maintain viewport position on first residue
2863     // of first sequence
2864     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2865     ViewportRanges ranges = viewport.getRanges();
2866     int startRes = seq.findPosition(ranges.getStartRes());
2867     // ShiftList shifts;
2868     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2869     // edit.alColumnChanges=shifts.getInverse();
2870     // if (viewport.hasHiddenColumns)
2871     // viewport.getColumnSelection().compensateForEdits(shifts);
2872     ranges.setStartRes(seq.findIndex(startRes) - 1);
2873     viewport.firePropertyChange("alignment", null,
2874             viewport.getAlignment().getSequences());
2875
2876   }
2877
2878   /**
2879    * DOCUMENT ME!
2880    *
2881    * @param e
2882    *          DOCUMENT ME!
2883    */
2884   @Override
2885   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2886   {
2887     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2888
2889     SequenceI[] seqs;
2890     if (viewport.getSelectionGroup() != null)
2891     {
2892       seqs = viewport.getSelectionGroup()
2893               .getSequencesAsArray(viewport.getHiddenRepSequences());
2894       start = viewport.getSelectionGroup().getStartRes();
2895       end = viewport.getSelectionGroup().getEndRes();
2896     }
2897     else
2898     {
2899       seqs = viewport.getAlignment().getSequencesArray();
2900     }
2901
2902     // This is to maintain viewport position on first residue
2903     // of first sequence
2904     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2905     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2906
2907     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2908             viewport.getAlignment()));
2909
2910     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2911
2912     viewport.firePropertyChange("alignment", null,
2913             viewport.getAlignment().getSequences());
2914
2915   }
2916
2917   /**
2918    * DOCUMENT ME!
2919    *
2920    * @param e
2921    *          DOCUMENT ME!
2922    */
2923   @Override
2924   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2925   {
2926     viewport.setPadGaps(padGapsMenuitem.isSelected());
2927     viewport.firePropertyChange("alignment", null,
2928             viewport.getAlignment().getSequences());
2929   }
2930
2931   /**
2932    * Opens a Finder dialog
2933    *
2934    * @param e
2935    */
2936   @Override
2937   public void findMenuItem_actionPerformed(ActionEvent e)
2938   {
2939     new Finder(alignPanel, false, null);
2940   }
2941
2942   /**
2943    * Create a new view of the current alignment.
2944    */
2945   @Override
2946   public void newView_actionPerformed(ActionEvent e)
2947   {
2948     newView(null, true);
2949   }
2950
2951   /**
2952    * Creates and shows a new view of the current alignment.
2953    *
2954    * @param viewTitle
2955    *          title of newly created view; if null, one will be generated
2956    * @param copyAnnotation
2957    *          if true then duplicate all annnotation, groups and settings
2958    * @return new alignment panel, already displayed.
2959    */
2960   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2961   {
2962     /*
2963      * Create a new AlignmentPanel (with its own, new Viewport)
2964      */
2965     AlignmentPanel newap = new jalview.project.Jalview2XML()
2966             .copyAlignPanel(alignPanel);
2967     if (!copyAnnotation)
2968     {
2969       /*
2970        * remove all groups and annotation except for the automatic stuff
2971        */
2972       newap.av.getAlignment().deleteAllGroups();
2973       newap.av.getAlignment().deleteAllAnnotations(false);
2974     }
2975
2976     newap.av.setGatherViewsHere(false);
2977
2978     if (viewport.getViewName() == null)
2979     {
2980       viewport.setViewName(
2981               MessageManager.getString("label.view_name_original"));
2982     }
2983
2984     /*
2985      * Views share the same edits undo and redo stacks
2986      */
2987     newap.av.setHistoryList(viewport.getHistoryList());
2988     newap.av.setRedoList(viewport.getRedoList());
2989
2990     /*
2991      * copy any visualisation settings that are not saved in the project
2992      */
2993     newap.av.setColourAppliesToAllGroups(
2994             viewport.getColourAppliesToAllGroups());
2995
2996     /*
2997      * Views share the same mappings; need to deregister any new mappings
2998      * created by copyAlignPanel, and register the new reference to the shared
2999      * mappings
3000      */
3001     newap.av.replaceMappings(viewport.getAlignment());
3002
3003     /*
3004      * start up cDNA consensus (if applicable) now mappings are in place
3005      */
3006     if (newap.av.initComplementConsensus())
3007     {
3008       newap.refresh(true); // adjust layout of annotations
3009     }
3010
3011     newap.av.setViewName(getNewViewName(viewTitle));
3012
3013     addAlignmentPanel(newap, true);
3014     newap.alignmentChanged();
3015
3016     if (alignPanels.size() == 2)
3017     {
3018       viewport.setGatherViewsHere(true);
3019     }
3020     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3021
3022     return newap;
3023   }
3024
3025   /**
3026    * Make a new name for the view, ensuring it is unique within the current
3027    * sequenceSetId. (This used to be essential for Jalview Project archives, but
3028    * these now use viewId. Unique view names are still desirable for usability.)
3029    *
3030    * @param viewTitle
3031    * @return
3032    */
3033   protected String getNewViewName(String viewTitle)
3034   {
3035     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3036     boolean addFirstIndex = false;
3037     if (viewTitle == null || viewTitle.trim().length() == 0)
3038     {
3039       viewTitle = MessageManager.getString("action.view");
3040       addFirstIndex = true;
3041     }
3042     else
3043     {
3044       index = 1;// we count from 1 if given a specific name
3045     }
3046     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3047
3048     List<Component> comps = PaintRefresher.components
3049             .get(viewport.getSequenceSetId());
3050
3051     List<String> existingNames = getExistingViewNames(comps);
3052
3053     while (existingNames.contains(newViewName))
3054     {
3055       newViewName = viewTitle + " " + (++index);
3056     }
3057     return newViewName;
3058   }
3059
3060   /**
3061    * Returns a list of distinct view names found in the given list of
3062    * components. View names are held on the viewport of an AlignmentPanel.
3063    *
3064    * @param comps
3065    * @return
3066    */
3067   protected List<String> getExistingViewNames(List<Component> comps)
3068   {
3069     List<String> existingNames = new ArrayList<>();
3070     for (Component comp : comps)
3071     {
3072       if (comp instanceof AlignmentPanel)
3073       {
3074         AlignmentPanel ap = (AlignmentPanel) comp;
3075         if (!existingNames.contains(ap.av.getViewName()))
3076         {
3077           existingNames.add(ap.av.getViewName());
3078         }
3079       }
3080     }
3081     return existingNames;
3082   }
3083
3084   /**
3085    * Explode tabbed views into separate windows.
3086    */
3087   @Override
3088   public void expandViews_actionPerformed(ActionEvent e)
3089   {
3090     Desktop.explodeViews(this);
3091   }
3092
3093   /**
3094    * Gather views in separate windows back into a tabbed presentation.
3095    */
3096   @Override
3097   public void gatherViews_actionPerformed(ActionEvent e)
3098   {
3099     Desktop.instance.gatherViews(this);
3100   }
3101
3102   /**
3103    * DOCUMENT ME!
3104    *
3105    * @param e
3106    *          DOCUMENT ME!
3107    */
3108   @Override
3109   public void font_actionPerformed(ActionEvent e)
3110   {
3111     new FontChooser(alignPanel);
3112   }
3113
3114   /**
3115    * DOCUMENT ME!
3116    *
3117    * @param e
3118    *          DOCUMENT ME!
3119    */
3120   @Override
3121   protected void seqLimit_actionPerformed(ActionEvent e)
3122   {
3123     viewport.setShowJVSuffix(seqLimits.isSelected());
3124
3125     alignPanel.getIdPanel().getIdCanvas()
3126             .setPreferredSize(alignPanel.calculateIdWidth());
3127     alignPanel.paintAlignment(true, false);
3128   }
3129
3130   @Override
3131   public void idRightAlign_actionPerformed(ActionEvent e)
3132   {
3133     viewport.setRightAlignIds(idRightAlign.isSelected());
3134     alignPanel.paintAlignment(false, false);
3135   }
3136
3137   @Override
3138   public void centreColumnLabels_actionPerformed(ActionEvent e)
3139   {
3140     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3141     alignPanel.paintAlignment(false, false);
3142   }
3143
3144   /*
3145    * (non-Javadoc)
3146    *
3147    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3148    */
3149   @Override
3150   protected void followHighlight_actionPerformed()
3151   {
3152     /*
3153      * Set the 'follow' flag on the Viewport (and scroll to position if now
3154      * true).
3155      */
3156     final boolean state = this.followHighlightMenuItem.getState();
3157     viewport.setFollowHighlight(state);
3158     if (state)
3159     {
3160       alignPanel.scrollToPosition(viewport.getSearchResults());
3161     }
3162   }
3163
3164   /**
3165    * DOCUMENT ME!
3166    *
3167    * @param e
3168    *          DOCUMENT ME!
3169    */
3170   @Override
3171   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3172   {
3173     viewport.setColourText(colourTextMenuItem.isSelected());
3174     alignPanel.paintAlignment(false, false);
3175   }
3176
3177   /**
3178    * DOCUMENT ME!
3179    *
3180    * @param e
3181    *          DOCUMENT ME!
3182    */
3183   @Override
3184   public void wrapMenuItem_actionPerformed(ActionEvent e)
3185   {
3186     scaleAbove.setVisible(wrapMenuItem.isSelected());
3187     scaleLeft.setVisible(wrapMenuItem.isSelected());
3188     scaleRight.setVisible(wrapMenuItem.isSelected());
3189     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3190     alignPanel.updateLayout();
3191   }
3192
3193   @Override
3194   public void showAllSeqs_actionPerformed(ActionEvent e)
3195   {
3196     viewport.showAllHiddenSeqs();
3197   }
3198
3199   @Override
3200   public void showAllColumns_actionPerformed(ActionEvent e)
3201   {
3202     viewport.showAllHiddenColumns();
3203     alignPanel.paintAlignment(true, true);
3204     viewport.sendSelection();
3205   }
3206
3207   @Override
3208   public void hideSelSequences_actionPerformed(ActionEvent e)
3209   {
3210     viewport.hideAllSelectedSeqs();
3211   }
3212
3213   /**
3214    * called by key handler and the hide all/show all menu items
3215    *
3216    * @param toggleSeqs
3217    * @param toggleCols
3218    */
3219   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3220   {
3221
3222     boolean hide = false;
3223     SequenceGroup sg = viewport.getSelectionGroup();
3224     if (!toggleSeqs && !toggleCols)
3225     {
3226       // Hide everything by the current selection - this is a hack - we do the
3227       // invert and then hide
3228       // first check that there will be visible columns after the invert.
3229       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3230               && sg.getStartRes() <= sg.getEndRes()))
3231       {
3232         // now invert the sequence set, if required - empty selection implies
3233         // that no hiding is required.
3234         if (sg != null)
3235         {
3236           invertSequenceMenuItem_actionPerformed(null);
3237           sg = viewport.getSelectionGroup();
3238           toggleSeqs = true;
3239
3240         }
3241         viewport.expandColSelection(sg, true);
3242         // finally invert the column selection and get the new sequence
3243         // selection.
3244         invertColSel_actionPerformed(null);
3245         toggleCols = true;
3246       }
3247     }
3248
3249     if (toggleSeqs)
3250     {
3251       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3252       {
3253         hideSelSequences_actionPerformed(null);
3254         hide = true;
3255       }
3256       else if (!(toggleCols && viewport.hasSelectedColumns()))
3257       {
3258         showAllSeqs_actionPerformed(null);
3259       }
3260     }
3261
3262     if (toggleCols)
3263     {
3264       if (viewport.hasSelectedColumns())
3265       {
3266         hideSelColumns_actionPerformed(null);
3267         if (!toggleSeqs)
3268         {
3269           viewport.setSelectionGroup(sg);
3270         }
3271       }
3272       else if (!hide)
3273       {
3274         showAllColumns_actionPerformed(null);
3275       }
3276     }
3277   }
3278
3279   /*
3280    * (non-Javadoc)
3281    *
3282    * @see
3283    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3284    * event.ActionEvent)
3285    */
3286   @Override
3287   public void hideAllButSelection_actionPerformed(ActionEvent e)
3288   {
3289     toggleHiddenRegions(false, false);
3290     viewport.sendSelection();
3291   }
3292
3293   /*
3294    * (non-Javadoc)
3295    *
3296    * @see
3297    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3298    * .ActionEvent)
3299    */
3300   @Override
3301   public void hideAllSelection_actionPerformed(ActionEvent e)
3302   {
3303     SequenceGroup sg = viewport.getSelectionGroup();
3304     viewport.expandColSelection(sg, false);
3305     viewport.hideAllSelectedSeqs();
3306     viewport.hideSelectedColumns();
3307     alignPanel.updateLayout();
3308     alignPanel.paintAlignment(true, true);
3309     viewport.sendSelection();
3310   }
3311
3312   /*
3313    * (non-Javadoc)
3314    *
3315    * @see
3316    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3317    * ActionEvent)
3318    */
3319   @Override
3320   public void showAllhidden_actionPerformed(ActionEvent e)
3321   {
3322     viewport.showAllHiddenColumns();
3323     viewport.showAllHiddenSeqs();
3324     alignPanel.paintAlignment(true, true);
3325     viewport.sendSelection();
3326   }
3327
3328   @Override
3329   public void hideSelColumns_actionPerformed(ActionEvent e)
3330   {
3331     viewport.hideSelectedColumns();
3332     alignPanel.updateLayout();
3333     alignPanel.paintAlignment(true, true);
3334     viewport.sendSelection();
3335   }
3336
3337   @Override
3338   public void hiddenMarkers_actionPerformed(ActionEvent e)
3339   {
3340     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3341     repaint();
3342   }
3343
3344   /**
3345    * DOCUMENT ME!
3346    *
3347    * @param e
3348    *          DOCUMENT ME!
3349    */
3350   @Override
3351   protected void scaleAbove_actionPerformed(ActionEvent e)
3352   {
3353     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3354     alignPanel.updateLayout();
3355     alignPanel.paintAlignment(true, false);
3356   }
3357
3358   /**
3359    * DOCUMENT ME!
3360    *
3361    * @param e
3362    *          DOCUMENT ME!
3363    */
3364   @Override
3365   protected void scaleLeft_actionPerformed(ActionEvent e)
3366   {
3367     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3368     alignPanel.updateLayout();
3369     alignPanel.paintAlignment(true, false);
3370   }
3371
3372   /**
3373    * DOCUMENT ME!
3374    *
3375    * @param e
3376    *          DOCUMENT ME!
3377    */
3378   @Override
3379   protected void scaleRight_actionPerformed(ActionEvent e)
3380   {
3381     viewport.setScaleRightWrapped(scaleRight.isSelected());
3382     alignPanel.updateLayout();
3383     alignPanel.paintAlignment(true, false);
3384   }
3385
3386   /**
3387    * DOCUMENT ME!
3388    *
3389    * @param e
3390    *          DOCUMENT ME!
3391    */
3392   @Override
3393   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3394   {
3395     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3396     alignPanel.paintAlignment(false, false);
3397   }
3398
3399   /**
3400    * DOCUMENT ME!
3401    *
3402    * @param e
3403    *          DOCUMENT ME!
3404    */
3405   @Override
3406   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3407   {
3408     viewport.setShowText(viewTextMenuItem.isSelected());
3409     alignPanel.paintAlignment(false, false);
3410   }
3411
3412   /**
3413    * DOCUMENT ME!
3414    *
3415    * @param e
3416    *          DOCUMENT ME!
3417    */
3418   @Override
3419   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3420   {
3421     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3422     alignPanel.paintAlignment(false, false);
3423   }
3424
3425   public FeatureSettings featureSettings;
3426
3427   @Override
3428   public FeatureSettingsControllerI getFeatureSettingsUI()
3429   {
3430     return featureSettings;
3431   }
3432
3433   @Override
3434   public void featureSettings_actionPerformed(ActionEvent e)
3435   {
3436     showFeatureSettingsUI();
3437   }
3438
3439   @Override
3440   public FeatureSettingsControllerI showFeatureSettingsUI()
3441   {
3442     if (featureSettings != null)
3443     {
3444       featureSettings.closeOldSettings();
3445       featureSettings = null;
3446     }
3447     if (!showSeqFeatures.isSelected())
3448     {
3449       // make sure features are actually displayed
3450       showSeqFeatures.setSelected(true);
3451       showSeqFeatures_actionPerformed(null);
3452     }
3453     featureSettings = new FeatureSettings(this);
3454     return featureSettings;
3455   }
3456
3457   /**
3458    * Set or clear 'Show Sequence Features'
3459    *
3460    * @param evt
3461    *          DOCUMENT ME!
3462    */
3463   @Override
3464   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3465   {
3466     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3467     alignPanel.paintAlignment(true, true);
3468   }
3469
3470   /**
3471    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3472    * the annotations panel as a whole.
3473    *
3474    * The options to show/hide all annotations should be enabled when the panel
3475    * is shown, and disabled when the panel is hidden.
3476    *
3477    * @param e
3478    */
3479   @Override
3480   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3481   {
3482     final boolean setVisible = annotationPanelMenuItem.isSelected();
3483     viewport.setShowAnnotation(setVisible);
3484     this.showAllSeqAnnotations.setEnabled(setVisible);
3485     this.hideAllSeqAnnotations.setEnabled(setVisible);
3486     this.showAllAlAnnotations.setEnabled(setVisible);
3487     this.hideAllAlAnnotations.setEnabled(setVisible);
3488     alignPanel.updateLayout();
3489   }
3490
3491   @Override
3492   public void alignmentProperties()
3493   {
3494     JComponent pane;
3495     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3496
3497             .formatAsHtml();
3498     String content = MessageManager.formatMessage("label.html_content",
3499             new Object[]
3500             { contents.toString() });
3501     contents = null;
3502
3503     if (Platform.isJS())
3504     {
3505       JLabel textLabel = new JLabel();
3506       textLabel.setText(content);
3507       textLabel.setBackground(Color.WHITE);
3508
3509       pane = new JPanel(new BorderLayout());
3510       ((JPanel) pane).setOpaque(true);
3511       pane.setBackground(Color.WHITE);
3512       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3513     }
3514     else
3515     /**
3516      * Java only
3517      *
3518      * @j2sIgnore
3519      */
3520     {
3521       JEditorPane editPane = new JEditorPane("text/html", "");
3522       editPane.setEditable(false);
3523       editPane.setText(content);
3524       pane = editPane;
3525     }
3526
3527     JInternalFrame frame = new JInternalFrame();
3528
3529     frame.getContentPane().add(new JScrollPane(pane));
3530
3531     Desktop.addInternalFrame(frame, MessageManager
3532             .formatMessage("label.alignment_properties", new Object[]
3533             { getTitle() }), 500, 400);
3534   }
3535
3536   /**
3537    * Opens an Overview panel for the alignment, unless one is open already
3538    *
3539    * @param e
3540    */
3541   @Override
3542   public void overviewMenuItem_actionPerformed(ActionEvent e)
3543   {
3544     boolean showHiddenRegions = Cache
3545             .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
3546     openOverviewPanel(showHiddenRegions);
3547   }
3548
3549   public OverviewPanel openOverviewPanel(boolean showHidden)
3550   {
3551     if (alignPanel.overviewPanel != null)
3552     {
3553       return alignPanel.overviewPanel;
3554     }
3555     JInternalFrame frame = new JInternalFrame();
3556     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
3557             showHidden);
3558     frame.setContentPane(overview);
3559     Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
3560             frame.getHeight(), true, true);
3561     frame.setFrameIcon(null);
3562     frame.pack();
3563     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3564     final AlignmentPanel thePanel = this.alignPanel;
3565     frame.addInternalFrameListener(
3566             new javax.swing.event.InternalFrameAdapter()
3567             {
3568               @Override
3569               public void internalFrameClosed(
3570                       javax.swing.event.InternalFrameEvent evt)
3571               {
3572                 overview.dispose();
3573                 thePanel.setOverviewPanel(null);
3574               }
3575             });
3576     if (getKeyListeners().length > 0)
3577     {
3578       frame.addKeyListener(getKeyListeners()[0]);
3579     }
3580
3581     alignPanel.setOverviewPanel(overview);
3582     alignPanel.setOverviewTitle(this);
3583
3584     return overview;
3585   }
3586
3587   @Override
3588   public void textColour_actionPerformed()
3589   {
3590     new TextColourChooser().chooseColour(alignPanel, null);
3591   }
3592
3593   /*
3594    * public void covariationColour_actionPerformed() {
3595    * changeColour(new
3596    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3597    * ()[0])); }
3598    */
3599   @Override
3600   public void annotationColour_actionPerformed()
3601   {
3602     new AnnotationColourChooser(viewport, alignPanel);
3603   }
3604
3605   @Override
3606   public void annotationColumn_actionPerformed(ActionEvent e)
3607   {
3608     new AnnotationColumnChooser(viewport, alignPanel);
3609   }
3610
3611   /**
3612    * Action on the user checking or unchecking the option to apply the selected
3613    * colour scheme to all groups. If unchecked, groups may have their own
3614    * independent colour schemes.
3615    *
3616    * @param selected
3617    */
3618   @Override
3619   public void applyToAllGroups_actionPerformed(boolean selected)
3620   {
3621     viewport.setColourAppliesToAllGroups(selected);
3622   }
3623
3624   /**
3625    * Action on user selecting a colour from the colour menu
3626    *
3627    * @param name
3628    *          the name (not the menu item label!) of the colour scheme
3629    */
3630   @Override
3631   public void changeColour_actionPerformed(String name)
3632   {
3633     /*
3634      * 'User Defined' opens a panel to configure or load a
3635      * user-defined colour scheme
3636      */
3637     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3638     {
3639       new UserDefinedColours(alignPanel);
3640       return;
3641     }
3642
3643     /*
3644      * otherwise set the chosen colour scheme (or null for 'None')
3645      */
3646     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3647             viewport, viewport.getAlignment(),
3648             viewport.getHiddenRepSequences());
3649     changeColour(cs);
3650   }
3651
3652   /**
3653    * Actions on setting or changing the alignment colour scheme
3654    *
3655    * @param cs
3656    */
3657   @Override
3658   public void changeColour(ColourSchemeI cs)
3659   {
3660     // TODO: pull up to controller method
3661     ColourMenuHelper.setColourSelected(colourMenu, cs);
3662
3663     viewport.setGlobalColourScheme(cs);
3664
3665     alignPanel.paintAlignment(true, true);
3666   }
3667
3668   /**
3669    * Show the PID threshold slider panel
3670    */
3671   @Override
3672   protected void modifyPID_actionPerformed()
3673   {
3674     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3675             alignPanel.getViewName());
3676     SliderPanel.showPIDSlider();
3677   }
3678
3679   /**
3680    * Show the Conservation slider panel
3681    */
3682   @Override
3683   protected void modifyConservation_actionPerformed()
3684   {
3685     SliderPanel.setConservationSlider(alignPanel,
3686             viewport.getResidueShading(), alignPanel.getViewName());
3687     SliderPanel.showConservationSlider();
3688   }
3689
3690   /**
3691    * Action on selecting or deselecting (Colour) By Conservation
3692    */
3693   @Override
3694   public void conservationMenuItem_actionPerformed(boolean selected)
3695   {
3696     modifyConservation.setEnabled(selected);
3697     viewport.setConservationSelected(selected);
3698     viewport.getResidueShading().setConservationApplied(selected);
3699
3700     changeColour(viewport.getGlobalColourScheme());
3701     if (selected)
3702     {
3703       modifyConservation_actionPerformed();
3704     }
3705     else
3706     {
3707       SliderPanel.hideConservationSlider();
3708     }
3709   }
3710
3711   /**
3712    * Action on selecting or deselecting (Colour) Above PID Threshold
3713    */
3714   @Override
3715   public void abovePIDThreshold_actionPerformed(boolean selected)
3716   {
3717     modifyPID.setEnabled(selected);
3718     viewport.setAbovePIDThreshold(selected);
3719     if (!selected)
3720     {
3721       viewport.getResidueShading().setThreshold(0,
3722               viewport.isIgnoreGapsConsensus());
3723     }
3724
3725     changeColour(viewport.getGlobalColourScheme());
3726     if (selected)
3727     {
3728       modifyPID_actionPerformed();
3729     }
3730     else
3731     {
3732       SliderPanel.hidePIDSlider();
3733     }
3734   }
3735
3736   /**
3737    * DOCUMENT ME!
3738    *
3739    * @param e
3740    *          DOCUMENT ME!
3741    */
3742   @Override
3743   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3744   {
3745     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3746     AlignmentSorter.sortByPID(viewport.getAlignment(),
3747             viewport.getAlignment().getSequenceAt(0));
3748     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3749             viewport.getAlignment()));
3750     alignPanel.paintAlignment(true, false);
3751   }
3752
3753   /**
3754    * DOCUMENT ME!
3755    *
3756    * @param e
3757    *          DOCUMENT ME!
3758    */
3759   @Override
3760   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3761   {
3762     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3763     AlignmentSorter.sortByID(viewport.getAlignment());
3764     addHistoryItem(
3765             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3766     alignPanel.paintAlignment(true, false);
3767   }
3768
3769   /**
3770    * DOCUMENT ME!
3771    *
3772    * @param e
3773    *          DOCUMENT ME!
3774    */
3775   @Override
3776   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3777   {
3778     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3779     AlignmentSorter.sortByLength(viewport.getAlignment());
3780     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3781             viewport.getAlignment()));
3782     alignPanel.paintAlignment(true, false);
3783   }
3784
3785   /**
3786    * DOCUMENT ME!
3787    *
3788    * @param e
3789    *          DOCUMENT ME!
3790    */
3791   @Override
3792   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3793   {
3794     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3795     AlignmentSorter.sortByGroup(viewport.getAlignment());
3796     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3797             viewport.getAlignment()));
3798
3799     alignPanel.paintAlignment(true, false);
3800   }
3801
3802   /**
3803    * DOCUMENT ME!
3804    *
3805    * @param e
3806    *          DOCUMENT ME!
3807    */
3808   @Override
3809   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3810   {
3811     new RedundancyPanel(alignPanel, this);
3812   }
3813
3814   /**
3815    * DOCUMENT ME!
3816    *
3817    * @param e
3818    *          DOCUMENT ME!
3819    */
3820   @Override
3821   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3822   {
3823     if ((viewport.getSelectionGroup() == null)
3824             || (viewport.getSelectionGroup().getSize() < 2))
3825     {
3826       JvOptionPane.showInternalMessageDialog(this,
3827               MessageManager.getString(
3828                       "label.you_must_select_least_two_sequences"),
3829               MessageManager.getString("label.invalid_selection"),
3830               JvOptionPane.WARNING_MESSAGE);
3831     }
3832     else
3833     {
3834       JInternalFrame frame = new JInternalFrame();
3835       frame.setContentPane(new PairwiseAlignPanel(viewport));
3836       Desktop.addInternalFrame(frame,
3837               MessageManager.getString("action.pairwise_alignment"), 600,
3838               500);
3839     }
3840   }
3841
3842   @Override
3843   public void autoCalculate_actionPerformed(ActionEvent e)
3844   {
3845     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3846     if (viewport.autoCalculateConsensus)
3847     {
3848       viewport.firePropertyChange("alignment", null,
3849               viewport.getAlignment().getSequences());
3850     }
3851   }
3852
3853   @Override
3854   public void sortByTreeOption_actionPerformed(ActionEvent e)
3855   {
3856     viewport.sortByTree = sortByTree.isSelected();
3857   }
3858
3859   @Override
3860   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3861   {
3862     viewport.followSelection = listenToViewSelections.isSelected();
3863   }
3864
3865   /**
3866    * Constructs a tree panel and adds it to the desktop
3867    *
3868    * @param type
3869    *          tree type (NJ or AV)
3870    * @param modelName
3871    *          name of score model used to compute the tree
3872    * @param options
3873    *          parameters for the distance or similarity calculation
3874    */
3875   void newTreePanel(String type, String modelName,
3876           SimilarityParamsI options)
3877   {
3878     String frameTitle = "";
3879     TreePanel tp;
3880
3881     boolean onSelection = false;
3882     if (viewport.getSelectionGroup() != null
3883             && viewport.getSelectionGroup().getSize() > 0)
3884     {
3885       SequenceGroup sg = viewport.getSelectionGroup();
3886
3887       /* Decide if the selection is a column region */
3888       for (SequenceI _s : sg.getSequences())
3889       {
3890         if (_s.getLength() < sg.getEndRes())
3891         {
3892           JvOptionPane.showMessageDialog(Desktop.desktop,
3893                   MessageManager.getString(
3894                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3895                   MessageManager.getString(
3896                           "label.sequences_selection_not_aligned"),
3897                   JvOptionPane.WARNING_MESSAGE);
3898
3899           return;
3900         }
3901       }
3902       onSelection = true;
3903     }
3904     else
3905     {
3906       if (viewport.getAlignment().getHeight() < 2)
3907       {
3908         return;
3909       }
3910     }
3911
3912     tp = new TreePanel(alignPanel, type, modelName, options);
3913     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3914
3915     frameTitle += " from ";
3916
3917     if (viewport.getViewName() != null)
3918     {
3919       frameTitle += viewport.getViewName() + " of ";
3920     }
3921
3922     frameTitle += this.title;
3923
3924     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3925   }
3926
3927   /**
3928    * DOCUMENT ME!
3929    *
3930    * @param title
3931    *          DOCUMENT ME!
3932    * @param order
3933    *          DOCUMENT ME!
3934    */
3935   public void addSortByOrderMenuItem(String title,
3936           final AlignmentOrder order)
3937   {
3938     final JMenuItem item = new JMenuItem(MessageManager
3939             .formatMessage("action.by_title_param", new Object[]
3940             { title }));
3941     sort.add(item);
3942     item.addActionListener(new java.awt.event.ActionListener()
3943     {
3944       @Override
3945       public void actionPerformed(ActionEvent e)
3946       {
3947         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3948
3949         // TODO: JBPNote - have to map order entries to curent SequenceI
3950         // pointers
3951         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3952
3953         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3954                 viewport.getAlignment()));
3955
3956         alignPanel.paintAlignment(true, false);
3957       }
3958     });
3959   }
3960
3961   /**
3962    * Add a new sort by annotation score menu item
3963    *
3964    * @param sort
3965    *          the menu to add the option to
3966    * @param scoreLabel
3967    *          the label used to retrieve scores for each sequence on the
3968    *          alignment
3969    */
3970   public void addSortByAnnotScoreMenuItem(JMenu sort,
3971           final String scoreLabel)
3972   {
3973     final JMenuItem item = new JMenuItem(scoreLabel);
3974     sort.add(item);
3975     item.addActionListener(new java.awt.event.ActionListener()
3976     {
3977       @Override
3978       public void actionPerformed(ActionEvent e)
3979       {
3980         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3981         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3982                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3983         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3984                 viewport.getAlignment()));
3985         alignPanel.paintAlignment(true, false);
3986       }
3987     });
3988   }
3989
3990   /**
3991    * last hash for alignment's annotation array - used to minimise cost of
3992    * rebuild.
3993    */
3994   protected int _annotationScoreVectorHash;
3995
3996   /**
3997    * search the alignment and rebuild the sort by annotation score submenu the
3998    * last alignment annotation vector hash is stored to minimize cost of
3999    * rebuilding in subsequence calls.
4000    *
4001    */
4002   @Override
4003   public void buildSortByAnnotationScoresMenu()
4004   {
4005     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4006     {
4007       return;
4008     }
4009
4010     if (viewport.getAlignment().getAlignmentAnnotation()
4011             .hashCode() != _annotationScoreVectorHash)
4012     {
4013       sortByAnnotScore.removeAll();
4014       // almost certainly a quicker way to do this - but we keep it simple
4015       Hashtable<String, String> scoreSorts = new Hashtable<>();
4016       AlignmentAnnotation aann[];
4017       for (SequenceI sqa : viewport.getAlignment().getSequences())
4018       {
4019         aann = sqa.getAnnotation();
4020         for (int i = 0; aann != null && i < aann.length; i++)
4021         {
4022           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4023           {
4024             scoreSorts.put(aann[i].label, aann[i].label);
4025           }
4026         }
4027       }
4028       Enumeration<String> labels = scoreSorts.keys();
4029       while (labels.hasMoreElements())
4030       {
4031         addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
4032       }
4033       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4034       scoreSorts.clear();
4035
4036       _annotationScoreVectorHash = viewport.getAlignment()
4037               .getAlignmentAnnotation().hashCode();
4038     }
4039   }
4040
4041   /**
4042    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4043    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4044    * call. Listeners are added to remove the menu item when the treePanel is
4045    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4046    * modified.
4047    */
4048   @Override
4049   public void buildTreeSortMenu()
4050   {
4051     sortByTreeMenu.removeAll();
4052
4053     List<Component> comps = PaintRefresher.components
4054             .get(viewport.getSequenceSetId());
4055     List<TreePanel> treePanels = new ArrayList<>();
4056     for (Component comp : comps)
4057     {
4058       if (comp instanceof TreePanel)
4059       {
4060         treePanels.add((TreePanel) comp);
4061       }
4062     }
4063
4064     if (treePanels.size() < 1)
4065     {
4066       sortByTreeMenu.setVisible(false);
4067       return;
4068     }
4069
4070     sortByTreeMenu.setVisible(true);
4071
4072     for (final TreePanel tp : treePanels)
4073     {
4074       final JMenuItem item = new JMenuItem(tp.getTitle());
4075       item.addActionListener(new java.awt.event.ActionListener()
4076       {
4077         @Override
4078         public void actionPerformed(ActionEvent e)
4079         {
4080           tp.sortByTree_actionPerformed();
4081           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4082
4083         }
4084       });
4085
4086       sortByTreeMenu.add(item);
4087     }
4088   }
4089
4090   public boolean sortBy(AlignmentOrder alorder, String undoname)
4091   {
4092     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4093     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4094     if (undoname != null)
4095     {
4096       addHistoryItem(new OrderCommand(undoname, oldOrder,
4097               viewport.getAlignment()));
4098     }
4099     alignPanel.paintAlignment(true, false);
4100     return true;
4101   }
4102
4103   /**
4104    * Work out whether the whole set of sequences or just the selected set will
4105    * be submitted for multiple alignment.
4106    *
4107    */
4108   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4109   {
4110     // Now, check we have enough sequences
4111     AlignmentView msa = null;
4112
4113     if ((viewport.getSelectionGroup() != null)
4114             && (viewport.getSelectionGroup().getSize() > 1))
4115     {
4116       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4117       // some common interface!
4118       /*
4119        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4120        * SequenceI[sz = seqs.getSize(false)];
4121        *
4122        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4123        * seqs.getSequenceAt(i); }
4124        */
4125       msa = viewport.getAlignmentView(true);
4126     }
4127     else if (viewport.getSelectionGroup() != null
4128             && viewport.getSelectionGroup().getSize() == 1)
4129     {
4130       int option = JvOptionPane.showConfirmDialog(this,
4131               MessageManager.getString("warn.oneseq_msainput_selection"),
4132               MessageManager.getString("label.invalid_selection"),
4133               JvOptionPane.OK_CANCEL_OPTION);
4134       if (option == JvOptionPane.OK_OPTION)
4135       {
4136         msa = viewport.getAlignmentView(false);
4137       }
4138     }
4139     else
4140     {
4141       msa = viewport.getAlignmentView(false);
4142     }
4143     return msa;
4144   }
4145
4146   /**
4147    * Decides what is submitted to a secondary structure prediction service: the
4148    * first sequence in the alignment, or in the current selection, or, if the
4149    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4150    * region or the whole alignment. (where the first sequence in the set is the
4151    * one that the prediction will be for).
4152    */
4153   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4154   {
4155     AlignmentView seqs = null;
4156
4157     if ((viewport.getSelectionGroup() != null)
4158             && (viewport.getSelectionGroup().getSize() > 0))
4159     {
4160       seqs = viewport.getAlignmentView(true);
4161     }
4162     else
4163     {
4164       seqs = viewport.getAlignmentView(false);
4165     }
4166     // limit sequences - JBPNote in future - could spawn multiple prediction
4167     // jobs
4168     // TODO: viewport.getAlignment().isAligned is a global state - the local
4169     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4170     if (!viewport.getAlignment().isAligned(false))
4171     {
4172       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4173       // TODO: if seqs.getSequences().length>1 then should really have warned
4174       // user!
4175
4176     }
4177     return seqs;
4178   }
4179
4180   /**
4181    * DOCUMENT ME!
4182    *
4183    * @param e
4184    *          DOCUMENT ME!
4185    */
4186   @Override
4187   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4188   {
4189     // Pick the tree file
4190     JalviewFileChooser chooser = new JalviewFileChooser(
4191             Cache.getProperty("LAST_DIRECTORY"));
4192     chooser.setFileView(new JalviewFileView());
4193     chooser.setDialogTitle(
4194             MessageManager.getString("label.select_newick_like_tree_file"));
4195     chooser.setToolTipText(
4196             MessageManager.getString("label.load_tree_file"));
4197
4198     chooser.setResponseHandler(0, () -> {
4199       String filePath = chooser.getSelectedFile().getPath();
4200       Cache.setProperty("LAST_DIRECTORY", filePath);
4201       NewickFile fin = null;
4202       try
4203       {
4204         fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4205                 DataSourceType.FILE));
4206         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4207       } catch (Exception ex)
4208       {
4209         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4210                 MessageManager.getString("label.problem_reading_tree_file"),
4211                 JvOptionPane.WARNING_MESSAGE);
4212         ex.printStackTrace();
4213       }
4214       if (fin != null && fin.hasWarningMessage())
4215       {
4216         JvOptionPane.showMessageDialog(Desktop.desktop,
4217                 fin.getWarningMessage(),
4218                 MessageManager
4219                         .getString("label.possible_problem_with_tree_file"),
4220                 JvOptionPane.WARNING_MESSAGE);
4221       }
4222     });
4223     chooser.showOpenDialog(this);
4224   }
4225
4226   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4227   {
4228     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4229   }
4230
4231   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4232           int h, int x, int y)
4233   {
4234     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4235   }
4236
4237   /**
4238    * Add a treeviewer for the tree extracted from a Newick file object to the
4239    * current alignment view
4240    *
4241    * @param nf
4242    *          the tree
4243    * @param title
4244    *          tree viewer title
4245    * @param input
4246    *          Associated alignment input data (or null)
4247    * @param w
4248    *          width
4249    * @param h
4250    *          height
4251    * @param x
4252    *          position
4253    * @param y
4254    *          position
4255    * @return TreePanel handle
4256    */
4257   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4258           AlignmentView input, int w, int h, int x, int y)
4259   {
4260     TreePanel tp = null;
4261
4262     try
4263     {
4264       nf.parse();
4265
4266       if (nf.getTree() != null)
4267       {
4268         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4269
4270         tp.setSize(w, h);
4271
4272         if (x > 0 && y > 0)
4273         {
4274           tp.setLocation(x, y);
4275         }
4276
4277         Desktop.addInternalFrame(tp, treeTitle, w, h);
4278       }
4279     } catch (Exception ex)
4280     {
4281       ex.printStackTrace();
4282     }
4283
4284     return tp;
4285   }
4286
4287   public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
4288   {
4289     int x = 4, y = 5;
4290     int w = 400, h = 500;
4291
4292     try
4293     {
4294       NewickFile fin = new NewickFile(
4295               new FileParse(cm.getNewick(), DataSourceType.PASTE));
4296       String title = aa.label + " " + cm.getTreeMethod() + " tree"
4297               + (aa.sequenceRef != null
4298                       ? (" for " + aa.sequenceRef.getDisplayId(false))
4299                       : "");
4300
4301       showColumnWiseTree(fin, aa, title, w, h, x, y);
4302     } catch (Throwable xx)
4303     {
4304       Console.error("Unexpected exception showing tree for contact matrix",
4305               xx);
4306     }
4307   }
4308
4309   public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
4310           String treeTitle, int w, int h, int x, int y)
4311   {
4312     try
4313     {
4314       nf.parse();
4315       if (nf.getTree() == null)
4316       {
4317         return null;
4318       }
4319       TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle);
4320
4321       tp.setSize(w, h);
4322
4323       if (x > 0 && y > 0)
4324       {
4325         tp.setLocation(x, y);
4326       }
4327
4328       Desktop.addInternalFrame(tp, treeTitle, w, h);
4329       return tp;
4330     } catch (Throwable xx)
4331     {
4332       Console.error("Unexpected exception showing tree for contact matrix",
4333               xx);
4334     }
4335     return null;
4336   }
4337
4338   private boolean buildingMenu = false;
4339
4340   /**
4341    * Generates menu items and listener event actions for web service clients
4342    *
4343    */
4344   public void BuildWebServiceMenu()
4345   {
4346     while (buildingMenu)
4347     {
4348       try
4349       {
4350         jalview.bin.Console
4351                 .errPrintln("Waiting for building menu to finish.");
4352         Thread.sleep(10);
4353       } catch (Exception e)
4354       {
4355       }
4356     }
4357     final AlignFrame me = this;
4358     buildingMenu = true;
4359     new Thread(new Runnable()
4360     {
4361       @Override
4362       public void run()
4363       {
4364         final List<JMenuItem> legacyItems = new ArrayList<>();
4365         try
4366         {
4367           // jalview.bin.Console.errPrintln("Building ws menu again "
4368           // + Thread.currentThread());
4369           // TODO: add support for context dependent disabling of services based
4370           // on
4371           // alignment and current selection
4372           // TODO: add additional serviceHandle parameter to specify abstract
4373           // handler
4374           // class independently of AbstractName
4375           // TODO: add in rediscovery GUI function to restart discoverer
4376           // TODO: group services by location as well as function and/or
4377           // introduce
4378           // object broker mechanism.
4379           final Vector<JMenu> wsmenu = new Vector<>();
4380           final IProgressIndicator af = me;
4381
4382           /*
4383            * do not i18n these strings - they are hard-coded in class
4384            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4385            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4386            */
4387           final JMenu msawsmenu = new JMenu("Alignment");
4388           final JMenu secstrmenu = new JMenu(
4389                   "Secondary Structure Prediction");
4390           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4391           final JMenu analymenu = new JMenu("Analysis");
4392           final JMenu dismenu = new JMenu("Protein Disorder");
4393           // JAL-940 - only show secondary structure prediction services from
4394           // the legacy server
4395           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4396               // &&
4397           Discoverer.services != null && (Discoverer.services.size() > 0))
4398           {
4399             // TODO: refactor to allow list of AbstractName/Handler bindings to
4400             // be
4401             // stored or retrieved from elsewhere
4402             // No MSAWS used any more:
4403             // Vector msaws = null; // (Vector)
4404             // Discoverer.services.get("MsaWS");
4405             Vector<ServiceHandle> secstrpr = Discoverer.services
4406                     .get("SecStrPred");
4407             if (secstrpr != null)
4408             {
4409               // Add any secondary structure prediction services
4410               for (int i = 0, j = secstrpr.size(); i < j; i++)
4411               {
4412                 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4413                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4414                         .getServiceClient(sh);
4415                 int p = secstrmenu.getItemCount();
4416                 impl.attachWSMenuEntry(secstrmenu, me);
4417                 int q = secstrmenu.getItemCount();
4418                 for (int litm = p; litm < q; litm++)
4419                 {
4420                   legacyItems.add(secstrmenu.getItem(litm));
4421                 }
4422               }
4423             }
4424           }
4425
4426           // Add all submenus in the order they should appear on the web
4427           // services menu
4428           wsmenu.add(msawsmenu);
4429           wsmenu.add(secstrmenu);
4430           wsmenu.add(dismenu);
4431           wsmenu.add(analymenu);
4432           // No search services yet
4433           // wsmenu.add(seqsrchmenu);
4434
4435           javax.swing.SwingUtilities.invokeLater(new Runnable()
4436           {
4437             @Override
4438             public void run()
4439             {
4440               try
4441               {
4442                 webService.removeAll();
4443                 // first, add discovered services onto the webservices menu
4444                 if (wsmenu.size() > 0)
4445                 {
4446                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4447                   {
4448                     webService.add(wsmenu.get(i));
4449                   }
4450                 }
4451                 else
4452                 {
4453                   webService.add(me.webServiceNoServices);
4454                 }
4455                 // TODO: move into separate menu builder class.
4456                 {
4457                   // logic for 2.11.1.4 is
4458                   // always look to see if there is a discover. if there isn't
4459                   // we can't show any Jws2 services
4460                   // if there are services available, show them - regardless of
4461                   // the 'show JWS2 preference'
4462                   // if the discoverer is running then say so
4463                   // otherwise offer to trigger discovery if 'show JWS2' is not
4464                   // enabled
4465                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4466                   if (jws2servs != null)
4467                   {
4468                     if (jws2servs.hasServices())
4469                     {
4470                       jws2servs.attachWSMenuEntry(webService, me);
4471                       for (Jws2Instance sv : jws2servs.getServices())
4472                       {
4473                         if (sv.description.toLowerCase(Locale.ROOT)
4474                                 .contains("jpred"))
4475                         {
4476                           for (JMenuItem jmi : legacyItems)
4477                           {
4478                             jmi.setVisible(false);
4479                           }
4480                         }
4481                       }
4482                     }
4483
4484                     if (jws2servs.isRunning())
4485                     {
4486                       JMenuItem tm = new JMenuItem(
4487                               "Still discovering JABA Services");
4488                       tm.setEnabled(false);
4489                       webService.add(tm);
4490                     }
4491                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4492                     {
4493                       JMenuItem enableJws2 = new JMenuItem(
4494                               "Discover Web Services");
4495                       enableJws2.setToolTipText(
4496                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4497                       enableJws2.setEnabled(true);
4498                       enableJws2.addActionListener(new ActionListener()
4499                       {
4500
4501                         @Override
4502                         public void actionPerformed(ActionEvent e)
4503                         {
4504                           // start service discoverer, but ignore preference
4505                           Desktop.instance.startServiceDiscovery(false,
4506                                   true);
4507                         }
4508                       });
4509                       webService.add(enableJws2);
4510                     }
4511                   }
4512                 }
4513                 build_urlServiceMenu(me.webService);
4514                 build_fetchdbmenu(webService);
4515                 for (JMenu item : wsmenu)
4516                 {
4517                   if (item.getItemCount() == 0)
4518                   {
4519                     item.setEnabled(false);
4520                   }
4521                   else
4522                   {
4523                     item.setEnabled(true);
4524                   }
4525                 }
4526               } catch (Exception e)
4527               {
4528                 Console.debug(
4529                         "Exception during web service menu building process.",
4530                         e);
4531               }
4532             }
4533           });
4534         } catch (Exception e)
4535         {
4536         }
4537         buildingMenu = false;
4538       }
4539     }).start();
4540
4541   }
4542
4543   /**
4544    * construct any groupURL type service menu entries.
4545    *
4546    * @param webService
4547    */
4548   protected void build_urlServiceMenu(JMenu webService)
4549   {
4550     // TODO: remove this code when 2.7 is released
4551     // DEBUG - alignmentView
4552     /*
4553      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4554      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4555      *
4556      * @Override public void actionPerformed(ActionEvent e) {
4557      * jalview.datamodel.AlignmentView
4558      * .testSelectionViews(af.viewport.getAlignment(),
4559      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4560      *
4561      * }); webService.add(testAlView);
4562      */
4563     // TODO: refactor to RestClient discoverer and merge menu entries for
4564     // rest-style services with other types of analysis/calculation service
4565     // SHmmr test client - still being implemented.
4566     // DEBUG - alignmentView
4567
4568     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4569             .getRestClients())
4570     {
4571       client.attachWSMenuEntry(
4572               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4573               this);
4574     }
4575   }
4576
4577   /**
4578    * Searches the alignment sequences for xRefs and builds the Show
4579    * Cross-References menu (formerly called Show Products), with database
4580    * sources for which cross-references are found (protein sources for a
4581    * nucleotide alignment and vice versa)
4582    *
4583    * @return true if Show Cross-references menu should be enabled
4584    */
4585   public boolean canShowProducts()
4586   {
4587     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4588     AlignmentI dataset = viewport.getAlignment().getDataset();
4589
4590     showProducts.removeAll();
4591     final boolean dna = viewport.getAlignment().isNucleotide();
4592
4593     if (seqs == null || seqs.length == 0)
4594     {
4595       // nothing to see here.
4596       return false;
4597     }
4598
4599     boolean showp = false;
4600     try
4601     {
4602       List<String> ptypes = new CrossRef(seqs, dataset)
4603               .findXrefSourcesForSequences(dna);
4604
4605       for (final String source : ptypes)
4606       {
4607         showp = true;
4608         final AlignFrame af = this;
4609         JMenuItem xtype = new JMenuItem(source);
4610         xtype.addActionListener(new ActionListener()
4611         {
4612           @Override
4613           public void actionPerformed(ActionEvent e)
4614           {
4615             showProductsFor(af.viewport.getSequenceSelection(), dna,
4616                     source);
4617           }
4618         });
4619         showProducts.add(xtype);
4620       }
4621       showProducts.setVisible(showp);
4622       showProducts.setEnabled(showp);
4623     } catch (Exception e)
4624     {
4625       Console.warn(
4626               "canShowProducts threw an exception - please report to help@jalview.org",
4627               e);
4628       return false;
4629     }
4630     return showp;
4631   }
4632
4633   /**
4634    * Finds and displays cross-references for the selected sequences (protein
4635    * products for nucleotide sequences, dna coding sequences for peptides).
4636    *
4637    * @param sel
4638    *          the sequences to show cross-references for
4639    * @param dna
4640    *          true if from a nucleotide alignment (so showing proteins)
4641    * @param source
4642    *          the database to show cross-references for
4643    */
4644   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4645           final String source)
4646   {
4647     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4648             .start();
4649   }
4650
4651   /**
4652    * Construct and display a new frame containing the translation of this
4653    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4654    */
4655   @Override
4656   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4657   {
4658     AlignmentI al = null;
4659     try
4660     {
4661       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4662
4663       al = dna.translateCdna(codeTable);
4664     } catch (Exception ex)
4665     {
4666       Console.error("Exception during translation. Please report this !",
4667               ex);
4668       final String msg = MessageManager.getString(
4669               "label.error_when_translating_sequences_submit_bug_report");
4670       final String errorTitle = MessageManager
4671               .getString("label.implementation_error")
4672               + MessageManager.getString("label.translation_failed");
4673       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4674               JvOptionPane.ERROR_MESSAGE);
4675       return;
4676     }
4677     if (al == null || al.getHeight() == 0)
4678     {
4679       final String msg = MessageManager.getString(
4680               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4681       final String errorTitle = MessageManager
4682               .getString("label.translation_failed");
4683       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4684               JvOptionPane.WARNING_MESSAGE);
4685     }
4686     else
4687     {
4688       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4689       af.setFileFormat(this.currentFileFormat);
4690       final String newTitle = MessageManager
4691               .formatMessage("label.translation_of_params", new Object[]
4692               { this.getTitle(), codeTable.getId() });
4693       af.setTitle(newTitle);
4694       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4695       {
4696         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4697         viewport.openSplitFrame(af, new Alignment(seqs));
4698       }
4699       else
4700       {
4701         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4702                 DEFAULT_HEIGHT);
4703       }
4704     }
4705   }
4706
4707   /**
4708    * Set the file format
4709    *
4710    * @param format
4711    */
4712   public void setFileFormat(FileFormatI format)
4713   {
4714     this.currentFileFormat = format;
4715   }
4716
4717   /**
4718    * Try to load a features file onto the alignment.
4719    *
4720    * @param file
4721    *          contents or path to retrieve file or a File object
4722    * @param sourceType
4723    *          access mode of file (see jalview.io.AlignFile)
4724    * @return true if features file was parsed correctly.
4725    */
4726   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4727   {
4728     // BH 2018
4729     return avc.parseFeaturesFile(file, sourceType,
4730             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4731
4732   }
4733
4734   @Override
4735   public void refreshFeatureUI(boolean enableIfNecessary)
4736   {
4737     // note - currently this is only still here rather than in the controller
4738     // because of the featureSettings hard reference that is yet to be
4739     // abstracted
4740     if (enableIfNecessary)
4741     {
4742       viewport.setShowSequenceFeatures(true);
4743       showSeqFeatures.setSelected(true);
4744     }
4745
4746   }
4747
4748   @Override
4749   public void dragEnter(DropTargetDragEvent evt)
4750   {
4751   }
4752
4753   @Override
4754   public void dragExit(DropTargetEvent evt)
4755   {
4756   }
4757
4758   @Override
4759   public void dragOver(DropTargetDragEvent evt)
4760   {
4761   }
4762
4763   @Override
4764   public void dropActionChanged(DropTargetDragEvent evt)
4765   {
4766   }
4767
4768   @Override
4769   public void drop(DropTargetDropEvent evt)
4770   {
4771     // JAL-1552 - acceptDrop required before getTransferable call for
4772     // Java's Transferable for native dnd
4773     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4774     Transferable t = evt.getTransferable();
4775
4776     final AlignFrame thisaf = this;
4777     final List<Object> files = new ArrayList<>();
4778     List<DataSourceType> protocols = new ArrayList<>();
4779
4780     try
4781     {
4782       Desktop.transferFromDropTarget(files, protocols, evt, t);
4783     } catch (Exception e)
4784     {
4785       e.printStackTrace();
4786     }
4787     if (files != null)
4788     {
4789       new Thread(new Runnable()
4790       {
4791         @Override
4792         public void run()
4793         {
4794           try
4795           {
4796             // check to see if any of these files have names matching sequences
4797             // in
4798             // the alignment
4799             SequenceIdMatcher idm = new SequenceIdMatcher(
4800                     viewport.getAlignment().getSequencesArray());
4801             /**
4802              * Object[] { String,SequenceI}
4803              */
4804             ArrayList<Object[]> filesmatched = new ArrayList<>();
4805             ArrayList<Object> filesnotmatched = new ArrayList<>();
4806             for (int i = 0; i < files.size(); i++)
4807             {
4808               // BH 2018
4809               Object file = files.get(i);
4810               String fileName = file.toString();
4811               String pdbfn = "";
4812               DataSourceType protocol = (file instanceof File
4813                       ? DataSourceType.FILE
4814                       : FormatAdapter.checkProtocol(fileName));
4815               if (protocol == DataSourceType.FILE)
4816               {
4817                 File fl;
4818                 if (file instanceof File)
4819                 {
4820                   fl = (File) file;
4821                   Platform.cacheFileData(fl);
4822                 }
4823                 else
4824                 {
4825                   fl = new File(fileName);
4826                 }
4827                 pdbfn = fl.getName();
4828               }
4829               else if (protocol == DataSourceType.URL)
4830               {
4831                 URL url = new URL(fileName);
4832                 pdbfn = url.getFile();
4833               }
4834               if (pdbfn.length() > 0)
4835               {
4836                 // attempt to find a match in the alignment
4837                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4838                 int l = 0, c = pdbfn.indexOf(".");
4839                 while (mtch == null && c != -1)
4840                 {
4841                   do
4842                   {
4843                     l = c;
4844                   } while ((c = pdbfn.indexOf(".", l)) > l);
4845                   if (l > -1)
4846                   {
4847                     pdbfn = pdbfn.substring(0, l);
4848                   }
4849                   mtch = idm.findAllIdMatches(pdbfn);
4850                 }
4851                 if (mtch != null)
4852                 {
4853                   FileFormatI type;
4854                   try
4855                   {
4856                     type = new IdentifyFile().identify(file, protocol);
4857                   } catch (Exception ex)
4858                   {
4859                     type = null;
4860                   }
4861                   if (type != null && type.isStructureFile())
4862                   {
4863                     filesmatched.add(new Object[] { file, protocol, mtch });
4864                     continue;
4865                   }
4866                 }
4867                 // File wasn't named like one of the sequences or wasn't a PDB
4868                 // file.
4869                 filesnotmatched.add(file);
4870               }
4871             }
4872             int assocfiles = 0;
4873             if (filesmatched.size() > 0)
4874             {
4875               boolean autoAssociate = Cache
4876                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4877               if (!autoAssociate)
4878               {
4879                 String msg = MessageManager.formatMessage(
4880                         "label.automatically_associate_structure_files_with_sequences_same_name",
4881                         new Object[]
4882                         { Integer.valueOf(filesmatched.size())
4883                                 .toString() });
4884                 String ttl = MessageManager.getString(
4885                         "label.automatically_associate_structure_files_by_name");
4886                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4887                         ttl, JvOptionPane.YES_NO_OPTION);
4888                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4889               }
4890               if (autoAssociate)
4891               {
4892                 for (Object[] fm : filesmatched)
4893                 {
4894                   // try and associate
4895                   // TODO: may want to set a standard ID naming formalism for
4896                   // associating PDB files which have no IDs.
4897                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4898                   {
4899                     PDBEntry pe = new AssociatePdbFileWithSeq()
4900                             .associatePdbWithSeq(fm[0].toString(),
4901                                     (DataSourceType) fm[1], toassoc, false,
4902                                     Desktop.instance);
4903                     if (pe != null)
4904                     {
4905                       jalview.bin.Console.errPrintln("Associated file : "
4906                               + (fm[0].toString()) + " with "
4907                               + toassoc.getDisplayId(true));
4908                       assocfiles++;
4909                     }
4910                   }
4911                   // TODO: do we need to update overview ? only if features are
4912                   // shown I guess
4913                   alignPanel.paintAlignment(true, false);
4914                 }
4915               }
4916               else
4917               {
4918                 /*
4919                  * add declined structures as sequences
4920                  */
4921                 for (Object[] o : filesmatched)
4922                 {
4923                   filesnotmatched.add(o[0]);
4924                 }
4925               }
4926             }
4927             if (filesnotmatched.size() > 0)
4928             {
4929               if (assocfiles > 0 && (Cache.getDefault(
4930                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4931                       || JvOptionPane.showConfirmDialog(thisaf,
4932                               "<html>" + MessageManager.formatMessage(
4933                                       "label.ignore_unmatched_dropped_files_info",
4934                                       new Object[]
4935                                       { Integer.valueOf(
4936                                               filesnotmatched.size())
4937                                               .toString() })
4938                                       + "</html>",
4939                               MessageManager.getString(
4940                                       "label.ignore_unmatched_dropped_files"),
4941                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4942               {
4943                 return;
4944               }
4945               for (Object fn : filesnotmatched)
4946               {
4947                 loadJalviewDataFile(fn, null, null, null);
4948               }
4949
4950             }
4951           } catch (Exception ex)
4952           {
4953             ex.printStackTrace();
4954           }
4955         }
4956       }).start();
4957     }
4958   }
4959
4960   /**
4961    * Attempt to load a "dropped" file or URL string, by testing in turn for
4962    * <ul>
4963    * <li>an Annotation file</li>
4964    * <li>a JNet file</li>
4965    * <li>a features file</li>
4966    * <li>else try to interpret as an alignment file</li>
4967    * </ul>
4968    *
4969    * @param file
4970    *          either a filename or a URL string.
4971    */
4972   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4973           FileFormatI format, SequenceI assocSeq)
4974   {
4975     // BH 2018 was String file
4976     try
4977     {
4978       if (sourceType == null)
4979       {
4980         sourceType = FormatAdapter.checkProtocol(file);
4981       }
4982       // if the file isn't identified, or not positively identified as some
4983       // other filetype (PFAM is default unidentified alignment file type) then
4984       // try to parse as annotation.
4985       boolean isAnnotation = (format == null
4986               || FileFormat.Pfam.equals(format))
4987                       ? new AnnotationFile().annotateAlignmentView(viewport,
4988                               file, sourceType)
4989                       : false;
4990
4991       if (!isAnnotation)
4992       {
4993         // first see if its a T-COFFEE score file
4994         TCoffeeScoreFile tcf = null;
4995         try
4996         {
4997           tcf = new TCoffeeScoreFile(file, sourceType);
4998           if (tcf.isValid())
4999           {
5000             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5001             {
5002               buildColourMenu();
5003               changeColour(
5004                       new TCoffeeColourScheme(viewport.getAlignment()));
5005               isAnnotation = true;
5006               setStatus(MessageManager.getString(
5007                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
5008             }
5009             else
5010             {
5011               // some problem - if no warning its probable that the ID matching
5012               // process didn't work
5013               JvOptionPane.showMessageDialog(Desktop.desktop,
5014                       tcf.getWarningMessage() == null
5015                               ? MessageManager.getString(
5016                                       "label.check_file_matches_sequence_ids_alignment")
5017                               : tcf.getWarningMessage(),
5018                       MessageManager.getString(
5019                               "label.problem_reading_tcoffee_score_file"),
5020                       JvOptionPane.WARNING_MESSAGE);
5021             }
5022           }
5023           else
5024           {
5025             tcf = null;
5026           }
5027         } catch (Exception x)
5028         {
5029           Console.debug(
5030                   "Exception when processing data source as T-COFFEE score file",
5031                   x);
5032           tcf = null;
5033         }
5034         if (tcf == null)
5035         {
5036           // try to see if its a JNet 'concise' style annotation file *before*
5037           // we
5038           // try to parse it as a features file
5039           if (format == null)
5040           {
5041             format = new IdentifyFile().identify(file, sourceType);
5042           }
5043           if (FileFormat.ScoreMatrix == format)
5044           {
5045             ScoreMatrixFile sm = new ScoreMatrixFile(
5046                     new FileParse(file, sourceType));
5047             sm.parse();
5048             // todo: i18n this message
5049             setStatus(MessageManager.formatMessage(
5050                     "label.successfully_loaded_matrix",
5051                     sm.getMatrixName()));
5052           }
5053           else if (FileFormat.Jnet.equals(format))
5054           {
5055             JPredFile predictions = new JPredFile(file, sourceType);
5056             new JnetAnnotationMaker();
5057             JnetAnnotationMaker.add_annotation(predictions,
5058                     viewport.getAlignment(), 0, false);
5059             viewport.getAlignment().setupJPredAlignment();
5060             isAnnotation = true;
5061           }
5062           // else if (IdentifyFile.FeaturesFile.equals(format))
5063           else if (FileFormat.Features.equals(format))
5064           {
5065             if (parseFeaturesFile(file, sourceType))
5066             {
5067               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
5068               if (splitFrame != null)
5069               {
5070                 splitFrame.repaint();
5071               }
5072               else
5073               {
5074                 alignPanel.paintAlignment(true, true);
5075               }
5076             }
5077           }
5078           else
5079           {
5080             new FileLoader().LoadFile(viewport, file, sourceType, format);
5081           }
5082         }
5083       }
5084       if (isAnnotation)
5085       {
5086
5087         alignPanel.adjustAnnotationHeight();
5088         viewport.updateSequenceIdColours();
5089         buildSortByAnnotationScoresMenu();
5090         alignPanel.paintAlignment(true, true);
5091       }
5092     } catch (Exception ex)
5093     {
5094       ex.printStackTrace();
5095     } catch (OutOfMemoryError oom)
5096     {
5097       try
5098       {
5099         System.gc();
5100       } catch (Exception x)
5101       {
5102       }
5103       new OOMWarning(
5104               "loading data "
5105                       + (sourceType != null
5106                               ? (sourceType == DataSourceType.PASTE
5107                                       ? "from clipboard."
5108                                       : "using " + sourceType + " from "
5109                                               + file)
5110                               : ".")
5111                       + (format != null
5112                               ? "(parsing as '" + format + "' file)"
5113                               : ""),
5114               oom, Desktop.desktop);
5115     }
5116   }
5117
5118   /**
5119    * Method invoked by the ChangeListener on the tabbed pane, in other words
5120    * when a different tabbed pane is selected by the user or programmatically.
5121    */
5122   @Override
5123   public void tabSelectionChanged(int index)
5124   {
5125     if (index > -1)
5126     {
5127       /*
5128        * update current Overview window title (if there is one)
5129        * to add view name "Original" if necessary
5130        */
5131       alignPanel.setOverviewTitle(this);
5132
5133       /*
5134        * switch panels and set Overview title (if there is one
5135        * because it was opened automatically)
5136        */
5137       alignPanel = alignPanels.get(index);
5138       alignPanel.setOverviewTitle(this);
5139
5140       viewport = alignPanel.av;
5141       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5142       setMenusFromViewport(viewport);
5143       if (featureSettings != null && featureSettings.isOpen()
5144               && featureSettings.fr.getViewport() != viewport)
5145       {
5146         if (viewport.isShowSequenceFeatures())
5147         {
5148           // refresh the featureSettings to reflect UI change
5149           showFeatureSettingsUI();
5150         }
5151         else
5152         {
5153           // close feature settings for this view.
5154           featureSettings.close();
5155         }
5156       }
5157
5158     }
5159
5160     /*
5161      * 'focus' any colour slider that is open to the selected viewport
5162      */
5163     if (viewport.getConservationSelected())
5164     {
5165       SliderPanel.setConservationSlider(alignPanel,
5166               viewport.getResidueShading(), alignPanel.getViewName());
5167     }
5168     else
5169     {
5170       SliderPanel.hideConservationSlider();
5171     }
5172     if (viewport.getAbovePIDThreshold())
5173     {
5174       SliderPanel.setPIDSliderSource(alignPanel,
5175               viewport.getResidueShading(), alignPanel.getViewName());
5176     }
5177     else
5178     {
5179       SliderPanel.hidePIDSlider();
5180     }
5181
5182     /*
5183      * If there is a frame linked to this one in a SplitPane, switch it to the
5184      * same view tab index. No infinite recursion of calls should happen, since
5185      * tabSelectionChanged() should not get invoked on setting the selected
5186      * index to an unchanged value. Guard against setting an invalid index
5187      * before the new view peer tab has been created.
5188      */
5189     final AlignViewportI peer = viewport.getCodingComplement();
5190     if (peer != null)
5191     {
5192       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5193               .getAlignPanel().alignFrame;
5194       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5195       {
5196         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5197       }
5198     }
5199   }
5200
5201   /**
5202    * On right mouse click on view tab, prompt for and set new view name.
5203    */
5204   @Override
5205   public void tabbedPane_mousePressed(MouseEvent e)
5206   {
5207     if (e.isPopupTrigger())
5208     {
5209       String msg = MessageManager.getString("label.enter_view_name");
5210       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5211       String reply = JvOptionPane.showInputDialog(msg, ttl);
5212
5213       if (reply != null)
5214       {
5215         viewport.setViewName(reply);
5216         // TODO warn if reply is in getExistingViewNames()?
5217         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5218       }
5219     }
5220   }
5221
5222   public AlignViewport getCurrentView()
5223   {
5224     return viewport;
5225   }
5226
5227   /**
5228    * Open the dialog for regex description parsing.
5229    */
5230   @Override
5231   protected void extractScores_actionPerformed(ActionEvent e)
5232   {
5233     ParseProperties pp = new jalview.analysis.ParseProperties(
5234             viewport.getAlignment());
5235     // TODO: verify regex and introduce GUI dialog for version 2.5
5236     // if (pp.getScoresFromDescription("col", "score column ",
5237     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5238     // true)>0)
5239     if (pp.getScoresFromDescription("description column",
5240             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5241     {
5242       buildSortByAnnotationScoresMenu();
5243     }
5244   }
5245
5246   /*
5247    * (non-Javadoc)
5248    *
5249    * @see
5250    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5251    * )
5252    */
5253   @Override
5254   protected void showDbRefs_actionPerformed(ActionEvent e)
5255   {
5256     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5257   }
5258
5259   /*
5260    * (non-Javadoc)
5261    *
5262    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5263    * ActionEvent)
5264    */
5265   @Override
5266   protected void showNpFeats_actionPerformed(ActionEvent e)
5267   {
5268     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5269   }
5270
5271   /**
5272    * find the viewport amongst the tabs in this alignment frame and close that
5273    * tab
5274    *
5275    * @param av
5276    */
5277   public boolean closeView(AlignViewportI av)
5278   {
5279     if (viewport == av)
5280     {
5281       this.closeMenuItem_actionPerformed(false);
5282       return true;
5283     }
5284     Component[] comp = tabbedPane.getComponents();
5285     for (int i = 0; comp != null && i < comp.length; i++)
5286     {
5287       if (comp[i] instanceof AlignmentPanel)
5288       {
5289         if (((AlignmentPanel) comp[i]).av == av)
5290         {
5291           // close the view.
5292           closeView((AlignmentPanel) comp[i]);
5293           return true;
5294         }
5295       }
5296     }
5297     return false;
5298   }
5299
5300   protected void build_fetchdbmenu(JMenu webService)
5301   {
5302     // Temporary hack - DBRef Fetcher always top level ws entry.
5303     // TODO We probably want to store a sequence database checklist in
5304     // preferences and have checkboxes.. rather than individual sources selected
5305     // here
5306     final JMenu rfetch = new JMenu(
5307             MessageManager.getString("action.fetch_db_references"));
5308     rfetch.setToolTipText(MessageManager.getString(
5309             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5310     webService.add(rfetch);
5311
5312     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5313             MessageManager.getString("option.trim_retrieved_seqs"));
5314     trimrs.setToolTipText(
5315             MessageManager.getString("label.trim_retrieved_sequences"));
5316     trimrs.setSelected(
5317             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5318     trimrs.addActionListener(new ActionListener()
5319     {
5320       @Override
5321       public void actionPerformed(ActionEvent e)
5322       {
5323         trimrs.setSelected(trimrs.isSelected());
5324         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5325                 Boolean.valueOf(trimrs.isSelected()).toString());
5326       }
5327     });
5328     rfetch.add(trimrs);
5329     JMenuItem fetchr = new JMenuItem(
5330             MessageManager.getString("label.standard_databases"));
5331     fetchr.setToolTipText(
5332             MessageManager.getString("label.fetch_embl_uniprot"));
5333     fetchr.addActionListener(new ActionListener()
5334     {
5335
5336       @Override
5337       public void actionPerformed(ActionEvent e)
5338       {
5339         new Thread(new Runnable()
5340         {
5341           @Override
5342           public void run()
5343           {
5344             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5345                     .getAlignment().isNucleotide();
5346             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5347                     alignPanel.av.getSequenceSelection(),
5348                     alignPanel.alignFrame, null,
5349                     alignPanel.alignFrame.featureSettings, isNucleotide);
5350             dbRefFetcher.addListener(new FetchFinishedListenerI()
5351             {
5352               @Override
5353               public void finished()
5354               {
5355
5356                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5357                         .getFeatureSettingsModels())
5358                 {
5359
5360                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5361                 }
5362                 AlignFrame.this.setMenusForViewport();
5363               }
5364             });
5365             dbRefFetcher.fetchDBRefs(false);
5366           }
5367         }).start();
5368
5369       }
5370
5371     });
5372     rfetch.add(fetchr);
5373     new Thread(new Runnable()
5374     {
5375       @Override
5376       public void run()
5377       {
5378         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5379                 .getSequenceFetcherSingleton();
5380         javax.swing.SwingUtilities.invokeLater(new Runnable()
5381         {
5382           @Override
5383           public void run()
5384           {
5385             String[] dbclasses = sf.getNonAlignmentSources();
5386             List<DbSourceProxy> otherdb;
5387             JMenu dfetch = new JMenu();
5388             JMenu ifetch = new JMenu();
5389             JMenuItem fetchr = null;
5390             int comp = 0, icomp = 0, mcomp = 15;
5391             String mname = null;
5392             int dbi = 0;
5393             for (String dbclass : dbclasses)
5394             {
5395               otherdb = sf.getSourceProxy(dbclass);
5396               // add a single entry for this class, or submenu allowing 'fetch
5397               // all' or pick one
5398               if (otherdb == null || otherdb.size() < 1)
5399               {
5400                 continue;
5401               }
5402               if (mname == null)
5403               {
5404                 mname = "From " + dbclass;
5405               }
5406               if (otherdb.size() == 1)
5407               {
5408                 final DbSourceProxy[] dassource = otherdb
5409                         .toArray(new DbSourceProxy[0]);
5410                 DbSourceProxy src = otherdb.get(0);
5411                 fetchr = new JMenuItem(src.getDbSource());
5412                 fetchr.addActionListener(new ActionListener()
5413                 {
5414
5415                   @Override
5416                   public void actionPerformed(ActionEvent e)
5417                   {
5418                     new Thread(new Runnable()
5419                     {
5420
5421                       @Override
5422                       public void run()
5423                       {
5424                         boolean isNucleotide = alignPanel.alignFrame
5425                                 .getViewport().getAlignment()
5426                                 .isNucleotide();
5427                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5428                                 alignPanel.av.getSequenceSelection(),
5429                                 alignPanel.alignFrame, dassource,
5430                                 alignPanel.alignFrame.featureSettings,
5431                                 isNucleotide);
5432                         dbRefFetcher
5433                                 .addListener(new FetchFinishedListenerI()
5434                                 {
5435                                   @Override
5436                                   public void finished()
5437                                   {
5438                                     FeatureSettingsModelI srcSettings = dassource[0]
5439                                             .getFeatureColourScheme();
5440                                     alignPanel.av.mergeFeaturesStyle(
5441                                             srcSettings);
5442                                     AlignFrame.this.setMenusForViewport();
5443                                   }
5444                                 });
5445                         dbRefFetcher.fetchDBRefs(false);
5446                       }
5447                     }).start();
5448                   }
5449
5450                 });
5451                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5452                         MessageManager.formatMessage(
5453                                 "label.fetch_retrieve_from", new Object[]
5454                                 { src.getDbName() })));
5455                 dfetch.add(fetchr);
5456                 comp++;
5457               }
5458               else
5459               {
5460                 final DbSourceProxy[] dassource = otherdb
5461                         .toArray(new DbSourceProxy[0]);
5462                 // fetch all entry
5463                 DbSourceProxy src = otherdb.get(0);
5464                 fetchr = new JMenuItem(MessageManager
5465                         .formatMessage("label.fetch_all_param", new Object[]
5466                         { src.getDbSource() }));
5467                 fetchr.addActionListener(new ActionListener()
5468                 {
5469                   @Override
5470                   public void actionPerformed(ActionEvent e)
5471                   {
5472                     new Thread(new Runnable()
5473                     {
5474
5475                       @Override
5476                       public void run()
5477                       {
5478                         boolean isNucleotide = alignPanel.alignFrame
5479                                 .getViewport().getAlignment()
5480                                 .isNucleotide();
5481                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5482                                 alignPanel.av.getSequenceSelection(),
5483                                 alignPanel.alignFrame, dassource,
5484                                 alignPanel.alignFrame.featureSettings,
5485                                 isNucleotide);
5486                         dbRefFetcher
5487                                 .addListener(new FetchFinishedListenerI()
5488                                 {
5489                                   @Override
5490                                   public void finished()
5491                                   {
5492                                     AlignFrame.this.setMenusForViewport();
5493                                   }
5494                                 });
5495                         dbRefFetcher.fetchDBRefs(false);
5496                       }
5497                     }).start();
5498                   }
5499                 });
5500
5501                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5502                         MessageManager.formatMessage(
5503                                 "label.fetch_retrieve_from_all_sources",
5504                                 new Object[]
5505                                 { Integer.valueOf(otherdb.size())
5506                                         .toString(),
5507                                     src.getDbSource(), src.getDbName() })));
5508                 dfetch.add(fetchr);
5509                 comp++;
5510                 // and then build the rest of the individual menus
5511                 ifetch = new JMenu(MessageManager.formatMessage(
5512                         "label.source_from_db_source", new Object[]
5513                         { src.getDbSource() }));
5514                 icomp = 0;
5515                 String imname = null;
5516                 int i = 0;
5517                 for (DbSourceProxy sproxy : otherdb)
5518                 {
5519                   String dbname = sproxy.getDbName();
5520                   String sname = dbname.length() > 5
5521                           ? dbname.substring(0, 5) + "..."
5522                           : dbname;
5523                   String msname = dbname.length() > 10
5524                           ? dbname.substring(0, 10) + "..."
5525                           : dbname;
5526                   if (imname == null)
5527                   {
5528                     imname = MessageManager
5529                             .formatMessage("label.from_msname", new Object[]
5530                             { sname });
5531                   }
5532                   fetchr = new JMenuItem(msname);
5533                   final DbSourceProxy[] dassrc = { sproxy };
5534                   fetchr.addActionListener(new ActionListener()
5535                   {
5536
5537                     @Override
5538                     public void actionPerformed(ActionEvent e)
5539                     {
5540                       new Thread(new Runnable()
5541                       {
5542
5543                         @Override
5544                         public void run()
5545                         {
5546                           boolean isNucleotide = alignPanel.alignFrame
5547                                   .getViewport().getAlignment()
5548                                   .isNucleotide();
5549                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5550                                   alignPanel.av.getSequenceSelection(),
5551                                   alignPanel.alignFrame, dassrc,
5552                                   alignPanel.alignFrame.featureSettings,
5553                                   isNucleotide);
5554                           dbRefFetcher
5555                                   .addListener(new FetchFinishedListenerI()
5556                                   {
5557                                     @Override
5558                                     public void finished()
5559                                     {
5560                                       AlignFrame.this.setMenusForViewport();
5561                                     }
5562                                   });
5563                           dbRefFetcher.fetchDBRefs(false);
5564                         }
5565                       }).start();
5566                     }
5567
5568                   });
5569                   fetchr.setToolTipText(
5570                           "<html>" + MessageManager.formatMessage(
5571                                   "label.fetch_retrieve_from", new Object[]
5572                                   { dbname }));
5573                   ifetch.add(fetchr);
5574                   ++i;
5575                   if (++icomp >= mcomp || i == (otherdb.size()))
5576                   {
5577                     ifetch.setText(MessageManager.formatMessage(
5578                             "label.source_to_target", imname, sname));
5579                     dfetch.add(ifetch);
5580                     ifetch = new JMenu();
5581                     imname = null;
5582                     icomp = 0;
5583                     comp++;
5584                   }
5585                 }
5586               }
5587               ++dbi;
5588               if (comp >= mcomp || dbi >= (dbclasses.length))
5589               {
5590                 dfetch.setText(MessageManager.formatMessage(
5591                         "label.source_to_target", mname, dbclass));
5592                 rfetch.add(dfetch);
5593                 dfetch = new JMenu();
5594                 mname = null;
5595                 comp = 0;
5596               }
5597             }
5598           }
5599         });
5600       }
5601     }).start();
5602
5603   }
5604
5605   /**
5606    * Left justify the whole alignment.
5607    */
5608   @Override
5609   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5610   {
5611     AlignmentI al = viewport.getAlignment();
5612     al.justify(false);
5613     viewport.firePropertyChange("alignment", null, al);
5614   }
5615
5616   /**
5617    * Right justify the whole alignment.
5618    */
5619   @Override
5620   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5621   {
5622     AlignmentI al = viewport.getAlignment();
5623     al.justify(true);
5624     viewport.firePropertyChange("alignment", null, al);
5625   }
5626
5627   @Override
5628   public void setShowSeqFeatures(boolean b)
5629   {
5630     showSeqFeatures.setSelected(b);
5631     viewport.setShowSequenceFeatures(b);
5632   }
5633
5634   /*
5635    * (non-Javadoc)
5636    *
5637    * @see
5638    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5639    * awt.event.ActionEvent)
5640    */
5641   @Override
5642   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5643   {
5644     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5645     alignPanel.paintAlignment(false, false);
5646   }
5647
5648   /*
5649    * (non-Javadoc)
5650    *
5651    * @see
5652    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5653    * .ActionEvent)
5654    */
5655   @Override
5656   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5657   {
5658     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5659     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5660
5661   }
5662
5663   /*
5664    * (non-Javadoc)
5665    *
5666    * @see
5667    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5668    * .event.ActionEvent)
5669    */
5670   @Override
5671   protected void showGroupConservation_actionPerformed(ActionEvent e)
5672   {
5673     viewport.setShowGroupConservation(showGroupConservation.getState());
5674     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5675   }
5676
5677   /*
5678    * (non-Javadoc)
5679    *
5680    * @see
5681    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5682    * .event.ActionEvent)
5683    */
5684   @Override
5685   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5686   {
5687     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5688     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5689   }
5690
5691   /*
5692    * (non-Javadoc)
5693    *
5694    * @see
5695    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5696    * .event.ActionEvent)
5697    */
5698   @Override
5699   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5700   {
5701     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5702     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5703   }
5704
5705   @Override
5706   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5707   {
5708     showSequenceLogo.setState(true);
5709     viewport.setShowSequenceLogo(true);
5710     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5711     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5712   }
5713
5714   @Override
5715   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5716   {
5717     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5718   }
5719
5720   /*
5721    * (non-Javadoc)
5722    *
5723    * @see
5724    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5725    * .event.ActionEvent)
5726    */
5727   @Override
5728   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5729   {
5730     if (avc.makeGroupsFromSelection())
5731     {
5732       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5733       alignPanel.updateAnnotation();
5734       alignPanel.paintAlignment(true,
5735               viewport.needToUpdateStructureViews());
5736     }
5737   }
5738
5739   public void clearAlignmentSeqRep()
5740   {
5741     // TODO refactor alignmentseqrep to controller
5742     if (viewport.getAlignment().hasSeqrep())
5743     {
5744       viewport.getAlignment().setSeqrep(null);
5745       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5746       alignPanel.updateAnnotation();
5747       alignPanel.paintAlignment(true, true);
5748     }
5749   }
5750
5751   @Override
5752   protected void createGroup_actionPerformed(ActionEvent e)
5753   {
5754     if (avc.createGroup())
5755     {
5756       if (applyAutoAnnotationSettings.isSelected())
5757       {
5758         alignPanel.updateAnnotation(true, false);
5759       }
5760       alignPanel.alignmentChanged();
5761     }
5762   }
5763
5764   @Override
5765   protected void unGroup_actionPerformed(ActionEvent e)
5766   {
5767     if (avc.unGroup())
5768     {
5769       alignPanel.alignmentChanged();
5770     }
5771   }
5772
5773   /**
5774    * make the given alignmentPanel the currently selected tab
5775    *
5776    * @param alignmentPanel
5777    */
5778   public void setDisplayedView(AlignmentPanel alignmentPanel)
5779   {
5780     if (!viewport.getSequenceSetId()
5781             .equals(alignmentPanel.av.getSequenceSetId()))
5782     {
5783       throw new Error(MessageManager.getString(
5784               "error.implementation_error_cannot_show_view_alignment_frame"));
5785     }
5786     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5787             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5788     {
5789       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5790     }
5791   }
5792
5793   /**
5794    * Action on selection of menu options to Show or Hide annotations.
5795    *
5796    * @param visible
5797    * @param forSequences
5798    *          update sequence-related annotations
5799    * @param forAlignment
5800    *          update non-sequence-related annotations
5801    */
5802   @Override
5803   public void setAnnotationsVisibility(boolean visible,
5804           boolean forSequences, boolean forAlignment)
5805   {
5806     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5807             .getAlignmentAnnotation();
5808     if (anns == null)
5809     {
5810       return;
5811     }
5812     for (AlignmentAnnotation aa : anns)
5813     {
5814       /*
5815        * don't display non-positional annotations on an alignment
5816        */
5817       if (aa.annotations == null)
5818       {
5819         continue;
5820       }
5821       boolean apply = (aa.sequenceRef == null && forAlignment)
5822               || (aa.sequenceRef != null && forSequences);
5823       if (apply)
5824       {
5825         aa.visible = visible;
5826       }
5827     }
5828     alignPanel.validateAnnotationDimensions(true);
5829     alignPanel.alignmentChanged();
5830   }
5831
5832   /**
5833    * Store selected annotation sort order for the view and repaint.
5834    */
5835   @Override
5836   protected void sortAnnotations_actionPerformed()
5837   {
5838     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5839     this.alignPanel.av
5840             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5841     alignPanel.paintAlignment(false, false);
5842   }
5843
5844   /**
5845    *
5846    * @return alignment panels in this alignment frame
5847    */
5848   public List<? extends AlignmentViewPanel> getAlignPanels()
5849   {
5850     // alignPanels is never null
5851     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5852     return alignPanels;
5853   }
5854
5855   /**
5856    * Open a new alignment window, with the cDNA associated with this (protein)
5857    * alignment, aligned as is the protein.
5858    */
5859   protected void viewAsCdna_actionPerformed()
5860   {
5861     // TODO no longer a menu action - refactor as required
5862     final AlignmentI alignment = getViewport().getAlignment();
5863     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5864     if (mappings == null)
5865     {
5866       return;
5867     }
5868     List<SequenceI> cdnaSeqs = new ArrayList<>();
5869     for (SequenceI aaSeq : alignment.getSequences())
5870     {
5871       for (AlignedCodonFrame acf : mappings)
5872       {
5873         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5874         if (dnaSeq != null)
5875         {
5876           /*
5877            * There is a cDNA mapping for this protein sequence - add to new
5878            * alignment. It will share the same dataset sequence as other mapped
5879            * cDNA (no new mappings need to be created).
5880            */
5881           final Sequence newSeq = new Sequence(dnaSeq);
5882           newSeq.setDatasetSequence(dnaSeq);
5883           cdnaSeqs.add(newSeq);
5884         }
5885       }
5886     }
5887     if (cdnaSeqs.size() == 0)
5888     {
5889       // show a warning dialog no mapped cDNA
5890       return;
5891     }
5892     AlignmentI cdna = new Alignment(
5893             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5894     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5895             AlignFrame.DEFAULT_HEIGHT);
5896     cdna.alignAs(alignment);
5897     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5898             + this.title;
5899     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5900             AlignFrame.DEFAULT_HEIGHT);
5901   }
5902
5903   /**
5904    * Set visibility of dna/protein complement view (available when shown in a
5905    * split frame).
5906    *
5907    * @param show
5908    */
5909   @Override
5910   protected void showComplement_actionPerformed(boolean show)
5911   {
5912     SplitContainerI sf = getSplitViewContainer();
5913     if (sf != null)
5914     {
5915       sf.setComplementVisible(this, show);
5916     }
5917   }
5918
5919   /**
5920    * Generate the reverse (optionally complemented) of the selected sequences,
5921    * and add them to the alignment
5922    */
5923   @Override
5924   protected void showReverse_actionPerformed(boolean complement)
5925   {
5926     AlignmentI al = null;
5927     try
5928     {
5929       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5930       al = dna.reverseCdna(complement);
5931       viewport.addAlignment(al, "");
5932       addHistoryItem(new EditCommand(
5933               MessageManager.getString("label.add_sequences"), Action.PASTE,
5934               al.getSequencesArray(), 0, al.getWidth(),
5935               viewport.getAlignment()));
5936     } catch (Exception ex)
5937     {
5938       jalview.bin.Console.errPrintln(ex.getMessage());
5939       return;
5940     }
5941   }
5942
5943   /**
5944    * Try to run a script in the Groovy console, having first ensured that this
5945    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5946    * be targeted at this alignment.
5947    */
5948   @Override
5949   protected void runGroovy_actionPerformed()
5950   {
5951     Jalview.setCurrentAlignFrame(this);
5952     groovy.ui.Console console = Desktop.getGroovyConsole();
5953     if (console != null)
5954     {
5955       try
5956       {
5957         console.runScript();
5958       } catch (Exception ex)
5959       {
5960         jalview.bin.Console.errPrintln((ex.toString()));
5961         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5962                 MessageManager.getString("label.couldnt_run_groovy_script"),
5963                 MessageManager.getString("label.groovy_support_failed"),
5964                 JvOptionPane.ERROR_MESSAGE);
5965       }
5966     }
5967     else
5968     {
5969       jalview.bin.Console
5970               .errPrintln("Can't run Groovy script as console not found");
5971     }
5972   }
5973
5974   /**
5975    * Hides columns containing (or not containing) a specified feature, provided
5976    * that would not leave all columns hidden
5977    *
5978    * @param featureType
5979    * @param columnsContaining
5980    * @return
5981    */
5982   public boolean hideFeatureColumns(String featureType,
5983           boolean columnsContaining)
5984   {
5985     boolean notForHiding = avc.markColumnsContainingFeatures(
5986             columnsContaining, false, false, featureType);
5987     if (notForHiding)
5988     {
5989       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5990               false, featureType))
5991       {
5992         getViewport().hideSelectedColumns();
5993         return true;
5994       }
5995     }
5996     return false;
5997   }
5998
5999   @Override
6000   protected void selectHighlightedColumns_actionPerformed(
6001           ActionEvent actionEvent)
6002   {
6003     // include key modifier check in case user selects from menu
6004     avc.markHighlightedColumns(
6005             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
6006             (actionEvent.getModifiers() & (ActionEvent.META_MASK
6007                     | ActionEvent.CTRL_MASK)) != 0);
6008   }
6009
6010   @Override
6011   protected void copyHighlightedColumns_actionPerformed(
6012           ActionEvent actionEvent)
6013   {
6014     avc.copyHighlightedRegionsToClipboard();
6015   }
6016
6017   /**
6018    * Rebuilds the Colour menu, including any user-defined colours which have
6019    * been loaded either on startup or during the session
6020    */
6021   public void buildColourMenu()
6022   {
6023     colourMenu.removeAll();
6024
6025     colourMenu.add(applyToAllGroups);
6026     colourMenu.add(textColour);
6027     colourMenu.addSeparator();
6028
6029     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
6030             viewport.getAlignment(), false);
6031
6032     colourMenu.add(annotationColour);
6033     bg.add(annotationColour);
6034     colourMenu.addSeparator();
6035     colourMenu.add(conservationMenuItem);
6036     colourMenu.add(modifyConservation);
6037     colourMenu.add(abovePIDThreshold);
6038     colourMenu.add(modifyPID);
6039
6040     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
6041     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
6042   }
6043
6044   /**
6045    * Open a dialog (if not already open) that allows the user to select and
6046    * calculate PCA or Tree analysis
6047    */
6048   protected void openTreePcaDialog()
6049   {
6050     if (alignPanel.getCalculationDialog() == null)
6051     {
6052       new CalculationChooser(AlignFrame.this);
6053     }
6054   }
6055
6056   @Override
6057   protected void loadVcf_actionPerformed()
6058   {
6059     JalviewFileChooser chooser = new JalviewFileChooser(
6060             Cache.getProperty("LAST_DIRECTORY"));
6061     chooser.setFileView(new JalviewFileView());
6062     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
6063     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
6064     final AlignFrame us = this;
6065     chooser.setResponseHandler(0, () -> {
6066       String choice = chooser.getSelectedFile().getPath();
6067       Cache.setProperty("LAST_DIRECTORY", choice);
6068       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
6069       new VCFLoader(choice).loadVCF(seqs, us);
6070     });
6071     chooser.showOpenDialog(null);
6072
6073   }
6074
6075   private Rectangle lastFeatureSettingsBounds = null;
6076
6077   @Override
6078   public void setFeatureSettingsGeometry(Rectangle bounds)
6079   {
6080     lastFeatureSettingsBounds = bounds;
6081   }
6082
6083   @Override
6084   public Rectangle getFeatureSettingsGeometry()
6085   {
6086     return lastFeatureSettingsBounds;
6087   }
6088
6089 }
6090
6091 class PrintThread extends Thread
6092 {
6093   AlignmentPanel ap;
6094
6095   public PrintThread(AlignmentPanel ap)
6096   {
6097     this.ap = ap;
6098   }
6099
6100   static PageFormat pf;
6101
6102   @Override
6103   public void run()
6104   {
6105     PrinterJob printJob = PrinterJob.getPrinterJob();
6106
6107     if (pf != null)
6108     {
6109       printJob.setPrintable(ap, pf);
6110     }
6111     else
6112     {
6113       printJob.setPrintable(ap);
6114     }
6115
6116     if (printJob.printDialog())
6117     {
6118       try
6119       {
6120         printJob.print();
6121       } catch (Exception PrintException)
6122       {
6123         PrintException.printStackTrace();
6124       }
6125     }
6126   }
6127 }