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    * DOCUMENT ME!
1786    *
1787    * @param up
1788    *          DOCUMENT ME!
1789    */
1790   public void moveSelectedSequences(boolean up)
1791   {
1792     SequenceGroup sg = viewport.getSelectionGroup();
1793
1794     if (sg == null)
1795     {
1796       return;
1797     }
1798     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1799             viewport.getHiddenRepSequences(), up);
1800     alignPanel.paintAlignment(true, false);
1801   }
1802
1803   synchronized void slideSequences(boolean right, int size)
1804   {
1805     List<SequenceI> sg = new ArrayList<>();
1806     if (viewport.cursorMode)
1807     {
1808       sg.add(viewport.getAlignment()
1809               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1810     }
1811     else if (viewport.getSelectionGroup() != null
1812             && viewport.getSelectionGroup().getSize() != viewport
1813                     .getAlignment().getHeight())
1814     {
1815       sg = viewport.getSelectionGroup()
1816               .getSequences(viewport.getHiddenRepSequences());
1817     }
1818
1819     if (sg.size() < 1)
1820     {
1821       return;
1822     }
1823
1824     List<SequenceI> invertGroup = new ArrayList<>();
1825
1826     for (SequenceI seq : viewport.getAlignment().getSequences())
1827     {
1828       if (!sg.contains(seq))
1829       {
1830         invertGroup.add(seq);
1831       }
1832     }
1833
1834     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1835
1836     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1837     for (int i = 0; i < invertGroup.size(); i++)
1838     {
1839       seqs2[i] = invertGroup.get(i);
1840     }
1841
1842     SlideSequencesCommand ssc;
1843     if (right)
1844     {
1845       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1846               viewport.getGapCharacter());
1847     }
1848     else
1849     {
1850       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1851               viewport.getGapCharacter());
1852     }
1853
1854     int groupAdjustment = 0;
1855     if (ssc.getGapsInsertedBegin() && right)
1856     {
1857       if (viewport.cursorMode)
1858       {
1859         alignPanel.getSeqPanel().moveCursor(size, 0);
1860       }
1861       else
1862       {
1863         groupAdjustment = size;
1864       }
1865     }
1866     else if (!ssc.getGapsInsertedBegin() && !right)
1867     {
1868       if (viewport.cursorMode)
1869       {
1870         alignPanel.getSeqPanel().moveCursor(-size, 0);
1871       }
1872       else
1873       {
1874         groupAdjustment = -size;
1875       }
1876     }
1877
1878     if (groupAdjustment != 0)
1879     {
1880       viewport.getSelectionGroup().setStartRes(
1881               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1882       viewport.getSelectionGroup().setEndRes(
1883               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1884     }
1885
1886     /*
1887      * just extend the last slide command if compatible; but not if in
1888      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1889      */
1890     boolean appendHistoryItem = false;
1891     Deque<CommandI> historyList = viewport.getHistoryList();
1892     boolean inSplitFrame = getSplitViewContainer() != null;
1893     if (!inSplitFrame && historyList != null && historyList.size() > 0
1894             && historyList.peek() instanceof SlideSequencesCommand)
1895     {
1896       appendHistoryItem = ssc.appendSlideCommand(
1897               (SlideSequencesCommand) historyList.peek());
1898     }
1899
1900     if (!appendHistoryItem)
1901     {
1902       addHistoryItem(ssc);
1903     }
1904
1905     repaint();
1906   }
1907
1908   /**
1909    * DOCUMENT ME!
1910    *
1911    * @param e
1912    *          DOCUMENT ME!
1913    */
1914   @Override
1915   protected void copy_actionPerformed()
1916   {
1917     if (viewport.getSelectionGroup() == null)
1918     {
1919       return;
1920     }
1921     // TODO: preserve the ordering of displayed alignment annotation in any
1922     // internal paste (particularly sequence associated annotation)
1923     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1924     String[] omitHidden = null;
1925
1926     if (viewport.hasHiddenColumns())
1927     {
1928       omitHidden = viewport.getViewAsString(true);
1929     }
1930
1931     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1932             seqs, omitHidden, null);
1933
1934     StringSelection ss = new StringSelection(output);
1935
1936     try
1937     {
1938       jalview.gui.Desktop.internalCopy = true;
1939       // Its really worth setting the clipboard contents
1940       // to empty before setting the large StringSelection!!
1941       Toolkit.getDefaultToolkit().getSystemClipboard()
1942               .setContents(new StringSelection(""), null);
1943
1944       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1945               Desktop.instance);
1946     } catch (OutOfMemoryError er)
1947     {
1948       new OOMWarning("copying region", er);
1949       return;
1950     }
1951
1952     HiddenColumns hiddenColumns = null;
1953     if (viewport.hasHiddenColumns())
1954     {
1955       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1956       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1957
1958       // create new HiddenColumns object with copy of hidden regions
1959       // between startRes and endRes, offset by startRes
1960       hiddenColumns = new HiddenColumns(
1961               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1962               hiddenCutoff, hiddenOffset);
1963     }
1964
1965     Desktop.jalviewClipboard = new Object[] { seqs,
1966         viewport.getAlignment().getDataset(), hiddenColumns };
1967     setStatus(MessageManager.formatMessage(
1968             "label.copied_sequences_to_clipboard", new Object[]
1969             { Integer.valueOf(seqs.length).toString() }));
1970   }
1971
1972   /**
1973    * DOCUMENT ME!
1974    *
1975    * @param e
1976    *          DOCUMENT ME!
1977    */
1978   @Override
1979   protected void pasteNew_actionPerformed(ActionEvent e)
1980   {
1981     paste(true);
1982   }
1983
1984   /**
1985    * DOCUMENT ME!
1986    *
1987    * @param e
1988    *          DOCUMENT ME!
1989    */
1990   @Override
1991   protected void pasteThis_actionPerformed(ActionEvent e)
1992   {
1993     paste(false);
1994   }
1995
1996   /**
1997    * Paste contents of Jalview clipboard
1998    *
1999    * @param newAlignment
2000    *          true to paste to a new alignment, otherwise add to this.
2001    */
2002   void paste(boolean newAlignment)
2003   {
2004     boolean externalPaste = true;
2005     try
2006     {
2007       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2008       Transferable contents = c.getContents(this);
2009
2010       if (contents == null)
2011       {
2012         return;
2013       }
2014
2015       String str;
2016       FileFormatI format;
2017       try
2018       {
2019         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2020         if (str.length() < 1)
2021         {
2022           return;
2023         }
2024
2025         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2026
2027       } catch (OutOfMemoryError er)
2028       {
2029         new OOMWarning("Out of memory pasting sequences!!", er);
2030         return;
2031       }
2032
2033       SequenceI[] sequences;
2034       boolean annotationAdded = false;
2035       AlignmentI alignment = null;
2036
2037       if (Desktop.jalviewClipboard != null)
2038       {
2039         // The clipboard was filled from within Jalview, we must use the
2040         // sequences
2041         // And dataset from the copied alignment
2042         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2043         // be doubly sure that we create *new* sequence objects.
2044         sequences = new SequenceI[newseq.length];
2045         for (int i = 0; i < newseq.length; i++)
2046         {
2047           sequences[i] = new Sequence(newseq[i]);
2048         }
2049         alignment = new Alignment(sequences);
2050         externalPaste = false;
2051       }
2052       else
2053       {
2054         // parse the clipboard as an alignment.
2055         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2056                 format);
2057         sequences = alignment.getSequencesArray();
2058       }
2059
2060       int alwidth = 0;
2061       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2062       int fgroup = -1;
2063
2064       if (newAlignment)
2065       {
2066
2067         if (Desktop.jalviewClipboard != null)
2068         {
2069           // dataset is inherited
2070           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2071         }
2072         else
2073         {
2074           // new dataset is constructed
2075           alignment.setDataset(null);
2076         }
2077         alwidth = alignment.getWidth() + 1;
2078       }
2079       else
2080       {
2081         AlignmentI pastedal = alignment; // preserve pasted alignment object
2082         // Add pasted sequences and dataset into existing alignment.
2083         alignment = viewport.getAlignment();
2084         alwidth = alignment.getWidth() + 1;
2085         // decide if we need to import sequences from an existing dataset
2086         boolean importDs = Desktop.jalviewClipboard != null
2087                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2088         // importDs==true instructs us to copy over new dataset sequences from
2089         // an existing alignment
2090         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2091                                                                       // create
2092         // minimum dataset set
2093
2094         for (int i = 0; i < sequences.length; i++)
2095         {
2096           if (importDs)
2097           {
2098             newDs.addElement(null);
2099           }
2100           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2101           // paste
2102           if (importDs && ds != null)
2103           {
2104             if (!newDs.contains(ds))
2105             {
2106               newDs.setElementAt(ds, i);
2107               ds = new Sequence(ds);
2108               // update with new dataset sequence
2109               sequences[i].setDatasetSequence(ds);
2110             }
2111             else
2112             {
2113               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2114             }
2115           }
2116           else
2117           {
2118             // copy and derive new dataset sequence
2119             sequences[i] = sequences[i].deriveSequence();
2120             alignment.getDataset()
2121                     .addSequence(sequences[i].getDatasetSequence());
2122             // TODO: avoid creation of duplicate dataset sequences with a
2123             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2124           }
2125           alignment.addSequence(sequences[i]); // merges dataset
2126         }
2127         if (newDs != null)
2128         {
2129           newDs.clear(); // tidy up
2130         }
2131         if (alignment.getAlignmentAnnotation() != null)
2132         {
2133           for (AlignmentAnnotation alan : alignment
2134                   .getAlignmentAnnotation())
2135           {
2136             if (alan.graphGroup > fgroup)
2137             {
2138               fgroup = alan.graphGroup;
2139             }
2140           }
2141         }
2142         if (pastedal.getAlignmentAnnotation() != null)
2143         {
2144           // Add any annotation attached to alignment.
2145           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2146           for (int i = 0; i < alann.length; i++)
2147           {
2148             annotationAdded = true;
2149             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2150             {
2151               AlignmentAnnotation newann = new AlignmentAnnotation(
2152                       alann[i]);
2153               if (newann.graphGroup > -1)
2154               {
2155                 if (newGraphGroups.size() <= newann.graphGroup
2156                         || newGraphGroups.get(newann.graphGroup) == null)
2157                 {
2158                   for (int q = newGraphGroups
2159                           .size(); q <= newann.graphGroup; q++)
2160                   {
2161                     newGraphGroups.add(q, null);
2162                   }
2163                   newGraphGroups.set(newann.graphGroup,
2164                           Integer.valueOf(++fgroup));
2165                 }
2166                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2167                         .intValue();
2168               }
2169
2170               newann.padAnnotation(alwidth);
2171               alignment.addAnnotation(newann);
2172             }
2173           }
2174         }
2175       }
2176       if (!newAlignment)
2177       {
2178         // /////
2179         // ADD HISTORY ITEM
2180         //
2181         addHistoryItem(new EditCommand(
2182                 MessageManager.getString("label.add_sequences"),
2183                 Action.PASTE, sequences, 0, alignment.getWidth(),
2184                 alignment));
2185       }
2186       // Add any annotations attached to sequences
2187       for (int i = 0; i < sequences.length; i++)
2188       {
2189         if (sequences[i].getAnnotation() != null)
2190         {
2191           AlignmentAnnotation newann;
2192           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2193           {
2194             annotationAdded = true;
2195             newann = sequences[i].getAnnotation()[a];
2196             newann.adjustForAlignment();
2197             newann.padAnnotation(alwidth);
2198             if (newann.graphGroup > -1)
2199             {
2200               if (newann.graphGroup > -1)
2201               {
2202                 if (newGraphGroups.size() <= newann.graphGroup
2203                         || newGraphGroups.get(newann.graphGroup) == null)
2204                 {
2205                   for (int q = newGraphGroups
2206                           .size(); q <= newann.graphGroup; q++)
2207                   {
2208                     newGraphGroups.add(q, null);
2209                   }
2210                   newGraphGroups.set(newann.graphGroup,
2211                           Integer.valueOf(++fgroup));
2212                 }
2213                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2214                         .intValue();
2215               }
2216             }
2217             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2218             // was
2219             // duplicated
2220             // earlier
2221             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2222                     a);
2223           }
2224         }
2225       }
2226       if (!newAlignment)
2227       {
2228
2229         // propagate alignment changed.
2230         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2231         if (annotationAdded)
2232         {
2233           // Duplicate sequence annotation in all views.
2234           AlignmentI[] alview = this.getViewAlignments();
2235           for (int i = 0; i < sequences.length; i++)
2236           {
2237             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2238             if (sann == null)
2239             {
2240               continue;
2241             }
2242             for (int avnum = 0; avnum < alview.length; avnum++)
2243             {
2244               if (alview[avnum] != alignment)
2245               {
2246                 // duplicate in a view other than the one with input focus
2247                 int avwidth = alview[avnum].getWidth() + 1;
2248                 // this relies on sann being preserved after we
2249                 // modify the sequence's annotation array for each duplication
2250                 for (int a = 0; a < sann.length; a++)
2251                 {
2252                   AlignmentAnnotation newann = new AlignmentAnnotation(
2253                           sann[a]);
2254                   sequences[i].addAlignmentAnnotation(newann);
2255                   newann.padAnnotation(avwidth);
2256                   alview[avnum].addAnnotation(newann); // annotation was
2257                   // duplicated earlier
2258                   // TODO JAL-1145 graphGroups are not updated for sequence
2259                   // annotation added to several views. This may cause
2260                   // strangeness
2261                   alview[avnum].setAnnotationIndex(newann, a);
2262                 }
2263               }
2264             }
2265           }
2266           buildSortByAnnotationScoresMenu();
2267         }
2268         viewport.firePropertyChange("alignment", null,
2269                 alignment.getSequences());
2270         if (alignPanels != null)
2271         {
2272           for (AlignmentPanel ap : alignPanels)
2273           {
2274             ap.validateAnnotationDimensions(false);
2275           }
2276         }
2277         else
2278         {
2279           alignPanel.validateAnnotationDimensions(false);
2280         }
2281
2282       }
2283       else
2284       {
2285         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2286                 DEFAULT_HEIGHT);
2287         String newtitle = new String("Copied sequences");
2288
2289         if (Desktop.jalviewClipboard != null
2290                 && Desktop.jalviewClipboard[2] != null)
2291         {
2292           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2293           af.viewport.setHiddenColumns(hc);
2294         }
2295
2296         // >>>This is a fix for the moment, until a better solution is
2297         // found!!<<<
2298         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2299                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2300                         .getFeatureRenderer());
2301
2302         // TODO: maintain provenance of an alignment, rather than just make the
2303         // title a concatenation of operations.
2304         if (!externalPaste)
2305         {
2306           if (title.startsWith("Copied sequences"))
2307           {
2308             newtitle = title;
2309           }
2310           else
2311           {
2312             newtitle = newtitle.concat("- from " + title);
2313           }
2314         }
2315         else
2316         {
2317           newtitle = new String("Pasted sequences");
2318         }
2319
2320         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2321                 DEFAULT_HEIGHT);
2322
2323       }
2324
2325     } catch (Exception ex)
2326     {
2327       ex.printStackTrace();
2328       System.out.println("Exception whilst pasting: " + ex);
2329       // could be anything being pasted in here
2330     }
2331
2332   }
2333
2334   @Override
2335   protected void expand_newalign(ActionEvent e)
2336   {
2337     try
2338     {
2339       AlignmentI alignment = AlignmentUtils
2340               .expandContext(getViewport().getAlignment(), -1);
2341       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2342               DEFAULT_HEIGHT);
2343       String newtitle = new String("Flanking alignment");
2344
2345       if (Desktop.jalviewClipboard != null
2346               && Desktop.jalviewClipboard[2] != null)
2347       {
2348         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2349         af.viewport.setHiddenColumns(hc);
2350       }
2351
2352       // >>>This is a fix for the moment, until a better solution is
2353       // found!!<<<
2354       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2355               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2356                       .getFeatureRenderer());
2357
2358       // TODO: maintain provenance of an alignment, rather than just make the
2359       // title a concatenation of operations.
2360       {
2361         if (title.startsWith("Copied sequences"))
2362         {
2363           newtitle = title;
2364         }
2365         else
2366         {
2367           newtitle = newtitle.concat("- from " + title);
2368         }
2369       }
2370
2371       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2372
2373     } catch (Exception ex)
2374     {
2375       ex.printStackTrace();
2376       System.out.println("Exception whilst pasting: " + ex);
2377       // could be anything being pasted in here
2378     } catch (OutOfMemoryError oom)
2379     {
2380       new OOMWarning("Viewing flanking region of alignment", oom);
2381     }
2382   }
2383
2384   /**
2385    * Action Cut (delete and copy) the selected region
2386    */
2387   @Override
2388   protected void cut_actionPerformed()
2389   {
2390     copy_actionPerformed();
2391     delete_actionPerformed();
2392   }
2393
2394   /**
2395    * Performs menu option to Delete the currently selected region
2396    */
2397   @Override
2398   protected void delete_actionPerformed()
2399   {
2400
2401     SequenceGroup sg = viewport.getSelectionGroup();
2402     if (sg == null)
2403     {
2404       return;
2405     }
2406
2407     Runnable okAction = new Runnable()
2408     {
2409                 @Override
2410                 public void run()
2411                 {
2412                     SequenceI[] cut = sg.getSequences()
2413                             .toArray(new SequenceI[sg.getSize()]);
2414
2415                     addHistoryItem(new EditCommand(
2416                             MessageManager.getString("label.cut_sequences"), Action.CUT,
2417                             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2418                             viewport.getAlignment()));
2419
2420                     viewport.setSelectionGroup(null);
2421                     viewport.sendSelection();
2422                     viewport.getAlignment().deleteGroup(sg);
2423
2424                     viewport.firePropertyChange("alignment", null,
2425                             viewport.getAlignment().getSequences());
2426                     if (viewport.getAlignment().getHeight() < 1)
2427                     {
2428                       try
2429                       {
2430                         AlignFrame.this.setClosed(true);
2431                       } catch (Exception ex)
2432                       {
2433                       }
2434                     }
2435                 }};
2436
2437     /*
2438      * If the cut affects all sequences, prompt for confirmation
2439      */
2440     boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2441     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2442             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2443         if (wholeHeight && wholeWidth)
2444         {
2445             JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2446                 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2447             Object[] options = new Object[] { MessageManager.getString("action.ok"),
2448                     MessageManager.getString("action.cancel") };
2449                 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2450                     MessageManager.getString("label.delete_all"),
2451                     JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2452                     options, options[0]);
2453         } else
2454         {
2455                 okAction.run();
2456         }
2457   }
2458
2459   /**
2460    * DOCUMENT ME!
2461    *
2462    * @param e
2463    *          DOCUMENT ME!
2464    */
2465   @Override
2466   protected void deleteGroups_actionPerformed(ActionEvent e)
2467   {
2468     if (avc.deleteGroups())
2469     {
2470       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2471       alignPanel.updateAnnotation();
2472       alignPanel.paintAlignment(true, true);
2473     }
2474   }
2475
2476   /**
2477    * DOCUMENT ME!
2478    *
2479    * @param e
2480    *          DOCUMENT ME!
2481    */
2482   @Override
2483   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2484   {
2485     SequenceGroup sg = new SequenceGroup(
2486             viewport.getAlignment().getSequences());
2487
2488     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2489     viewport.setSelectionGroup(sg);
2490     viewport.isSelectionGroupChanged(true);
2491     viewport.sendSelection();
2492     // JAL-2034 - should delegate to
2493     // alignPanel to decide if overview needs
2494     // updating.
2495     alignPanel.paintAlignment(false, false);
2496     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2497   }
2498
2499   /**
2500    * DOCUMENT ME!
2501    *
2502    * @param e
2503    *          DOCUMENT ME!
2504    */
2505   @Override
2506   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2507   {
2508     if (viewport.cursorMode)
2509     {
2510       alignPanel.getSeqPanel().keyboardNo1 = null;
2511       alignPanel.getSeqPanel().keyboardNo2 = null;
2512     }
2513     viewport.setSelectionGroup(null);
2514     viewport.getColumnSelection().clear();
2515     viewport.setSearchResults(null);
2516     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2517     // JAL-2034 - should delegate to
2518     // alignPanel to decide if overview needs
2519     // updating.
2520     alignPanel.paintAlignment(false, false);
2521     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2522     viewport.sendSelection();
2523   }
2524
2525   /**
2526    * DOCUMENT ME!
2527    *
2528    * @param e
2529    *          DOCUMENT ME!
2530    */
2531   @Override
2532   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2533   {
2534     SequenceGroup sg = viewport.getSelectionGroup();
2535
2536     if (sg == null)
2537     {
2538       selectAllSequenceMenuItem_actionPerformed(null);
2539
2540       return;
2541     }
2542
2543     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2544     {
2545       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2546     }
2547     // JAL-2034 - should delegate to
2548     // alignPanel to decide if overview needs
2549     // updating.
2550
2551     alignPanel.paintAlignment(true, false);
2552     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2553     viewport.sendSelection();
2554   }
2555
2556   @Override
2557   public void invertColSel_actionPerformed(ActionEvent e)
2558   {
2559     viewport.invertColumnSelection();
2560     alignPanel.paintAlignment(true, false);
2561     viewport.sendSelection();
2562   }
2563
2564   /**
2565    * DOCUMENT ME!
2566    *
2567    * @param e
2568    *          DOCUMENT ME!
2569    */
2570   @Override
2571   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2572   {
2573     trimAlignment(true);
2574   }
2575
2576   /**
2577    * DOCUMENT ME!
2578    *
2579    * @param e
2580    *          DOCUMENT ME!
2581    */
2582   @Override
2583   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2584   {
2585     trimAlignment(false);
2586   }
2587
2588   void trimAlignment(boolean trimLeft)
2589   {
2590     ColumnSelection colSel = viewport.getColumnSelection();
2591     int column;
2592
2593     if (!colSel.isEmpty())
2594     {
2595       if (trimLeft)
2596       {
2597         column = colSel.getMin();
2598       }
2599       else
2600       {
2601         column = colSel.getMax();
2602       }
2603
2604       SequenceI[] seqs;
2605       if (viewport.getSelectionGroup() != null)
2606       {
2607         seqs = viewport.getSelectionGroup()
2608                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2609       }
2610       else
2611       {
2612         seqs = viewport.getAlignment().getSequencesArray();
2613       }
2614
2615       TrimRegionCommand trimRegion;
2616       if (trimLeft)
2617       {
2618         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2619                 column, viewport.getAlignment());
2620         viewport.getRanges().setStartRes(0);
2621       }
2622       else
2623       {
2624         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2625                 column, viewport.getAlignment());
2626       }
2627
2628       setStatus(MessageManager
2629               .formatMessage("label.removed_columns", new String[]
2630               { Integer.valueOf(trimRegion.getSize()).toString() }));
2631
2632       addHistoryItem(trimRegion);
2633
2634       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2635       {
2636         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2637                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2638         {
2639           viewport.getAlignment().deleteGroup(sg);
2640         }
2641       }
2642
2643       viewport.firePropertyChange("alignment", null,
2644               viewport.getAlignment().getSequences());
2645     }
2646   }
2647
2648   /**
2649    * DOCUMENT ME!
2650    *
2651    * @param e
2652    *          DOCUMENT ME!
2653    */
2654   @Override
2655   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2656   {
2657     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2658
2659     SequenceI[] seqs;
2660     if (viewport.getSelectionGroup() != null)
2661     {
2662       seqs = viewport.getSelectionGroup()
2663               .getSequencesAsArray(viewport.getHiddenRepSequences());
2664       start = viewport.getSelectionGroup().getStartRes();
2665       end = viewport.getSelectionGroup().getEndRes();
2666     }
2667     else
2668     {
2669       seqs = viewport.getAlignment().getSequencesArray();
2670     }
2671
2672     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2673             "Remove Gapped Columns", seqs, start, end,
2674             viewport.getAlignment());
2675
2676     addHistoryItem(removeGapCols);
2677
2678     setStatus(MessageManager
2679             .formatMessage("label.removed_empty_columns", new Object[]
2680             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2681
2682     // This is to maintain viewport position on first residue
2683     // of first sequence
2684     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2685     ViewportRanges ranges = viewport.getRanges();
2686     int startRes = seq.findPosition(ranges.getStartRes());
2687     // ShiftList shifts;
2688     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2689     // edit.alColumnChanges=shifts.getInverse();
2690     // if (viewport.hasHiddenColumns)
2691     // viewport.getColumnSelection().compensateForEdits(shifts);
2692     ranges.setStartRes(seq.findIndex(startRes) - 1);
2693     viewport.firePropertyChange("alignment", null,
2694             viewport.getAlignment().getSequences());
2695
2696   }
2697
2698   /**
2699    * DOCUMENT ME!
2700    *
2701    * @param e
2702    *          DOCUMENT ME!
2703    */
2704   @Override
2705   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2706   {
2707     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2708
2709     SequenceI[] seqs;
2710     if (viewport.getSelectionGroup() != null)
2711     {
2712       seqs = viewport.getSelectionGroup()
2713               .getSequencesAsArray(viewport.getHiddenRepSequences());
2714       start = viewport.getSelectionGroup().getStartRes();
2715       end = viewport.getSelectionGroup().getEndRes();
2716     }
2717     else
2718     {
2719       seqs = viewport.getAlignment().getSequencesArray();
2720     }
2721
2722     // This is to maintain viewport position on first residue
2723     // of first sequence
2724     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2725     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2726
2727     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2728             viewport.getAlignment()));
2729
2730     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2731
2732     viewport.firePropertyChange("alignment", null,
2733             viewport.getAlignment().getSequences());
2734
2735   }
2736
2737   /**
2738    * DOCUMENT ME!
2739    *
2740    * @param e
2741    *          DOCUMENT ME!
2742    */
2743   @Override
2744   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2745   {
2746     viewport.setPadGaps(padGapsMenuitem.isSelected());
2747     viewport.firePropertyChange("alignment", null,
2748             viewport.getAlignment().getSequences());
2749   }
2750
2751   /**
2752    * Opens a Finder dialog
2753    *
2754    * @param e
2755    */
2756   @Override
2757   public void findMenuItem_actionPerformed(ActionEvent e)
2758   {
2759     new Finder(alignPanel);
2760   }
2761
2762   /**
2763    * Create a new view of the current alignment.
2764    */
2765   @Override
2766   public void newView_actionPerformed(ActionEvent e)
2767   {
2768     newView(null, true);
2769   }
2770
2771   /**
2772    * Creates and shows a new view of the current alignment.
2773    *
2774    * @param viewTitle
2775    *          title of newly created view; if null, one will be generated
2776    * @param copyAnnotation
2777    *          if true then duplicate all annnotation, groups and settings
2778    * @return new alignment panel, already displayed.
2779    */
2780   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2781   {
2782     /*
2783      * Create a new AlignmentPanel (with its own, new Viewport)
2784      */
2785     AlignmentPanel newap = new jalview.project.Jalview2XML()
2786             .copyAlignPanel(alignPanel);
2787     if (!copyAnnotation)
2788     {
2789       /*
2790        * remove all groups and annotation except for the automatic stuff
2791        */
2792       newap.av.getAlignment().deleteAllGroups();
2793       newap.av.getAlignment().deleteAllAnnotations(false);
2794     }
2795
2796     newap.av.setGatherViewsHere(false);
2797
2798     if (viewport.getViewName() == null)
2799     {
2800       viewport.setViewName(MessageManager
2801               .getString("label.view_name_original"));
2802     }
2803
2804     /*
2805      * Views share the same edits undo and redo stacks
2806      */
2807     newap.av.setHistoryList(viewport.getHistoryList());
2808     newap.av.setRedoList(viewport.getRedoList());
2809
2810     /*
2811      * copy any visualisation settings that are not saved in the project
2812      */
2813     newap.av.setColourAppliesToAllGroups(
2814             viewport.getColourAppliesToAllGroups());
2815
2816     /*
2817      * Views share the same mappings; need to deregister any new mappings
2818      * created by copyAlignPanel, and register the new reference to the shared
2819      * mappings
2820      */
2821     newap.av.replaceMappings(viewport.getAlignment());
2822
2823     /*
2824      * start up cDNA consensus (if applicable) now mappings are in place
2825      */
2826     if (newap.av.initComplementConsensus())
2827     {
2828       newap.refresh(true); // adjust layout of annotations
2829     }
2830
2831     newap.av.setViewName(getNewViewName(viewTitle));
2832
2833     addAlignmentPanel(newap, true);
2834     newap.alignmentChanged();
2835
2836     if (alignPanels.size() == 2)
2837     {
2838       viewport.setGatherViewsHere(true);
2839     }
2840     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2841     return newap;
2842   }
2843
2844   /**
2845    * Make a new name for the view, ensuring it is unique within the current
2846    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2847    * these now use viewId. Unique view names are still desirable for usability.)
2848    *
2849    * @param viewTitle
2850    * @return
2851    */
2852   protected String getNewViewName(String viewTitle)
2853   {
2854     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2855     boolean addFirstIndex = false;
2856     if (viewTitle == null || viewTitle.trim().length() == 0)
2857     {
2858       viewTitle = MessageManager.getString("action.view");
2859       addFirstIndex = true;
2860     }
2861     else
2862     {
2863       index = 1;// we count from 1 if given a specific name
2864     }
2865     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2866
2867     List<Component> comps = PaintRefresher.components
2868             .get(viewport.getSequenceSetId());
2869
2870     List<String> existingNames = getExistingViewNames(comps);
2871
2872     while (existingNames.contains(newViewName))
2873     {
2874       newViewName = viewTitle + " " + (++index);
2875     }
2876     return newViewName;
2877   }
2878
2879   /**
2880    * Returns a list of distinct view names found in the given list of
2881    * components. View names are held on the viewport of an AlignmentPanel.
2882    *
2883    * @param comps
2884    * @return
2885    */
2886   protected List<String> getExistingViewNames(List<Component> comps)
2887   {
2888     List<String> existingNames = new ArrayList<>();
2889     for (Component comp : comps)
2890     {
2891       if (comp instanceof AlignmentPanel)
2892       {
2893         AlignmentPanel ap = (AlignmentPanel) comp;
2894         if (!existingNames.contains(ap.av.getViewName()))
2895         {
2896           existingNames.add(ap.av.getViewName());
2897         }
2898       }
2899     }
2900     return existingNames;
2901   }
2902
2903   /**
2904    * Explode tabbed views into separate windows.
2905    */
2906   @Override
2907   public void expandViews_actionPerformed(ActionEvent e)
2908   {
2909     Desktop.explodeViews(this);
2910   }
2911
2912   /**
2913    * Gather views in separate windows back into a tabbed presentation.
2914    */
2915   @Override
2916   public void gatherViews_actionPerformed(ActionEvent e)
2917   {
2918     Desktop.instance.gatherViews(this);
2919   }
2920
2921   /**
2922    * DOCUMENT ME!
2923    *
2924    * @param e
2925    *          DOCUMENT ME!
2926    */
2927   @Override
2928   public void font_actionPerformed(ActionEvent e)
2929   {
2930     new FontChooser(alignPanel);
2931   }
2932
2933   /**
2934    * DOCUMENT ME!
2935    *
2936    * @param e
2937    *          DOCUMENT ME!
2938    */
2939   @Override
2940   protected void seqLimit_actionPerformed(ActionEvent e)
2941   {
2942     viewport.setShowJVSuffix(seqLimits.isSelected());
2943
2944     alignPanel.getIdPanel().getIdCanvas()
2945             .setPreferredSize(alignPanel.calculateIdWidth());
2946     alignPanel.paintAlignment(true, false);
2947   }
2948
2949   @Override
2950   public void idRightAlign_actionPerformed(ActionEvent e)
2951   {
2952     viewport.setRightAlignIds(idRightAlign.isSelected());
2953     alignPanel.paintAlignment(false, false);
2954   }
2955
2956   @Override
2957   public void centreColumnLabels_actionPerformed(ActionEvent e)
2958   {
2959     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2960     alignPanel.paintAlignment(false, false);
2961   }
2962
2963   /*
2964    * (non-Javadoc)
2965    *
2966    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2967    */
2968   @Override
2969   protected void followHighlight_actionPerformed()
2970   {
2971     /*
2972      * Set the 'follow' flag on the Viewport (and scroll to position if now
2973      * true).
2974      */
2975     final boolean state = this.followHighlightMenuItem.getState();
2976     viewport.setFollowHighlight(state);
2977     if (state)
2978     {
2979       alignPanel.scrollToPosition(viewport.getSearchResults());
2980     }
2981   }
2982
2983   /**
2984    * DOCUMENT ME!
2985    *
2986    * @param e
2987    *          DOCUMENT ME!
2988    */
2989   @Override
2990   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2991   {
2992     viewport.setColourText(colourTextMenuItem.isSelected());
2993     alignPanel.paintAlignment(false, false);
2994   }
2995
2996   /**
2997    * DOCUMENT ME!
2998    *
2999    * @param e
3000    *          DOCUMENT ME!
3001    */
3002   @Override
3003   public void wrapMenuItem_actionPerformed(ActionEvent e)
3004   {
3005     scaleAbove.setVisible(wrapMenuItem.isSelected());
3006     scaleLeft.setVisible(wrapMenuItem.isSelected());
3007     scaleRight.setVisible(wrapMenuItem.isSelected());
3008     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3009     alignPanel.updateLayout();
3010   }
3011
3012   @Override
3013   public void showAllSeqs_actionPerformed(ActionEvent e)
3014   {
3015     viewport.showAllHiddenSeqs();
3016   }
3017
3018   @Override
3019   public void showAllColumns_actionPerformed(ActionEvent e)
3020   {
3021     viewport.showAllHiddenColumns();
3022     alignPanel.paintAlignment(true, true);
3023     viewport.sendSelection();
3024   }
3025
3026   @Override
3027   public void hideSelSequences_actionPerformed(ActionEvent e)
3028   {
3029     viewport.hideAllSelectedSeqs();
3030   }
3031
3032   /**
3033    * called by key handler and the hide all/show all menu items
3034    *
3035    * @param toggleSeqs
3036    * @param toggleCols
3037    */
3038   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3039   {
3040
3041     boolean hide = false;
3042     SequenceGroup sg = viewport.getSelectionGroup();
3043     if (!toggleSeqs && !toggleCols)
3044     {
3045       // Hide everything by the current selection - this is a hack - we do the
3046       // invert and then hide
3047       // first check that there will be visible columns after the invert.
3048       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3049               && sg.getStartRes() <= sg.getEndRes()))
3050       {
3051         // now invert the sequence set, if required - empty selection implies
3052         // that no hiding is required.
3053         if (sg != null)
3054         {
3055           invertSequenceMenuItem_actionPerformed(null);
3056           sg = viewport.getSelectionGroup();
3057           toggleSeqs = true;
3058
3059         }
3060         viewport.expandColSelection(sg, true);
3061         // finally invert the column selection and get the new sequence
3062         // selection.
3063         invertColSel_actionPerformed(null);
3064         toggleCols = true;
3065       }
3066     }
3067
3068     if (toggleSeqs)
3069     {
3070       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3071       {
3072         hideSelSequences_actionPerformed(null);
3073         hide = true;
3074       }
3075       else if (!(toggleCols && viewport.hasSelectedColumns()))
3076       {
3077         showAllSeqs_actionPerformed(null);
3078       }
3079     }
3080
3081     if (toggleCols)
3082     {
3083       if (viewport.hasSelectedColumns())
3084       {
3085         hideSelColumns_actionPerformed(null);
3086         if (!toggleSeqs)
3087         {
3088           viewport.setSelectionGroup(sg);
3089         }
3090       }
3091       else if (!hide)
3092       {
3093         showAllColumns_actionPerformed(null);
3094       }
3095     }
3096   }
3097
3098   /*
3099    * (non-Javadoc)
3100    *
3101    * @see
3102    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3103    * event.ActionEvent)
3104    */
3105   @Override
3106   public void hideAllButSelection_actionPerformed(ActionEvent e)
3107   {
3108     toggleHiddenRegions(false, false);
3109     viewport.sendSelection();
3110   }
3111
3112   /*
3113    * (non-Javadoc)
3114    *
3115    * @see
3116    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3117    * .ActionEvent)
3118    */
3119   @Override
3120   public void hideAllSelection_actionPerformed(ActionEvent e)
3121   {
3122     SequenceGroup sg = viewport.getSelectionGroup();
3123     viewport.expandColSelection(sg, false);
3124     viewport.hideAllSelectedSeqs();
3125     viewport.hideSelectedColumns();
3126     alignPanel.updateLayout();
3127     alignPanel.paintAlignment(true, true);
3128     viewport.sendSelection();
3129   }
3130
3131   /*
3132    * (non-Javadoc)
3133    *
3134    * @see
3135    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3136    * ActionEvent)
3137    */
3138   @Override
3139   public void showAllhidden_actionPerformed(ActionEvent e)
3140   {
3141     viewport.showAllHiddenColumns();
3142     viewport.showAllHiddenSeqs();
3143     alignPanel.paintAlignment(true, true);
3144     viewport.sendSelection();
3145   }
3146
3147   @Override
3148   public void hideSelColumns_actionPerformed(ActionEvent e)
3149   {
3150     viewport.hideSelectedColumns();
3151     alignPanel.updateLayout();
3152     alignPanel.paintAlignment(true, true);
3153     viewport.sendSelection();
3154   }
3155
3156   @Override
3157   public void hiddenMarkers_actionPerformed(ActionEvent e)
3158   {
3159     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3160     repaint();
3161   }
3162
3163   /**
3164    * DOCUMENT ME!
3165    *
3166    * @param e
3167    *          DOCUMENT ME!
3168    */
3169   @Override
3170   protected void scaleAbove_actionPerformed(ActionEvent e)
3171   {
3172     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3173     alignPanel.updateLayout();
3174     alignPanel.paintAlignment(true, false);
3175   }
3176
3177   /**
3178    * DOCUMENT ME!
3179    *
3180    * @param e
3181    *          DOCUMENT ME!
3182    */
3183   @Override
3184   protected void scaleLeft_actionPerformed(ActionEvent e)
3185   {
3186     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3187     alignPanel.updateLayout();
3188     alignPanel.paintAlignment(true, false);
3189   }
3190
3191   /**
3192    * DOCUMENT ME!
3193    *
3194    * @param e
3195    *          DOCUMENT ME!
3196    */
3197   @Override
3198   protected void scaleRight_actionPerformed(ActionEvent e)
3199   {
3200     viewport.setScaleRightWrapped(scaleRight.isSelected());
3201     alignPanel.updateLayout();
3202     alignPanel.paintAlignment(true, false);
3203   }
3204
3205   /**
3206    * DOCUMENT ME!
3207    *
3208    * @param e
3209    *          DOCUMENT ME!
3210    */
3211   @Override
3212   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3213   {
3214     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3215     alignPanel.paintAlignment(false, false);
3216   }
3217
3218   /**
3219    * DOCUMENT ME!
3220    *
3221    * @param e
3222    *          DOCUMENT ME!
3223    */
3224   @Override
3225   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3226   {
3227     viewport.setShowText(viewTextMenuItem.isSelected());
3228     alignPanel.paintAlignment(false, false);
3229   }
3230
3231   /**
3232    * DOCUMENT ME!
3233    *
3234    * @param e
3235    *          DOCUMENT ME!
3236    */
3237   @Override
3238   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3239   {
3240     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3241     alignPanel.paintAlignment(false, false);
3242   }
3243
3244   public FeatureSettings featureSettings;
3245
3246   @Override
3247   public FeatureSettingsControllerI getFeatureSettingsUI()
3248   {
3249     return featureSettings;
3250   }
3251
3252   @Override
3253   public void featureSettings_actionPerformed(ActionEvent e)
3254   {
3255     showFeatureSettingsUI();
3256   }
3257
3258   @Override
3259   public FeatureSettingsControllerI showFeatureSettingsUI()
3260   {
3261     if (featureSettings != null)
3262     {
3263       featureSettings.closeOldSettings();
3264       featureSettings = null;
3265     }
3266     if (!showSeqFeatures.isSelected())
3267     {
3268       // make sure features are actually displayed
3269       showSeqFeatures.setSelected(true);
3270       showSeqFeatures_actionPerformed(null);
3271     }
3272     featureSettings = new FeatureSettings(this);
3273     return featureSettings;
3274   }
3275
3276   /**
3277    * Set or clear 'Show Sequence Features'
3278    *
3279    * @param evt
3280    *          DOCUMENT ME!
3281    */
3282   @Override
3283   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3284   {
3285     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3286     alignPanel.paintAlignment(true, true);
3287   }
3288
3289   /**
3290    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3291    * the annotations panel as a whole.
3292    *
3293    * The options to show/hide all annotations should be enabled when the panel
3294    * is shown, and disabled when the panel is hidden.
3295    *
3296    * @param e
3297    */
3298   @Override
3299   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3300   {
3301     final boolean setVisible = annotationPanelMenuItem.isSelected();
3302     viewport.setShowAnnotation(setVisible);
3303     this.showAllSeqAnnotations.setEnabled(setVisible);
3304     this.hideAllSeqAnnotations.setEnabled(setVisible);
3305     this.showAllAlAnnotations.setEnabled(setVisible);
3306     this.hideAllAlAnnotations.setEnabled(setVisible);
3307     alignPanel.updateLayout();
3308   }
3309
3310   @Override
3311   public void alignmentProperties()
3312   {
3313     JComponent pane;
3314     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3315
3316             .formatAsHtml();
3317     String content = MessageManager.formatMessage("label.html_content",
3318             new Object[]
3319             { contents.toString() });
3320     contents = null;
3321
3322     if (Platform.isJS())
3323     {
3324       JLabel textLabel = new JLabel();
3325       textLabel.setText(content);
3326       textLabel.setBackground(Color.WHITE);
3327
3328       pane = new JPanel(new BorderLayout());
3329       ((JPanel) pane).setOpaque(true);
3330       pane.setBackground(Color.WHITE);
3331       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3332     }
3333     else
3334     /**
3335      * Java only
3336      *
3337      * @j2sIgnore
3338      */
3339     {
3340       JEditorPane editPane = new JEditorPane("text/html", "");
3341       editPane.setEditable(false);
3342       editPane.setText(content);
3343       pane = editPane;
3344     }
3345
3346     JInternalFrame frame = new JInternalFrame();
3347
3348     frame.getContentPane().add(new JScrollPane(pane));
3349
3350     Desktop.addInternalFrame(frame, MessageManager
3351             .formatMessage("label.alignment_properties", new Object[]
3352             { getTitle() }), 500, 400);
3353   }
3354
3355   /**
3356    * DOCUMENT ME!
3357    *
3358    * @param e
3359    *          DOCUMENT ME!
3360    */
3361   @Override
3362   public void overviewMenuItem_actionPerformed(ActionEvent e)
3363   {
3364     if (alignPanel.overviewPanel != null)
3365     {
3366       return;
3367     }
3368
3369     JInternalFrame frame = new JInternalFrame();
3370     final OverviewPanel overview = new OverviewPanel(alignPanel);
3371     frame.setContentPane(overview);
3372     Desktop.addInternalFrame(frame, MessageManager
3373             .formatMessage("label.overview_params", new Object[]
3374             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3375             true, true);
3376     frame.pack();
3377     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3378     frame.addInternalFrameListener(
3379             new javax.swing.event.InternalFrameAdapter()
3380             {
3381               @Override
3382               public void internalFrameClosed(
3383                       javax.swing.event.InternalFrameEvent evt)
3384               {
3385                 overview.dispose();
3386                 alignPanel.setOverviewPanel(null);
3387               }
3388             });
3389     if (getKeyListeners().length > 0)
3390     {
3391       frame.addKeyListener(getKeyListeners()[0]);
3392     }
3393
3394     alignPanel.setOverviewPanel(overview);
3395   }
3396
3397   @Override
3398   public void textColour_actionPerformed()
3399   {
3400     new TextColourChooser().chooseColour(alignPanel, null);
3401   }
3402
3403   /*
3404    * public void covariationColour_actionPerformed() {
3405    * changeColour(new
3406    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3407    * ()[0])); }
3408    */
3409   @Override
3410   public void annotationColour_actionPerformed()
3411   {
3412     new AnnotationColourChooser(viewport, alignPanel);
3413   }
3414
3415   @Override
3416   public void annotationColumn_actionPerformed(ActionEvent e)
3417   {
3418     new AnnotationColumnChooser(viewport, alignPanel);
3419   }
3420
3421   /**
3422    * Action on the user checking or unchecking the option to apply the selected
3423    * colour scheme to all groups. If unchecked, groups may have their own
3424    * independent colour schemes.
3425    *
3426    * @param selected
3427    */
3428   @Override
3429   public void applyToAllGroups_actionPerformed(boolean selected)
3430   {
3431     viewport.setColourAppliesToAllGroups(selected);
3432   }
3433
3434   /**
3435    * Action on user selecting a colour from the colour menu
3436    *
3437    * @param name
3438    *          the name (not the menu item label!) of the colour scheme
3439    */
3440   @Override
3441   public void changeColour_actionPerformed(String name)
3442   {
3443     /*
3444      * 'User Defined' opens a panel to configure or load a
3445      * user-defined colour scheme
3446      */
3447     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3448     {
3449       new UserDefinedColours(alignPanel);
3450       return;
3451     }
3452
3453     /*
3454      * otherwise set the chosen colour scheme (or null for 'None')
3455      */
3456     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3457             viewport,
3458             viewport.getAlignment(), viewport.getHiddenRepSequences());
3459     changeColour(cs);
3460   }
3461
3462   /**
3463    * Actions on setting or changing the alignment colour scheme
3464    *
3465    * @param cs
3466    */
3467   @Override
3468   public void changeColour(ColourSchemeI cs)
3469   {
3470     // TODO: pull up to controller method
3471     ColourMenuHelper.setColourSelected(colourMenu, cs);
3472
3473     viewport.setGlobalColourScheme(cs);
3474
3475     alignPanel.paintAlignment(true, true);
3476   }
3477
3478   /**
3479    * Show the PID threshold slider panel
3480    */
3481   @Override
3482   protected void modifyPID_actionPerformed()
3483   {
3484     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3485             alignPanel.getViewName());
3486     SliderPanel.showPIDSlider();
3487   }
3488
3489   /**
3490    * Show the Conservation slider panel
3491    */
3492   @Override
3493   protected void modifyConservation_actionPerformed()
3494   {
3495     SliderPanel.setConservationSlider(alignPanel,
3496             viewport.getResidueShading(), alignPanel.getViewName());
3497     SliderPanel.showConservationSlider();
3498   }
3499
3500   /**
3501    * Action on selecting or deselecting (Colour) By Conservation
3502    */
3503   @Override
3504   public void conservationMenuItem_actionPerformed(boolean selected)
3505   {
3506     modifyConservation.setEnabled(selected);
3507     viewport.setConservationSelected(selected);
3508     viewport.getResidueShading().setConservationApplied(selected);
3509
3510     changeColour(viewport.getGlobalColourScheme());
3511     if (selected)
3512     {
3513       modifyConservation_actionPerformed();
3514     }
3515     else
3516     {
3517       SliderPanel.hideConservationSlider();
3518     }
3519   }
3520
3521   /**
3522    * Action on selecting or deselecting (Colour) Above PID Threshold
3523    */
3524   @Override
3525   public void abovePIDThreshold_actionPerformed(boolean selected)
3526   {
3527     modifyPID.setEnabled(selected);
3528     viewport.setAbovePIDThreshold(selected);
3529     if (!selected)
3530     {
3531       viewport.getResidueShading().setThreshold(0,
3532               viewport.isIgnoreGapsConsensus());
3533     }
3534
3535     changeColour(viewport.getGlobalColourScheme());
3536     if (selected)
3537     {
3538       modifyPID_actionPerformed();
3539     }
3540     else
3541     {
3542       SliderPanel.hidePIDSlider();
3543     }
3544   }
3545
3546   /**
3547    * DOCUMENT ME!
3548    *
3549    * @param e
3550    *          DOCUMENT ME!
3551    */
3552   @Override
3553   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3554   {
3555     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3556     AlignmentSorter.sortByPID(viewport.getAlignment(),
3557             viewport.getAlignment().getSequenceAt(0));
3558     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3559             viewport.getAlignment()));
3560     alignPanel.paintAlignment(true, false);
3561   }
3562
3563   /**
3564    * DOCUMENT ME!
3565    *
3566    * @param e
3567    *          DOCUMENT ME!
3568    */
3569   @Override
3570   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3571   {
3572     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3573     AlignmentSorter.sortByID(viewport.getAlignment());
3574     addHistoryItem(
3575             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3576     alignPanel.paintAlignment(true, false);
3577   }
3578
3579   /**
3580    * DOCUMENT ME!
3581    *
3582    * @param e
3583    *          DOCUMENT ME!
3584    */
3585   @Override
3586   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3587   {
3588     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3589     AlignmentSorter.sortByLength(viewport.getAlignment());
3590     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3591             viewport.getAlignment()));
3592     alignPanel.paintAlignment(true, false);
3593   }
3594
3595   /**
3596    * DOCUMENT ME!
3597    *
3598    * @param e
3599    *          DOCUMENT ME!
3600    */
3601   @Override
3602   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3603   {
3604     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3605     AlignmentSorter.sortByGroup(viewport.getAlignment());
3606     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3607             viewport.getAlignment()));
3608
3609     alignPanel.paintAlignment(true, false);
3610   }
3611
3612   /**
3613    * DOCUMENT ME!
3614    *
3615    * @param e
3616    *          DOCUMENT ME!
3617    */
3618   @Override
3619   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3620   {
3621     new RedundancyPanel(alignPanel, this);
3622   }
3623
3624   /**
3625    * DOCUMENT ME!
3626    *
3627    * @param e
3628    *          DOCUMENT ME!
3629    */
3630   @Override
3631   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3632   {
3633     if ((viewport.getSelectionGroup() == null)
3634             || (viewport.getSelectionGroup().getSize() < 2))
3635     {
3636       JvOptionPane.showInternalMessageDialog(this,
3637               MessageManager.getString(
3638                       "label.you_must_select_least_two_sequences"),
3639               MessageManager.getString("label.invalid_selection"),
3640               JvOptionPane.WARNING_MESSAGE);
3641     }
3642     else
3643     {
3644       JInternalFrame frame = new JInternalFrame();
3645       frame.setContentPane(new PairwiseAlignPanel(viewport));
3646       Desktop.addInternalFrame(frame,
3647               MessageManager.getString("action.pairwise_alignment"), 600,
3648               500);
3649     }
3650   }
3651
3652   @Override
3653   public void autoCalculate_actionPerformed(ActionEvent e)
3654   {
3655     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3656     if (viewport.autoCalculateConsensus)
3657     {
3658       viewport.firePropertyChange("alignment", null,
3659               viewport.getAlignment().getSequences());
3660     }
3661   }
3662
3663   @Override
3664   public void sortByTreeOption_actionPerformed(ActionEvent e)
3665   {
3666     viewport.sortByTree = sortByTree.isSelected();
3667   }
3668
3669   @Override
3670   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3671   {
3672     viewport.followSelection = listenToViewSelections.isSelected();
3673   }
3674
3675   /**
3676    * Constructs a tree panel and adds it to the desktop
3677    *
3678    * @param type
3679    *          tree type (NJ or AV)
3680    * @param modelName
3681    *          name of score model used to compute the tree
3682    * @param options
3683    *          parameters for the distance or similarity calculation
3684    */
3685   void newTreePanel(String type, String modelName,
3686           SimilarityParamsI options)
3687   {
3688     String frameTitle = "";
3689     TreePanel tp;
3690
3691     boolean onSelection = false;
3692     if (viewport.getSelectionGroup() != null
3693             && viewport.getSelectionGroup().getSize() > 0)
3694     {
3695       SequenceGroup sg = viewport.getSelectionGroup();
3696
3697       /* Decide if the selection is a column region */
3698       for (SequenceI _s : sg.getSequences())
3699       {
3700         if (_s.getLength() < sg.getEndRes())
3701         {
3702           JvOptionPane.showMessageDialog(Desktop.desktop,
3703                   MessageManager.getString(
3704                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3705                   MessageManager.getString(
3706                           "label.sequences_selection_not_aligned"),
3707                   JvOptionPane.WARNING_MESSAGE);
3708
3709           return;
3710         }
3711       }
3712       onSelection = true;
3713     }
3714     else
3715     {
3716       if (viewport.getAlignment().getHeight() < 2)
3717       {
3718         return;
3719       }
3720     }
3721
3722     tp = new TreePanel(alignPanel, type, modelName, options);
3723     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3724
3725     frameTitle += " from ";
3726
3727     if (viewport.getViewName() != null)
3728     {
3729       frameTitle += viewport.getViewName() + " of ";
3730     }
3731
3732     frameTitle += this.title;
3733
3734     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3735   }
3736
3737   /**
3738    * DOCUMENT ME!
3739    *
3740    * @param title
3741    *          DOCUMENT ME!
3742    * @param order
3743    *          DOCUMENT ME!
3744    */
3745   public void addSortByOrderMenuItem(String title,
3746           final AlignmentOrder order)
3747   {
3748     final JMenuItem item = new JMenuItem(MessageManager
3749             .formatMessage("action.by_title_param", new Object[]
3750             { title }));
3751     sort.add(item);
3752     item.addActionListener(new java.awt.event.ActionListener()
3753     {
3754       @Override
3755       public void actionPerformed(ActionEvent e)
3756       {
3757         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3758
3759         // TODO: JBPNote - have to map order entries to curent SequenceI
3760         // pointers
3761         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3762
3763         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3764                 viewport.getAlignment()));
3765
3766         alignPanel.paintAlignment(true, false);
3767       }
3768     });
3769   }
3770
3771   /**
3772    * Add a new sort by annotation score menu item
3773    *
3774    * @param sort
3775    *          the menu to add the option to
3776    * @param scoreLabel
3777    *          the label used to retrieve scores for each sequence on the
3778    *          alignment
3779    */
3780   public void addSortByAnnotScoreMenuItem(JMenu sort,
3781           final String scoreLabel)
3782   {
3783     final JMenuItem item = new JMenuItem(scoreLabel);
3784     sort.add(item);
3785     item.addActionListener(new java.awt.event.ActionListener()
3786     {
3787       @Override
3788       public void actionPerformed(ActionEvent e)
3789       {
3790         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3791         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3792                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3793         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3794                 viewport.getAlignment()));
3795         alignPanel.paintAlignment(true, false);
3796       }
3797     });
3798   }
3799
3800   /**
3801    * last hash for alignment's annotation array - used to minimise cost of
3802    * rebuild.
3803    */
3804   protected int _annotationScoreVectorHash;
3805
3806   /**
3807    * search the alignment and rebuild the sort by annotation score submenu the
3808    * last alignment annotation vector hash is stored to minimize cost of
3809    * rebuilding in subsequence calls.
3810    *
3811    */
3812   @Override
3813   public void buildSortByAnnotationScoresMenu()
3814   {
3815     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3816     {
3817       return;
3818     }
3819
3820     if (viewport.getAlignment().getAlignmentAnnotation()
3821             .hashCode() != _annotationScoreVectorHash)
3822     {
3823       sortByAnnotScore.removeAll();
3824       // almost certainly a quicker way to do this - but we keep it simple
3825       Hashtable<String, String> scoreSorts = new Hashtable<>();
3826       AlignmentAnnotation aann[];
3827       for (SequenceI sqa : viewport.getAlignment().getSequences())
3828       {
3829         aann = sqa.getAnnotation();
3830         for (int i = 0; aann != null && i < aann.length; i++)
3831         {
3832           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3833           {
3834             scoreSorts.put(aann[i].label, aann[i].label);
3835           }
3836         }
3837       }
3838       Enumeration<String> labels = scoreSorts.keys();
3839       while (labels.hasMoreElements())
3840       {
3841         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3842                 labels.nextElement());
3843       }
3844       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3845       scoreSorts.clear();
3846
3847       _annotationScoreVectorHash = viewport.getAlignment()
3848               .getAlignmentAnnotation().hashCode();
3849     }
3850   }
3851
3852   /**
3853    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3854    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3855    * call. Listeners are added to remove the menu item when the treePanel is
3856    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3857    * modified.
3858    */
3859   @Override
3860   public void buildTreeSortMenu()
3861   {
3862     sortByTreeMenu.removeAll();
3863
3864     List<Component> comps = PaintRefresher.components
3865             .get(viewport.getSequenceSetId());
3866     List<TreePanel> treePanels = new ArrayList<>();
3867     for (Component comp : comps)
3868     {
3869       if (comp instanceof TreePanel)
3870       {
3871         treePanels.add((TreePanel) comp);
3872       }
3873     }
3874
3875     if (treePanels.size() < 1)
3876     {
3877       sortByTreeMenu.setVisible(false);
3878       return;
3879     }
3880
3881     sortByTreeMenu.setVisible(true);
3882
3883     for (final TreePanel tp : treePanels)
3884     {
3885       final JMenuItem item = new JMenuItem(tp.getTitle());
3886       item.addActionListener(new java.awt.event.ActionListener()
3887       {
3888         @Override
3889         public void actionPerformed(ActionEvent e)
3890         {
3891           tp.sortByTree_actionPerformed();
3892           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3893
3894         }
3895       });
3896
3897       sortByTreeMenu.add(item);
3898     }
3899   }
3900
3901   public boolean sortBy(AlignmentOrder alorder, String undoname)
3902   {
3903     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3904     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3905     if (undoname != null)
3906     {
3907       addHistoryItem(new OrderCommand(undoname, oldOrder,
3908               viewport.getAlignment()));
3909     }
3910     alignPanel.paintAlignment(true, false);
3911     return true;
3912   }
3913
3914   /**
3915    * Work out whether the whole set of sequences or just the selected set will
3916    * be submitted for multiple alignment.
3917    *
3918    */
3919   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3920   {
3921     // Now, check we have enough sequences
3922     AlignmentView msa = null;
3923
3924     if ((viewport.getSelectionGroup() != null)
3925             && (viewport.getSelectionGroup().getSize() > 1))
3926     {
3927       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3928       // some common interface!
3929       /*
3930        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3931        * SequenceI[sz = seqs.getSize(false)];
3932        *
3933        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3934        * seqs.getSequenceAt(i); }
3935        */
3936       msa = viewport.getAlignmentView(true);
3937     }
3938     else if (viewport.getSelectionGroup() != null
3939             && viewport.getSelectionGroup().getSize() == 1)
3940     {
3941       int option = JvOptionPane.showConfirmDialog(this,
3942               MessageManager.getString("warn.oneseq_msainput_selection"),
3943               MessageManager.getString("label.invalid_selection"),
3944               JvOptionPane.OK_CANCEL_OPTION);
3945       if (option == JvOptionPane.OK_OPTION)
3946       {
3947         msa = viewport.getAlignmentView(false);
3948       }
3949     }
3950     else
3951     {
3952       msa = viewport.getAlignmentView(false);
3953     }
3954     return msa;
3955   }
3956
3957   /**
3958    * Decides what is submitted to a secondary structure prediction service: the
3959    * first sequence in the alignment, or in the current selection, or, if the
3960    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3961    * region or the whole alignment. (where the first sequence in the set is the
3962    * one that the prediction will be for).
3963    */
3964   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3965   {
3966     AlignmentView seqs = null;
3967
3968     if ((viewport.getSelectionGroup() != null)
3969             && (viewport.getSelectionGroup().getSize() > 0))
3970     {
3971       seqs = viewport.getAlignmentView(true);
3972     }
3973     else
3974     {
3975       seqs = viewport.getAlignmentView(false);
3976     }
3977     // limit sequences - JBPNote in future - could spawn multiple prediction
3978     // jobs
3979     // TODO: viewport.getAlignment().isAligned is a global state - the local
3980     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3981     if (!viewport.getAlignment().isAligned(false))
3982     {
3983       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3984       // TODO: if seqs.getSequences().length>1 then should really have warned
3985       // user!
3986
3987     }
3988     return seqs;
3989   }
3990
3991   /**
3992    * DOCUMENT ME!
3993    *
3994    * @param e
3995    *          DOCUMENT ME!
3996    */
3997   @Override
3998   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3999   {
4000     // Pick the tree file
4001     JalviewFileChooser chooser = new JalviewFileChooser(
4002             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4003     chooser.setFileView(new JalviewFileView());
4004     chooser.setDialogTitle(
4005             MessageManager.getString("label.select_newick_like_tree_file"));
4006     chooser.setToolTipText(
4007             MessageManager.getString("label.load_tree_file"));
4008
4009     chooser.setResponseHandler(0,new Runnable()
4010     {
4011       @Override
4012       public void run()
4013       {
4014         String filePath = chooser.getSelectedFile().getPath();
4015         Cache.setProperty("LAST_DIRECTORY", filePath);
4016         NewickFile fin = null;
4017         try
4018         {
4019           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4020                   DataSourceType.FILE));
4021           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4022         } catch (Exception ex)
4023         {
4024           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4025                   MessageManager
4026                           .getString("label.problem_reading_tree_file"),
4027                   JvOptionPane.WARNING_MESSAGE);
4028           ex.printStackTrace();
4029         }
4030         if (fin != null && fin.hasWarningMessage())
4031         {
4032           JvOptionPane.showMessageDialog(Desktop.desktop,
4033                   fin.getWarningMessage(),
4034                   MessageManager.getString(
4035                           "label.possible_problem_with_tree_file"),
4036                   JvOptionPane.WARNING_MESSAGE);
4037         }
4038       }
4039     });
4040     chooser.showOpenDialog(this);
4041   }
4042
4043   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4044   {
4045     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4046   }
4047
4048   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4049           int h, int x, int y)
4050   {
4051     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4052   }
4053
4054   /**
4055    * Add a treeviewer for the tree extracted from a Newick file object to the
4056    * current alignment view
4057    *
4058    * @param nf
4059    *          the tree
4060    * @param title
4061    *          tree viewer title
4062    * @param input
4063    *          Associated alignment input data (or null)
4064    * @param w
4065    *          width
4066    * @param h
4067    *          height
4068    * @param x
4069    *          position
4070    * @param y
4071    *          position
4072    * @return TreePanel handle
4073    */
4074   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4075           AlignmentView input, int w, int h, int x, int y)
4076   {
4077     TreePanel tp = null;
4078
4079     try
4080     {
4081       nf.parse();
4082
4083       if (nf.getTree() != null)
4084       {
4085         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4086
4087         tp.setSize(w, h);
4088
4089         if (x > 0 && y > 0)
4090         {
4091           tp.setLocation(x, y);
4092         }
4093
4094         Desktop.addInternalFrame(tp, treeTitle, w, h);
4095       }
4096     } catch (Exception ex)
4097     {
4098       ex.printStackTrace();
4099     }
4100
4101     return tp;
4102   }
4103
4104   private boolean buildingMenu = false;
4105
4106   /**
4107    * Generates menu items and listener event actions for web service clients
4108    *
4109    */
4110   public void BuildWebServiceMenu()
4111   {
4112     while (buildingMenu)
4113     {
4114       try
4115       {
4116         System.err.println("Waiting for building menu to finish.");
4117         Thread.sleep(10);
4118       } catch (Exception e)
4119       {
4120       }
4121     }
4122     final AlignFrame me = this;
4123     buildingMenu = true;
4124     new Thread(new Runnable()
4125     {
4126       @Override
4127       public void run()
4128       {
4129         final List<JMenuItem> legacyItems = new ArrayList<>();
4130         try
4131         {
4132           // System.err.println("Building ws menu again "
4133           // + Thread.currentThread());
4134           // TODO: add support for context dependent disabling of services based
4135           // on
4136           // alignment and current selection
4137           // TODO: add additional serviceHandle parameter to specify abstract
4138           // handler
4139           // class independently of AbstractName
4140           // TODO: add in rediscovery GUI function to restart discoverer
4141           // TODO: group services by location as well as function and/or
4142           // introduce
4143           // object broker mechanism.
4144           final Vector<JMenu> wsmenu = new Vector<>();
4145           final IProgressIndicator af = me;
4146
4147           /*
4148            * do not i18n these strings - they are hard-coded in class
4149            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4150            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4151            */
4152           final JMenu msawsmenu = new JMenu("Alignment");
4153           final JMenu secstrmenu = new JMenu(
4154                   "Secondary Structure Prediction");
4155           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4156           final JMenu analymenu = new JMenu("Analysis");
4157           final JMenu dismenu = new JMenu("Protein Disorder");
4158           // JAL-940 - only show secondary structure prediction services from
4159           // the legacy server
4160           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4161               // &&
4162           Discoverer.services != null && (Discoverer.services.size() > 0))
4163           {
4164             // TODO: refactor to allow list of AbstractName/Handler bindings to
4165             // be
4166             // stored or retrieved from elsewhere
4167             // No MSAWS used any more:
4168             // Vector msaws = null; // (Vector)
4169             // Discoverer.services.get("MsaWS");
4170             Vector<ServiceHandle> secstrpr = Discoverer.services
4171                     .get("SecStrPred");
4172             if (secstrpr != null)
4173             {
4174               // Add any secondary structure prediction services
4175               for (int i = 0, j = secstrpr.size(); i < j; i++)
4176               {
4177                 final ext.vamsas.ServiceHandle sh = secstrpr
4178                         .get(i);
4179                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4180                         .getServiceClient(sh);
4181                 int p = secstrmenu.getItemCount();
4182                 impl.attachWSMenuEntry(secstrmenu, me);
4183                 int q = secstrmenu.getItemCount();
4184                 for (int litm = p; litm < q; litm++)
4185                 {
4186                   legacyItems.add(secstrmenu.getItem(litm));
4187                 }
4188               }
4189             }
4190           }
4191
4192           // Add all submenus in the order they should appear on the web
4193           // services menu
4194           wsmenu.add(msawsmenu);
4195           wsmenu.add(secstrmenu);
4196           wsmenu.add(dismenu);
4197           wsmenu.add(analymenu);
4198           // No search services yet
4199           // wsmenu.add(seqsrchmenu);
4200
4201           javax.swing.SwingUtilities.invokeLater(new Runnable()
4202           {
4203             @Override
4204             public void run()
4205             {
4206               try
4207               {
4208                 webService.removeAll();
4209                 // first, add discovered services onto the webservices menu
4210                 if (wsmenu.size() > 0)
4211                 {
4212                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4213                   {
4214                     webService.add(wsmenu.get(i));
4215                   }
4216                 }
4217                 else
4218                 {
4219                   webService.add(me.webServiceNoServices);
4220                 }
4221                 // TODO: move into separate menu builder class.
4222                 boolean new_sspred = false;
4223                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4224                 {
4225                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4226                   if (jws2servs != null)
4227                   {
4228                     if (jws2servs.hasServices())
4229                     {
4230                       jws2servs.attachWSMenuEntry(webService, me);
4231                       for (Jws2Instance sv : jws2servs.getServices())
4232                       {
4233                         if (sv.description.toLowerCase().contains("jpred"))
4234                         {
4235                           for (JMenuItem jmi : legacyItems)
4236                           {
4237                             jmi.setVisible(false);
4238                           }
4239                         }
4240                       }
4241
4242                     }
4243                     if (jws2servs.isRunning())
4244                     {
4245                       JMenuItem tm = new JMenuItem(
4246                               "Still discovering JABA Services");
4247                       tm.setEnabled(false);
4248                       webService.add(tm);
4249                     }
4250                   }
4251                 }
4252                 build_urlServiceMenu(me.webService);
4253                 build_fetchdbmenu(webService);
4254                 for (JMenu item : wsmenu)
4255                 {
4256                   if (item.getItemCount() == 0)
4257                   {
4258                     item.setEnabled(false);
4259                   }
4260                   else
4261                   {
4262                     item.setEnabled(true);
4263                   }
4264                 }
4265               } catch (Exception e)
4266               {
4267                 Cache.log.debug(
4268                         "Exception during web service menu building process.",
4269                         e);
4270               }
4271             }
4272           });
4273         } catch (Exception e)
4274         {
4275         }
4276         buildingMenu = false;
4277       }
4278     }).start();
4279
4280   }
4281
4282   /**
4283    * construct any groupURL type service menu entries.
4284    *
4285    * @param webService
4286    */
4287   protected void build_urlServiceMenu(JMenu webService)
4288   {
4289     // TODO: remove this code when 2.7 is released
4290     // DEBUG - alignmentView
4291     /*
4292      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4293      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4294      *
4295      * @Override public void actionPerformed(ActionEvent e) {
4296      * jalview.datamodel.AlignmentView
4297      * .testSelectionViews(af.viewport.getAlignment(),
4298      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4299      *
4300      * }); webService.add(testAlView);
4301      */
4302     // TODO: refactor to RestClient discoverer and merge menu entries for
4303     // rest-style services with other types of analysis/calculation service
4304     // SHmmr test client - still being implemented.
4305     // DEBUG - alignmentView
4306
4307     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4308             .getRestClients())
4309     {
4310       client.attachWSMenuEntry(
4311               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4312               this);
4313     }
4314   }
4315
4316   /**
4317    * Searches the alignment sequences for xRefs and builds the Show
4318    * Cross-References menu (formerly called Show Products), with database
4319    * sources for which cross-references are found (protein sources for a
4320    * nucleotide alignment and vice versa)
4321    *
4322    * @return true if Show Cross-references menu should be enabled
4323    */
4324   public boolean canShowProducts()
4325   {
4326     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4327     AlignmentI dataset = viewport.getAlignment().getDataset();
4328
4329     showProducts.removeAll();
4330     final boolean dna = viewport.getAlignment().isNucleotide();
4331
4332     if (seqs == null || seqs.length == 0)
4333     {
4334       // nothing to see here.
4335       return false;
4336     }
4337
4338     boolean showp = false;
4339     try
4340     {
4341       List<String> ptypes = new CrossRef(seqs, dataset)
4342               .findXrefSourcesForSequences(dna);
4343
4344       for (final String source : ptypes)
4345       {
4346         showp = true;
4347         final AlignFrame af = this;
4348         JMenuItem xtype = new JMenuItem(source);
4349         xtype.addActionListener(new ActionListener()
4350         {
4351           @Override
4352           public void actionPerformed(ActionEvent e)
4353           {
4354             showProductsFor(af.viewport.getSequenceSelection(), dna,
4355                     source);
4356           }
4357         });
4358         showProducts.add(xtype);
4359       }
4360       showProducts.setVisible(showp);
4361       showProducts.setEnabled(showp);
4362     } catch (Exception e)
4363     {
4364       Cache.log.warn(
4365               "canShowProducts threw an exception - please report to help@jalview.org",
4366               e);
4367       return false;
4368     }
4369     return showp;
4370   }
4371
4372   /**
4373    * Finds and displays cross-references for the selected sequences (protein
4374    * products for nucleotide sequences, dna coding sequences for peptides).
4375    *
4376    * @param sel
4377    *          the sequences to show cross-references for
4378    * @param dna
4379    *          true if from a nucleotide alignment (so showing proteins)
4380    * @param source
4381    *          the database to show cross-references for
4382    */
4383   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4384           final String source)
4385   {
4386     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4387             .start();
4388   }
4389
4390   /**
4391    * Construct and display a new frame containing the translation of this
4392    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4393    */
4394   @Override
4395   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4396   {
4397     AlignmentI al = null;
4398     try
4399     {
4400       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4401
4402       al = dna.translateCdna(codeTable);
4403     } catch (Exception ex)
4404     {
4405       jalview.bin.Cache.log.error(
4406               "Exception during translation. Please report this !", ex);
4407       final String msg = MessageManager.getString(
4408               "label.error_when_translating_sequences_submit_bug_report");
4409       final String errorTitle = MessageManager
4410               .getString("label.implementation_error")
4411               + MessageManager.getString("label.translation_failed");
4412       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4413               JvOptionPane.ERROR_MESSAGE);
4414       return;
4415     }
4416     if (al == null || al.getHeight() == 0)
4417     {
4418       final String msg = MessageManager.getString(
4419               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4420       final String errorTitle = MessageManager
4421               .getString("label.translation_failed");
4422       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4423               JvOptionPane.WARNING_MESSAGE);
4424     }
4425     else
4426     {
4427       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4428       af.setFileFormat(this.currentFileFormat);
4429       final String newTitle = MessageManager
4430               .formatMessage("label.translation_of_params", new Object[]
4431               { this.getTitle(), codeTable.getId() });
4432       af.setTitle(newTitle);
4433       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4434       {
4435         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4436         viewport.openSplitFrame(af, new Alignment(seqs));
4437       }
4438       else
4439       {
4440         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4441                 DEFAULT_HEIGHT);
4442       }
4443     }
4444   }
4445
4446   /**
4447    * Set the file format
4448    *
4449    * @param format
4450    */
4451   public void setFileFormat(FileFormatI format)
4452   {
4453     this.currentFileFormat = format;
4454   }
4455
4456   /**
4457    * Try to load a features file onto the alignment.
4458    *
4459    * @param file
4460    *          contents or path to retrieve file or a File object
4461    * @param sourceType
4462    *          access mode of file (see jalview.io.AlignFile)
4463    * @return true if features file was parsed correctly.
4464    */
4465   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4466   {
4467     // BH 2018
4468     return avc.parseFeaturesFile(file, sourceType,
4469             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4470
4471   }
4472
4473   @Override
4474   public void refreshFeatureUI(boolean enableIfNecessary)
4475   {
4476     // note - currently this is only still here rather than in the controller
4477     // because of the featureSettings hard reference that is yet to be
4478     // abstracted
4479     if (enableIfNecessary)
4480     {
4481       viewport.setShowSequenceFeatures(true);
4482       showSeqFeatures.setSelected(true);
4483     }
4484
4485   }
4486
4487   @Override
4488   public void dragEnter(DropTargetDragEvent evt)
4489   {
4490   }
4491
4492   @Override
4493   public void dragExit(DropTargetEvent evt)
4494   {
4495   }
4496
4497   @Override
4498   public void dragOver(DropTargetDragEvent evt)
4499   {
4500   }
4501
4502   @Override
4503   public void dropActionChanged(DropTargetDragEvent evt)
4504   {
4505   }
4506
4507   @Override
4508   public void drop(DropTargetDropEvent evt)
4509   {
4510     // JAL-1552 - acceptDrop required before getTransferable call for
4511     // Java's Transferable for native dnd
4512     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4513     Transferable t = evt.getTransferable();
4514
4515     final AlignFrame thisaf = this;
4516     final List<Object> files = new ArrayList<>();
4517     List<DataSourceType> protocols = new ArrayList<>();
4518
4519     try
4520     {
4521       Desktop.transferFromDropTarget(files, protocols, evt, t);
4522     } catch (Exception e)
4523     {
4524       e.printStackTrace();
4525     }
4526     if (files != null)
4527     {
4528       new Thread(new Runnable()
4529       {
4530         @Override
4531         public void run()
4532         {
4533           try
4534           {
4535             // check to see if any of these files have names matching sequences
4536             // in
4537             // the alignment
4538             SequenceIdMatcher idm = new SequenceIdMatcher(
4539                     viewport.getAlignment().getSequencesArray());
4540             /**
4541              * Object[] { String,SequenceI}
4542              */
4543             ArrayList<Object[]> filesmatched = new ArrayList<>();
4544             ArrayList<Object> filesnotmatched = new ArrayList<>();
4545             for (int i = 0; i < files.size(); i++)
4546             {
4547               // BH 2018
4548               Object file = files.get(i);
4549               String fileName = file.toString();
4550               String pdbfn = "";
4551               DataSourceType protocol = (file instanceof File
4552                       ? DataSourceType.FILE
4553                       : FormatAdapter.checkProtocol(fileName));
4554               if (protocol == DataSourceType.FILE)
4555               {
4556                 File fl;
4557                 if (file instanceof File) {
4558                   fl = (File) file;
4559                   Platform.cacheFileData(fl);
4560                 } else {
4561                   fl = new File(fileName);
4562                 }
4563                 pdbfn = fl.getName();
4564               }
4565               else if (protocol == DataSourceType.URL)
4566               {
4567                 URL url = new URL(fileName);
4568                 pdbfn = url.getFile();
4569               }
4570               if (pdbfn.length() > 0)
4571               {
4572                 // attempt to find a match in the alignment
4573                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4574                 int l = 0, c = pdbfn.indexOf(".");
4575                 while (mtch == null && c != -1)
4576                 {
4577                   do
4578                   {
4579                     l = c;
4580                   } while ((c = pdbfn.indexOf(".", l)) > l);
4581                   if (l > -1)
4582                   {
4583                     pdbfn = pdbfn.substring(0, l);
4584                   }
4585                   mtch = idm.findAllIdMatches(pdbfn);
4586                 }
4587                 if (mtch != null)
4588                 {
4589                   FileFormatI type;
4590                   try
4591                   {
4592                     type = new IdentifyFile().identify(file, protocol);
4593                   } catch (Exception ex)
4594                   {
4595                     type = null;
4596                   }
4597                   if (type != null && type.isStructureFile())
4598                   {
4599                     filesmatched.add(new Object[] { file, protocol, mtch });
4600                     continue;
4601                   }
4602                 }
4603                 // File wasn't named like one of the sequences or wasn't a PDB
4604                 // file.
4605                 filesnotmatched.add(file);
4606               }
4607             }
4608             int assocfiles = 0;
4609             if (filesmatched.size() > 0)
4610             {
4611               boolean autoAssociate = Cache
4612                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4613               if (!autoAssociate)
4614               {
4615                 String msg = MessageManager.formatMessage(
4616                         "label.automatically_associate_structure_files_with_sequences_same_name",
4617                         new Object[]
4618                         { Integer.valueOf(filesmatched.size())
4619                                 .toString() });
4620                 String ttl = MessageManager.getString(
4621                         "label.automatically_associate_structure_files_by_name");
4622                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4623                         ttl, JvOptionPane.YES_NO_OPTION);
4624                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4625               }
4626               if (autoAssociate)
4627               {
4628                 for (Object[] fm : filesmatched)
4629                 {
4630                   // try and associate
4631                   // TODO: may want to set a standard ID naming formalism for
4632                   // associating PDB files which have no IDs.
4633                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4634                   {
4635                     PDBEntry pe = new AssociatePdbFileWithSeq()
4636                             .associatePdbWithSeq(fm[0].toString(),
4637                                     (DataSourceType) fm[1], toassoc, false,
4638                                     Desktop.instance);
4639                     if (pe != null)
4640                     {
4641                       System.err.println("Associated file : "
4642                               + (fm[0].toString()) + " with "
4643                               + toassoc.getDisplayId(true));
4644                       assocfiles++;
4645                     }
4646                   }
4647                   // TODO: do we need to update overview ? only if features are
4648                   // shown I guess
4649                   alignPanel.paintAlignment(true, false);
4650                 }
4651               }
4652               else
4653               {
4654                 /*
4655                  * add declined structures as sequences
4656                  */
4657                 for (Object[] o : filesmatched)
4658                 {
4659                   filesnotmatched.add(o[0]);
4660                 }
4661               }
4662             }
4663             if (filesnotmatched.size() > 0)
4664             {
4665               if (assocfiles > 0 && (Cache.getDefault(
4666                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4667                       || JvOptionPane.showConfirmDialog(thisaf,
4668                               "<html>" + MessageManager.formatMessage(
4669                                       "label.ignore_unmatched_dropped_files_info",
4670                                       new Object[]
4671                                       { Integer.valueOf(
4672                                               filesnotmatched.size())
4673                                               .toString() })
4674                                       + "</html>",
4675                               MessageManager.getString(
4676                                       "label.ignore_unmatched_dropped_files"),
4677                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4678               {
4679                 return;
4680               }
4681               for (Object fn : filesnotmatched)
4682               {
4683                 loadJalviewDataFile(fn, null, null, null);
4684               }
4685
4686             }
4687           } catch (Exception ex)
4688           {
4689             ex.printStackTrace();
4690           }
4691         }
4692       }).start();
4693     }
4694   }
4695
4696   /**
4697    * Attempt to load a "dropped" file or URL string, by testing in turn for
4698    * <ul>
4699    * <li>an Annotation file</li>
4700    * <li>a JNet file</li>
4701    * <li>a features file</li>
4702    * <li>else try to interpret as an alignment file</li>
4703    * </ul>
4704    *
4705    * @param file
4706    *          either a filename or a URL string.
4707    */
4708   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4709           FileFormatI format, SequenceI assocSeq)
4710   {
4711     // BH 2018 was String file
4712     try
4713     {
4714       if (sourceType == null)
4715       {
4716         sourceType = FormatAdapter.checkProtocol(file);
4717       }
4718       // if the file isn't identified, or not positively identified as some
4719       // other filetype (PFAM is default unidentified alignment file type) then
4720       // try to parse as annotation.
4721       boolean isAnnotation = (format == null
4722               || FileFormat.Pfam.equals(format))
4723                       ? new AnnotationFile().annotateAlignmentView(viewport,
4724                               file, sourceType)
4725                       : false;
4726
4727       if (!isAnnotation)
4728       {
4729         // first see if its a T-COFFEE score file
4730         TCoffeeScoreFile tcf = null;
4731         try
4732         {
4733           tcf = new TCoffeeScoreFile(file, sourceType);
4734           if (tcf.isValid())
4735           {
4736             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4737             {
4738               buildColourMenu();
4739               changeColour(
4740                       new TCoffeeColourScheme(viewport.getAlignment()));
4741               isAnnotation = true;
4742               setStatus(MessageManager.getString(
4743                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4744             }
4745             else
4746             {
4747               // some problem - if no warning its probable that the ID matching
4748               // process didn't work
4749               JvOptionPane.showMessageDialog(Desktop.desktop,
4750                       tcf.getWarningMessage() == null
4751                               ? MessageManager.getString(
4752                                       "label.check_file_matches_sequence_ids_alignment")
4753                               : tcf.getWarningMessage(),
4754                       MessageManager.getString(
4755                               "label.problem_reading_tcoffee_score_file"),
4756                       JvOptionPane.WARNING_MESSAGE);
4757             }
4758           }
4759           else
4760           {
4761             tcf = null;
4762           }
4763         } catch (Exception x)
4764         {
4765           Cache.log.debug(
4766                   "Exception when processing data source as T-COFFEE score file",
4767                   x);
4768           tcf = null;
4769         }
4770         if (tcf == null)
4771         {
4772           // try to see if its a JNet 'concise' style annotation file *before*
4773           // we
4774           // try to parse it as a features file
4775           if (format == null)
4776           {
4777             format = new IdentifyFile().identify(file, sourceType);
4778           }
4779           if (FileFormat.ScoreMatrix == format)
4780           {
4781             ScoreMatrixFile sm = new ScoreMatrixFile(
4782                     new FileParse(file, sourceType));
4783             sm.parse();
4784             // todo: i18n this message
4785             setStatus(MessageManager.formatMessage(
4786                     "label.successfully_loaded_matrix",
4787                     sm.getMatrixName()));
4788           }
4789           else if (FileFormat.Jnet.equals(format))
4790           {
4791             JPredFile predictions = new JPredFile(file, sourceType);
4792             new JnetAnnotationMaker();
4793             JnetAnnotationMaker.add_annotation(predictions,
4794                     viewport.getAlignment(), 0, false);
4795             viewport.getAlignment().setupJPredAlignment();
4796             isAnnotation = true;
4797           }
4798           // else if (IdentifyFile.FeaturesFile.equals(format))
4799           else if (FileFormat.Features.equals(format))
4800           {
4801             if (parseFeaturesFile(file, sourceType))
4802             {
4803               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4804               if (splitFrame != null)
4805               {
4806                 splitFrame.repaint();
4807               }
4808               else
4809               {
4810                 alignPanel.paintAlignment(true, true);
4811               }
4812             }
4813           }
4814           else
4815           {
4816             new FileLoader().LoadFile(viewport, file, sourceType, format);
4817           }
4818         }
4819       }
4820       if (isAnnotation)
4821       {
4822
4823         alignPanel.adjustAnnotationHeight();
4824         viewport.updateSequenceIdColours();
4825         buildSortByAnnotationScoresMenu();
4826         alignPanel.paintAlignment(true, true);
4827       }
4828     } catch (Exception ex)
4829     {
4830       ex.printStackTrace();
4831     } catch (OutOfMemoryError oom)
4832     {
4833       try
4834       {
4835         System.gc();
4836       } catch (Exception x)
4837       {
4838       }
4839       new OOMWarning(
4840               "loading data "
4841                       + (sourceType != null
4842                               ? (sourceType == DataSourceType.PASTE
4843                                       ? "from clipboard."
4844                                       : "using " + sourceType + " from "
4845                                               + file)
4846                               : ".")
4847                       + (format != null
4848                               ? "(parsing as '" + format + "' file)"
4849                               : ""),
4850               oom, Desktop.desktop);
4851     }
4852   }
4853
4854   /**
4855    * Method invoked by the ChangeListener on the tabbed pane, in other words
4856    * when a different tabbed pane is selected by the user or programmatically.
4857    */
4858   @Override
4859   public void tabSelectionChanged(int index)
4860   {
4861     if (index > -1)
4862     {
4863       alignPanel = alignPanels.get(index);
4864       viewport = alignPanel.av;
4865       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4866       setMenusFromViewport(viewport);
4867       if (featureSettings != null && featureSettings.isOpen()
4868               && featureSettings.fr.getViewport() != viewport)
4869       {
4870         if (viewport.isShowSequenceFeatures())
4871         {
4872           // refresh the featureSettings to reflect UI change
4873           showFeatureSettingsUI();
4874         }
4875         else
4876         {
4877           // close feature settings for this view.
4878           featureSettings.close();
4879         }
4880       }
4881
4882     }
4883
4884     /*
4885      * 'focus' any colour slider that is open to the selected viewport
4886      */
4887     if (viewport.getConservationSelected())
4888     {
4889       SliderPanel.setConservationSlider(alignPanel,
4890               viewport.getResidueShading(), alignPanel.getViewName());
4891     }
4892     else
4893     {
4894       SliderPanel.hideConservationSlider();
4895     }
4896     if (viewport.getAbovePIDThreshold())
4897     {
4898       SliderPanel.setPIDSliderSource(alignPanel,
4899               viewport.getResidueShading(), alignPanel.getViewName());
4900     }
4901     else
4902     {
4903       SliderPanel.hidePIDSlider();
4904     }
4905
4906     /*
4907      * If there is a frame linked to this one in a SplitPane, switch it to the
4908      * same view tab index. No infinite recursion of calls should happen, since
4909      * tabSelectionChanged() should not get invoked on setting the selected
4910      * index to an unchanged value. Guard against setting an invalid index
4911      * before the new view peer tab has been created.
4912      */
4913     final AlignViewportI peer = viewport.getCodingComplement();
4914     if (peer != null)
4915     {
4916       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4917               .getAlignPanel().alignFrame;
4918       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4919       {
4920         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4921       }
4922     }
4923   }
4924
4925   /**
4926    * On right mouse click on view tab, prompt for and set new view name.
4927    */
4928   @Override
4929   public void tabbedPane_mousePressed(MouseEvent e)
4930   {
4931     if (e.isPopupTrigger())
4932     {
4933       String msg = MessageManager.getString("label.enter_view_name");
4934       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4935       String reply = JvOptionPane.showInputDialog(msg, ttl);
4936
4937       if (reply != null)
4938       {
4939         viewport.setViewName(reply);
4940         // TODO warn if reply is in getExistingViewNames()?
4941         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4942       }
4943     }
4944   }
4945
4946   public AlignViewport getCurrentView()
4947   {
4948     return viewport;
4949   }
4950
4951   /**
4952    * Open the dialog for regex description parsing.
4953    */
4954   @Override
4955   protected void extractScores_actionPerformed(ActionEvent e)
4956   {
4957     ParseProperties pp = new jalview.analysis.ParseProperties(
4958             viewport.getAlignment());
4959     // TODO: verify regex and introduce GUI dialog for version 2.5
4960     // if (pp.getScoresFromDescription("col", "score column ",
4961     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4962     // true)>0)
4963     if (pp.getScoresFromDescription("description column",
4964             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4965     {
4966       buildSortByAnnotationScoresMenu();
4967     }
4968   }
4969
4970   /*
4971    * (non-Javadoc)
4972    *
4973    * @see
4974    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4975    * )
4976    */
4977   @Override
4978   protected void showDbRefs_actionPerformed(ActionEvent e)
4979   {
4980     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4981   }
4982
4983   /*
4984    * (non-Javadoc)
4985    *
4986    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4987    * ActionEvent)
4988    */
4989   @Override
4990   protected void showNpFeats_actionPerformed(ActionEvent e)
4991   {
4992     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4993   }
4994
4995   /**
4996    * find the viewport amongst the tabs in this alignment frame and close that
4997    * tab
4998    *
4999    * @param av
5000    */
5001   public boolean closeView(AlignViewportI av)
5002   {
5003     if (viewport == av)
5004     {
5005       this.closeMenuItem_actionPerformed(false);
5006       return true;
5007     }
5008     Component[] comp = tabbedPane.getComponents();
5009     for (int i = 0; comp != null && i < comp.length; i++)
5010     {
5011       if (comp[i] instanceof AlignmentPanel)
5012       {
5013         if (((AlignmentPanel) comp[i]).av == av)
5014         {
5015           // close the view.
5016           closeView((AlignmentPanel) comp[i]);
5017           return true;
5018         }
5019       }
5020     }
5021     return false;
5022   }
5023
5024   protected void build_fetchdbmenu(JMenu webService)
5025   {
5026     // Temporary hack - DBRef Fetcher always top level ws entry.
5027     // TODO We probably want to store a sequence database checklist in
5028     // preferences and have checkboxes.. rather than individual sources selected
5029     // here
5030     final JMenu rfetch = new JMenu(
5031             MessageManager.getString("action.fetch_db_references"));
5032     rfetch.setToolTipText(MessageManager.getString(
5033             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5034     webService.add(rfetch);
5035
5036     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5037             MessageManager.getString("option.trim_retrieved_seqs"));
5038     trimrs.setToolTipText(
5039             MessageManager.getString("label.trim_retrieved_sequences"));
5040     trimrs.setSelected(
5041             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5042     trimrs.addActionListener(new ActionListener()
5043     {
5044       @Override
5045       public void actionPerformed(ActionEvent e)
5046       {
5047         trimrs.setSelected(trimrs.isSelected());
5048         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5049                 Boolean.valueOf(trimrs.isSelected()).toString());
5050       }
5051     });
5052     rfetch.add(trimrs);
5053     JMenuItem fetchr = new JMenuItem(
5054             MessageManager.getString("label.standard_databases"));
5055     fetchr.setToolTipText(
5056             MessageManager.getString("label.fetch_embl_uniprot"));
5057     fetchr.addActionListener(new ActionListener()
5058     {
5059
5060       @Override
5061       public void actionPerformed(ActionEvent e)
5062       {
5063         new Thread(new Runnable()
5064         {
5065           @Override
5066           public void run()
5067           {
5068             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5069                     .getAlignment().isNucleotide();
5070             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5071                     alignPanel.av.getSequenceSelection(),
5072                     alignPanel.alignFrame, null,
5073                     alignPanel.alignFrame.featureSettings, isNucleotide);
5074             dbRefFetcher.addListener(new FetchFinishedListenerI()
5075             {
5076               @Override
5077               public void finished()
5078               {
5079
5080                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5081                         .getFeatureSettingsModels())
5082                 {
5083
5084                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5085                 }
5086                 AlignFrame.this.setMenusForViewport();
5087               }
5088             });
5089             dbRefFetcher.fetchDBRefs(false);
5090           }
5091         }).start();
5092
5093       }
5094
5095     });
5096     rfetch.add(fetchr);
5097     new Thread(new Runnable()
5098     {
5099       @Override
5100       public void run()
5101       {
5102         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5103                 .getSequenceFetcherSingleton();
5104         javax.swing.SwingUtilities.invokeLater(new Runnable()
5105         {
5106           @Override
5107           public void run()
5108           {
5109             String[] dbclasses = sf.getNonAlignmentSources();
5110             List<DbSourceProxy> otherdb;
5111             JMenu dfetch = new JMenu();
5112             JMenu ifetch = new JMenu();
5113             JMenuItem fetchr = null;
5114             int comp = 0, icomp = 0, mcomp = 15;
5115             String mname = null;
5116             int dbi = 0;
5117             for (String dbclass : dbclasses)
5118             {
5119               otherdb = sf.getSourceProxy(dbclass);
5120               // add a single entry for this class, or submenu allowing 'fetch
5121               // all' or pick one
5122               if (otherdb == null || otherdb.size() < 1)
5123               {
5124                 continue;
5125               }
5126               if (mname == null)
5127               {
5128                 mname = "From " + dbclass;
5129               }
5130               if (otherdb.size() == 1)
5131               {
5132                 final DbSourceProxy[] dassource = otherdb
5133                         .toArray(new DbSourceProxy[0]);
5134                 DbSourceProxy src = otherdb.get(0);
5135                 fetchr = new JMenuItem(src.getDbSource());
5136                 fetchr.addActionListener(new ActionListener()
5137                 {
5138
5139                   @Override
5140                   public void actionPerformed(ActionEvent e)
5141                   {
5142                     new Thread(new Runnable()
5143                     {
5144
5145                       @Override
5146                       public void run()
5147                       {
5148                         boolean isNucleotide = alignPanel.alignFrame
5149                                 .getViewport().getAlignment()
5150                                 .isNucleotide();
5151                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5152                                 alignPanel.av.getSequenceSelection(),
5153                                 alignPanel.alignFrame, dassource,
5154                                 alignPanel.alignFrame.featureSettings,
5155                                 isNucleotide);
5156                         dbRefFetcher
5157                                 .addListener(new FetchFinishedListenerI()
5158                                 {
5159                                   @Override
5160                                   public void finished()
5161                                   {
5162                                     FeatureSettingsModelI srcSettings = dassource[0]
5163                                             .getFeatureColourScheme();
5164                                     alignPanel.av.mergeFeaturesStyle(
5165                                             srcSettings);
5166                                     AlignFrame.this.setMenusForViewport();
5167                                   }
5168                                 });
5169                         dbRefFetcher.fetchDBRefs(false);
5170                       }
5171                     }).start();
5172                   }
5173
5174                 });
5175                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5176                         MessageManager.formatMessage(
5177                                 "label.fetch_retrieve_from", new Object[]
5178                                 { src.getDbName() })));
5179                 dfetch.add(fetchr);
5180                 comp++;
5181               }
5182               else
5183               {
5184                 final DbSourceProxy[] dassource = otherdb
5185                         .toArray(new DbSourceProxy[0]);
5186                 // fetch all entry
5187                 DbSourceProxy src = otherdb.get(0);
5188                 fetchr = new JMenuItem(MessageManager
5189                         .formatMessage("label.fetch_all_param", new Object[]
5190                         { src.getDbSource() }));
5191                 fetchr.addActionListener(new ActionListener()
5192                 {
5193                   @Override
5194                   public void actionPerformed(ActionEvent e)
5195                   {
5196                     new Thread(new Runnable()
5197                     {
5198
5199                       @Override
5200                       public void run()
5201                       {
5202                         boolean isNucleotide = alignPanel.alignFrame
5203                                 .getViewport().getAlignment()
5204                                 .isNucleotide();
5205                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5206                                 alignPanel.av.getSequenceSelection(),
5207                                 alignPanel.alignFrame, dassource,
5208                                 alignPanel.alignFrame.featureSettings,
5209                                 isNucleotide);
5210                         dbRefFetcher
5211                                 .addListener(new FetchFinishedListenerI()
5212                                 {
5213                                   @Override
5214                                   public void finished()
5215                                   {
5216                                     AlignFrame.this.setMenusForViewport();
5217                                   }
5218                                 });
5219                         dbRefFetcher.fetchDBRefs(false);
5220                       }
5221                     }).start();
5222                   }
5223                 });
5224
5225                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5226                         MessageManager.formatMessage(
5227                                 "label.fetch_retrieve_from_all_sources",
5228                                 new Object[]
5229                                 { Integer.valueOf(otherdb.size())
5230                                         .toString(),
5231                                     src.getDbSource(), src.getDbName() })));
5232                 dfetch.add(fetchr);
5233                 comp++;
5234                 // and then build the rest of the individual menus
5235                 ifetch = new JMenu(MessageManager.formatMessage(
5236                         "label.source_from_db_source", new Object[]
5237                         { src.getDbSource() }));
5238                 icomp = 0;
5239                 String imname = null;
5240                 int i = 0;
5241                 for (DbSourceProxy sproxy : otherdb)
5242                 {
5243                   String dbname = sproxy.getDbName();
5244                   String sname = dbname.length() > 5
5245                           ? dbname.substring(0, 5) + "..."
5246                           : dbname;
5247                   String msname = dbname.length() > 10
5248                           ? dbname.substring(0, 10) + "..."
5249                           : dbname;
5250                   if (imname == null)
5251                   {
5252                     imname = MessageManager
5253                             .formatMessage("label.from_msname", new Object[]
5254                             { sname });
5255                   }
5256                   fetchr = new JMenuItem(msname);
5257                   final DbSourceProxy[] dassrc = { sproxy };
5258                   fetchr.addActionListener(new ActionListener()
5259                   {
5260
5261                     @Override
5262                     public void actionPerformed(ActionEvent e)
5263                     {
5264                       new Thread(new Runnable()
5265                       {
5266
5267                         @Override
5268                         public void run()
5269                         {
5270                           boolean isNucleotide = alignPanel.alignFrame
5271                                   .getViewport().getAlignment()
5272                                   .isNucleotide();
5273                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5274                                   alignPanel.av.getSequenceSelection(),
5275                                   alignPanel.alignFrame, dassrc,
5276                                   alignPanel.alignFrame.featureSettings,
5277                                   isNucleotide);
5278                           dbRefFetcher
5279                                   .addListener(new FetchFinishedListenerI()
5280                                   {
5281                                     @Override
5282                                     public void finished()
5283                                     {
5284                                       AlignFrame.this.setMenusForViewport();
5285                                     }
5286                                   });
5287                           dbRefFetcher.fetchDBRefs(false);
5288                         }
5289                       }).start();
5290                     }
5291
5292                   });
5293                   fetchr.setToolTipText(
5294                           "<html>" + MessageManager.formatMessage(
5295                                   "label.fetch_retrieve_from", new Object[]
5296                                   { dbname }));
5297                   ifetch.add(fetchr);
5298                   ++i;
5299                   if (++icomp >= mcomp || i == (otherdb.size()))
5300                   {
5301                     ifetch.setText(MessageManager.formatMessage(
5302                             "label.source_to_target", imname, sname));
5303                     dfetch.add(ifetch);
5304                     ifetch = new JMenu();
5305                     imname = null;
5306                     icomp = 0;
5307                     comp++;
5308                   }
5309                 }
5310               }
5311               ++dbi;
5312               if (comp >= mcomp || dbi >= (dbclasses.length))
5313               {
5314                 dfetch.setText(MessageManager.formatMessage(
5315                         "label.source_to_target", mname, dbclass));
5316                 rfetch.add(dfetch);
5317                 dfetch = new JMenu();
5318                 mname = null;
5319                 comp = 0;
5320               }
5321             }
5322           }
5323         });
5324       }
5325     }).start();
5326
5327   }
5328
5329   /**
5330    * Left justify the whole alignment.
5331    */
5332   @Override
5333   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5334   {
5335     AlignmentI al = viewport.getAlignment();
5336     al.justify(false);
5337     viewport.firePropertyChange("alignment", null, al);
5338   }
5339
5340   /**
5341    * Right justify the whole alignment.
5342    */
5343   @Override
5344   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5345   {
5346     AlignmentI al = viewport.getAlignment();
5347     al.justify(true);
5348     viewport.firePropertyChange("alignment", null, al);
5349   }
5350
5351   @Override
5352   public void setShowSeqFeatures(boolean b)
5353   {
5354     showSeqFeatures.setSelected(b);
5355     viewport.setShowSequenceFeatures(b);
5356   }
5357
5358   /*
5359    * (non-Javadoc)
5360    *
5361    * @see
5362    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5363    * awt.event.ActionEvent)
5364    */
5365   @Override
5366   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5367   {
5368     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5369     alignPanel.paintAlignment(false, false);
5370   }
5371
5372   /*
5373    * (non-Javadoc)
5374    *
5375    * @see
5376    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5377    * .ActionEvent)
5378    */
5379   @Override
5380   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5381   {
5382     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5383     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5384
5385   }
5386
5387   /*
5388    * (non-Javadoc)
5389    *
5390    * @see
5391    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5392    * .event.ActionEvent)
5393    */
5394   @Override
5395   protected void showGroupConservation_actionPerformed(ActionEvent e)
5396   {
5397     viewport.setShowGroupConservation(showGroupConservation.getState());
5398     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5399   }
5400
5401   /*
5402    * (non-Javadoc)
5403    *
5404    * @see
5405    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5406    * .event.ActionEvent)
5407    */
5408   @Override
5409   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5410   {
5411     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5412     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5413   }
5414
5415   /*
5416    * (non-Javadoc)
5417    *
5418    * @see
5419    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5420    * .event.ActionEvent)
5421    */
5422   @Override
5423   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5424   {
5425     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5426     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5427   }
5428
5429   @Override
5430   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5431   {
5432     showSequenceLogo.setState(true);
5433     viewport.setShowSequenceLogo(true);
5434     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5435     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5436   }
5437
5438   @Override
5439   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5440   {
5441     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5442   }
5443
5444   /*
5445    * (non-Javadoc)
5446    *
5447    * @see
5448    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5449    * .event.ActionEvent)
5450    */
5451   @Override
5452   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5453   {
5454     if (avc.makeGroupsFromSelection())
5455     {
5456       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5457       alignPanel.updateAnnotation();
5458       alignPanel.paintAlignment(true,
5459               viewport.needToUpdateStructureViews());
5460     }
5461   }
5462
5463   public void clearAlignmentSeqRep()
5464   {
5465     // TODO refactor alignmentseqrep to controller
5466     if (viewport.getAlignment().hasSeqrep())
5467     {
5468       viewport.getAlignment().setSeqrep(null);
5469       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5470       alignPanel.updateAnnotation();
5471       alignPanel.paintAlignment(true, true);
5472     }
5473   }
5474
5475   @Override
5476   protected void createGroup_actionPerformed(ActionEvent e)
5477   {
5478     if (avc.createGroup())
5479     {
5480       if (applyAutoAnnotationSettings.isSelected())
5481       {
5482         alignPanel.updateAnnotation(true, false);
5483       }
5484       alignPanel.alignmentChanged();
5485     }
5486   }
5487
5488   @Override
5489   protected void unGroup_actionPerformed(ActionEvent e)
5490   {
5491     if (avc.unGroup())
5492     {
5493       alignPanel.alignmentChanged();
5494     }
5495   }
5496
5497   /**
5498    * make the given alignmentPanel the currently selected tab
5499    *
5500    * @param alignmentPanel
5501    */
5502   public void setDisplayedView(AlignmentPanel alignmentPanel)
5503   {
5504     if (!viewport.getSequenceSetId()
5505             .equals(alignmentPanel.av.getSequenceSetId()))
5506     {
5507       throw new Error(MessageManager.getString(
5508               "error.implementation_error_cannot_show_view_alignment_frame"));
5509     }
5510     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5511             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5512     {
5513       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5514     }
5515   }
5516
5517   /**
5518    * Action on selection of menu options to Show or Hide annotations.
5519    *
5520    * @param visible
5521    * @param forSequences
5522    *          update sequence-related annotations
5523    * @param forAlignment
5524    *          update non-sequence-related annotations
5525    */
5526   @Override
5527   protected void setAnnotationsVisibility(boolean visible,
5528           boolean forSequences, boolean forAlignment)
5529   {
5530     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5531             .getAlignmentAnnotation();
5532     if (anns == null)
5533     {
5534       return;
5535     }
5536     for (AlignmentAnnotation aa : anns)
5537     {
5538       /*
5539        * don't display non-positional annotations on an alignment
5540        */
5541       if (aa.annotations == null)
5542       {
5543         continue;
5544       }
5545       boolean apply = (aa.sequenceRef == null && forAlignment)
5546               || (aa.sequenceRef != null && forSequences);
5547       if (apply)
5548       {
5549         aa.visible = visible;
5550       }
5551     }
5552     alignPanel.validateAnnotationDimensions(true);
5553     alignPanel.alignmentChanged();
5554   }
5555
5556   /**
5557    * Store selected annotation sort order for the view and repaint.
5558    */
5559   @Override
5560   protected void sortAnnotations_actionPerformed()
5561   {
5562     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5563     this.alignPanel.av
5564             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5565     alignPanel.paintAlignment(false, false);
5566   }
5567
5568   /**
5569    *
5570    * @return alignment panels in this alignment frame
5571    */
5572   public List<? extends AlignmentViewPanel> getAlignPanels()
5573   {
5574     // alignPanels is never null
5575     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5576     return alignPanels;
5577   }
5578
5579   /**
5580    * Open a new alignment window, with the cDNA associated with this (protein)
5581    * alignment, aligned as is the protein.
5582    */
5583   protected void viewAsCdna_actionPerformed()
5584   {
5585     // TODO no longer a menu action - refactor as required
5586     final AlignmentI alignment = getViewport().getAlignment();
5587     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5588     if (mappings == null)
5589     {
5590       return;
5591     }
5592     List<SequenceI> cdnaSeqs = new ArrayList<>();
5593     for (SequenceI aaSeq : alignment.getSequences())
5594     {
5595       for (AlignedCodonFrame acf : mappings)
5596       {
5597         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5598         if (dnaSeq != null)
5599         {
5600           /*
5601            * There is a cDNA mapping for this protein sequence - add to new
5602            * alignment. It will share the same dataset sequence as other mapped
5603            * cDNA (no new mappings need to be created).
5604            */
5605           final Sequence newSeq = new Sequence(dnaSeq);
5606           newSeq.setDatasetSequence(dnaSeq);
5607           cdnaSeqs.add(newSeq);
5608         }
5609       }
5610     }
5611     if (cdnaSeqs.size() == 0)
5612     {
5613       // show a warning dialog no mapped cDNA
5614       return;
5615     }
5616     AlignmentI cdna = new Alignment(
5617             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5618     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5619             AlignFrame.DEFAULT_HEIGHT);
5620     cdna.alignAs(alignment);
5621     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5622             + this.title;
5623     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5624             AlignFrame.DEFAULT_HEIGHT);
5625   }
5626
5627   /**
5628    * Set visibility of dna/protein complement view (available when shown in a
5629    * split frame).
5630    *
5631    * @param show
5632    */
5633   @Override
5634   protected void showComplement_actionPerformed(boolean show)
5635   {
5636     SplitContainerI sf = getSplitViewContainer();
5637     if (sf != null)
5638     {
5639       sf.setComplementVisible(this, show);
5640     }
5641   }
5642
5643   /**
5644    * Generate the reverse (optionally complemented) of the selected sequences,
5645    * and add them to the alignment
5646    */
5647   @Override
5648   protected void showReverse_actionPerformed(boolean complement)
5649   {
5650     AlignmentI al = null;
5651     try
5652     {
5653       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5654       al = dna.reverseCdna(complement);
5655       viewport.addAlignment(al, "");
5656       addHistoryItem(new EditCommand(
5657               MessageManager.getString("label.add_sequences"), Action.PASTE,
5658               al.getSequencesArray(), 0, al.getWidth(),
5659               viewport.getAlignment()));
5660     } catch (Exception ex)
5661     {
5662       System.err.println(ex.getMessage());
5663       return;
5664     }
5665   }
5666
5667   /**
5668    * Try to run a script in the Groovy console, having first ensured that this
5669    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5670    * be targeted at this alignment.
5671    */
5672   @Override
5673   protected void runGroovy_actionPerformed()
5674   {
5675     Jalview.setCurrentAlignFrame(this);
5676     groovy.ui.Console console = Desktop.getGroovyConsole();
5677     if (console != null)
5678     {
5679       try
5680       {
5681         console.runScript();
5682       } catch (Exception ex)
5683       {
5684         System.err.println((ex.toString()));
5685         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5686                 MessageManager.getString("label.couldnt_run_groovy_script"),
5687                 MessageManager.getString("label.groovy_support_failed"),
5688                 JvOptionPane.ERROR_MESSAGE);
5689       }
5690     }
5691     else
5692     {
5693       System.err.println("Can't run Groovy script as console not found");
5694     }
5695   }
5696
5697   /**
5698    * Hides columns containing (or not containing) a specified feature, provided
5699    * that would not leave all columns hidden
5700    *
5701    * @param featureType
5702    * @param columnsContaining
5703    * @return
5704    */
5705   public boolean hideFeatureColumns(String featureType,
5706           boolean columnsContaining)
5707   {
5708     boolean notForHiding = avc.markColumnsContainingFeatures(
5709             columnsContaining, false, false, featureType);
5710     if (notForHiding)
5711     {
5712       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5713               false, featureType))
5714       {
5715         getViewport().hideSelectedColumns();
5716         return true;
5717       }
5718     }
5719     return false;
5720   }
5721
5722   @Override
5723   protected void selectHighlightedColumns_actionPerformed(
5724           ActionEvent actionEvent)
5725   {
5726     // include key modifier check in case user selects from menu
5727     avc.markHighlightedColumns(
5728             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5729             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5730                     | ActionEvent.CTRL_MASK)) != 0);
5731   }
5732
5733   /**
5734    * Rebuilds the Colour menu, including any user-defined colours which have
5735    * been loaded either on startup or during the session
5736    */
5737   public void buildColourMenu()
5738   {
5739     colourMenu.removeAll();
5740
5741     colourMenu.add(applyToAllGroups);
5742     colourMenu.add(textColour);
5743     colourMenu.addSeparator();
5744
5745     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5746             viewport.getAlignment(), false);
5747
5748     colourMenu.add(annotationColour);
5749     bg.add(annotationColour);
5750     colourMenu.addSeparator();
5751     colourMenu.add(conservationMenuItem);
5752     colourMenu.add(modifyConservation);
5753     colourMenu.add(abovePIDThreshold);
5754     colourMenu.add(modifyPID);
5755
5756     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5757     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5758   }
5759
5760   /**
5761    * Open a dialog (if not already open) that allows the user to select and
5762    * calculate PCA or Tree analysis
5763    */
5764   protected void openTreePcaDialog()
5765   {
5766     if (alignPanel.getCalculationDialog() == null)
5767     {
5768       new CalculationChooser(AlignFrame.this);
5769     }
5770   }
5771
5772   @Override
5773   protected void loadVcf_actionPerformed()
5774   {
5775     JalviewFileChooser chooser = new JalviewFileChooser(
5776             Cache.getProperty("LAST_DIRECTORY"));
5777     chooser.setFileView(new JalviewFileView());
5778     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5779     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5780     final AlignFrame us = this;
5781     chooser.setResponseHandler(0, new Runnable()
5782     {
5783       @Override
5784       public void run()
5785       {
5786         String choice = chooser.getSelectedFile().getPath();
5787         Cache.setProperty("LAST_DIRECTORY", choice);
5788         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5789         new VCFLoader(choice).loadVCF(seqs, us);
5790       }
5791     });
5792     chooser.showOpenDialog(null);
5793
5794   }
5795
5796   private Rectangle lastFeatureSettingsBounds = null;
5797   @Override
5798   public void setFeatureSettingsGeometry(Rectangle bounds)
5799   {
5800     lastFeatureSettingsBounds = bounds;
5801   }
5802
5803   @Override
5804   public Rectangle getFeatureSettingsGeometry()
5805   {
5806     return lastFeatureSettingsBounds;
5807   }
5808 }
5809
5810 class PrintThread extends Thread
5811 {
5812   AlignmentPanel ap;
5813
5814   public PrintThread(AlignmentPanel ap)
5815   {
5816     this.ap = ap;
5817   }
5818
5819   static PageFormat pf;
5820
5821   @Override
5822   public void run()
5823   {
5824     PrinterJob printJob = PrinterJob.getPrinterJob();
5825
5826     if (pf != null)
5827     {
5828       printJob.setPrintable(ap, pf);
5829     }
5830     else
5831     {
5832       printJob.setPrintable(ap);
5833     }
5834
5835     if (printJob.printDialog())
5836     {
5837       try
5838       {
5839         printJob.print();
5840       } catch (Exception PrintException)
5841       {
5842         PrintException.printStackTrace();
5843       }
5844     }
5845   }
5846 }