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