src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Rectangle;
  27 import java.awt.Toolkit;
  28 import java.awt.datatransfer.Clipboard;
  29 import java.awt.datatransfer.DataFlavor;
  30 import java.awt.datatransfer.StringSelection;
  31 import java.awt.datatransfer.Transferable;
  32 import java.awt.dnd.DnDConstants;
  33 import java.awt.dnd.DropTargetDragEvent;
  34 import java.awt.dnd.DropTargetDropEvent;
  35 import java.awt.dnd.DropTargetEvent;
  36 import java.awt.dnd.DropTargetListener;
  37 import java.awt.event.ActionEvent;
  38 import java.awt.event.ActionListener;
  39 import java.awt.event.FocusAdapter;
  40 import java.awt.event.FocusEvent;
  41 import java.awt.event.ItemEvent;
  42 import java.awt.event.ItemListener;
  43 import java.awt.event.KeyAdapter;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.print.PageFormat;
  47 import java.awt.print.PrinterJob;
  48 import java.beans.PropertyChangeEvent;
  49 import java.io.File;
  50 import java.io.FileWriter;
  51 import java.io.PrintWriter;
  52 import java.net.URL;
  53 import java.util.ArrayList;
  54 import java.util.Arrays;
  55 import java.util.Deque;
  56 import java.util.Enumeration;
  57 import java.util.Hashtable;
  58 import java.util.List;
  59 import java.util.Vector;
  60
  61 import javax.swing.ButtonGroup;
  62 import javax.swing.JCheckBoxMenuItem;
  63 import javax.swing.JComponent;
  64 import javax.swing.JEditorPane;
  65 import javax.swing.JInternalFrame;
  66 import javax.swing.JLabel;
  67 import javax.swing.JLayeredPane;
  68 import javax.swing.JMenu;
  69 import javax.swing.JMenuItem;
  70 import javax.swing.JPanel;
  71 import javax.swing.JScrollPane;
  72 import javax.swing.SwingUtilities;
  73
  74 import ext.vamsas.ServiceHandle;
  75 import jalview.analysis.AlignmentSorter;
  76 import jalview.analysis.AlignmentUtils;
  77 import jalview.analysis.CrossRef;
  78 import jalview.analysis.Dna;
  79 import jalview.analysis.GeneticCodeI;
  80 import jalview.analysis.ParseProperties;
  81 import jalview.analysis.SequenceIdMatcher;
  82 import jalview.api.AlignExportSettingsI;
  83 import jalview.api.AlignViewControllerGuiI;
  84 import jalview.api.AlignViewControllerI;
  85 import jalview.api.AlignViewportI;
  86 import jalview.api.AlignmentViewPanel;
  87 import jalview.api.FeatureSettingsControllerI;
  88 import jalview.api.FeatureSettingsModelI;
  89 import jalview.api.SplitContainerI;
  90 import jalview.api.ViewStyleI;
  91 import jalview.api.analysis.SimilarityParamsI;
  92 import jalview.bin.Cache;
  93 import jalview.bin.Jalview;
  94 import jalview.commands.CommandI;
  95 import jalview.commands.EditCommand;
  96 import jalview.commands.EditCommand.Action;
  97 import jalview.commands.OrderCommand;
  98 import jalview.commands.RemoveGapColCommand;
  99 import jalview.commands.RemoveGapsCommand;
 100 import jalview.commands.SlideSequencesCommand;
 101 import jalview.commands.TrimRegionCommand;
 102 import jalview.datamodel.AlignExportSettingsAdapter;
 103 import jalview.datamodel.AlignedCodonFrame;
 104 import jalview.datamodel.Alignment;
 105 import jalview.datamodel.AlignmentAnnotation;
 106 import jalview.datamodel.AlignmentExportData;
 107 import jalview.datamodel.AlignmentI;
 108 import jalview.datamodel.AlignmentOrder;
 109 import jalview.datamodel.AlignmentView;
 110 import jalview.datamodel.ColumnSelection;
 111 import jalview.datamodel.HiddenColumns;
 112 import jalview.datamodel.PDBEntry;
 113 import jalview.datamodel.SeqCigar;
 114 import jalview.datamodel.Sequence;
 115 import jalview.datamodel.SequenceGroup;
 116 import jalview.datamodel.SequenceI;
 117 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 118 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 119 import jalview.io.AlignmentProperties;
 120 import jalview.io.AnnotationFile;
 121 import jalview.io.BackupFiles;
 122 import jalview.io.BioJsHTMLOutput;
 123 import jalview.io.DataSourceType;
 124 import jalview.io.FileFormat;
 125 import jalview.io.FileFormatI;
 126 import jalview.io.FileFormats;
 127 import jalview.io.FileLoader;
 128 import jalview.io.FileParse;
 129 import jalview.io.FormatAdapter;
 130 import jalview.io.HtmlSvgOutput;
 131 import jalview.io.IdentifyFile;
 132 import jalview.io.JPredFile;
 133 import jalview.io.JalviewFileChooser;
 134 import jalview.io.JalviewFileView;
 135 import jalview.io.JnetAnnotationMaker;
 136 import jalview.io.NewickFile;
 137 import jalview.io.ScoreMatrixFile;
 138 import jalview.io.TCoffeeScoreFile;
 139 import jalview.io.vcf.VCFLoader;
 140 import jalview.jbgui.GAlignFrame;
 141 import jalview.project.Jalview2XML;
 142 import jalview.schemes.ColourSchemeI;
 143 import jalview.schemes.ColourSchemes;
 144 import jalview.schemes.ResidueColourScheme;
 145 import jalview.schemes.TCoffeeColourScheme;
 146 import jalview.util.ImageMaker.TYPE;
 147 import jalview.util.MessageManager;
 148 import jalview.util.Platform;
 149 import jalview.viewmodel.AlignmentViewport;
 150 import jalview.viewmodel.ViewportRanges;
 151 import jalview.ws.DBRefFetcher;
 152 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 153 import jalview.ws.jws1.Discoverer;
 154 import jalview.ws.jws2.Jws2Discoverer;
 155 import jalview.ws.jws2.jabaws2.Jws2Instance;
 156 import jalview.ws.seqfetcher.DbSourceProxy;
 157
 158 /**
 159  * DOCUMENT ME!
 160  *
 161  * @author $author$
 162  * @version $Revision$
 163  */
 164 @SuppressWarnings("serial")
 165 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 166         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 167 {
 168
 169   public static final int DEFAULT_WIDTH = 700;
 170
 171   public static final int DEFAULT_HEIGHT = 500;
 172
 173   /*
 174    * The currently displayed panel (selected tabbed view if more than one)
 175    */
 176   public AlignmentPanel alignPanel;
 177
 178   AlignViewport viewport;
 179
 180   public AlignViewControllerI avc;
 181
 182   List<AlignmentPanel> alignPanels = new ArrayList<>();
 183
 184   /**
 185    * Last format used to load or save alignments in this window
 186    */
 187   FileFormatI currentFileFormat = null;
 188
 189   /**
 190    * Current filename for this alignment
 191    */
 192   String fileName = null;
 193
 194   File fileObject;
 195
 196   /**
 197    * Creates a new AlignFrame object with specific width and height.
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    */
 203   public AlignFrame(AlignmentI al, int width, int height)
 204   {
 205     this(al, null, width, height);
 206   }
 207
 208   /**
 209    * Creates a new AlignFrame object with specific width, height and
 210    * sequenceSetId
 211    *
 212    * @param al
 213    * @param width
 214    * @param height
 215    * @param sequenceSetId
 216    */
 217   public AlignFrame(AlignmentI al, int width, int height,
 218           String sequenceSetId)
 219   {
 220     this(al, null, width, height, sequenceSetId);
 221   }
 222
 223   /**
 224    * Creates a new AlignFrame object with specific width, height and
 225    * sequenceSetId
 226    *
 227    * @param al
 228    * @param width
 229    * @param height
 230    * @param sequenceSetId
 231    * @param viewId
 232    */
 233   public AlignFrame(AlignmentI al, int width, int height,
 234           String sequenceSetId, String viewId)
 235   {
 236     this(al, null, width, height, sequenceSetId, viewId);
 237   }
 238
 239   /**
 240    * new alignment window with hidden columns
 241    *
 242    * @param al
 243    *          AlignmentI
 244    * @param hiddenColumns
 245    *          ColumnSelection or null
 246    * @param width
 247    *          Width of alignment frame
 248    * @param height
 249    *          height of frame.
 250    */
 251   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 252           int height)
 253   {
 254     this(al, hiddenColumns, width, height, null);
 255   }
 256
 257   /**
 258    * Create alignment frame for al with hiddenColumns, a specific width and
 259    * height, and specific sequenceId
 260    *
 261    * @param al
 262    * @param hiddenColumns
 263    * @param width
 264    * @param height
 265    * @param sequenceSetId
 266    *          (may be null)
 267    */
 268   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 269           int height, String sequenceSetId)
 270   {
 271     this(al, hiddenColumns, width, height, sequenceSetId, null);
 272   }
 273
 274   /**
 275    * Create alignment frame for al with hiddenColumns, a specific width and
 276    * height, and specific sequenceId
 277    *
 278    * @param al
 279    * @param hiddenColumns
 280    * @param width
 281    * @param height
 282    * @param sequenceSetId
 283    *          (may be null)
 284    * @param viewId
 285    *          (may be null)
 286    */
 287   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 288           int height, String sequenceSetId, String viewId)
 289   {
 290     setSize(width, height);
 291
 292     if (al.getDataset() == null)
 293     {
 294       al.setDataset(null);
 295     }
 296
 297     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 298
 299     alignPanel = new AlignmentPanel(this, viewport);
 300
 301     addAlignmentPanel(alignPanel, true);
 302     init();
 303   }
 304
 305   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 306           HiddenColumns hiddenColumns, int width, int height)
 307   {
 308     setSize(width, height);
 309
 310     if (al.getDataset() == null)
 311     {
 312       al.setDataset(null);
 313     }
 314
 315     viewport = new AlignViewport(al, hiddenColumns);
 316
 317     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 318     {
 319       viewport.hideSequence(hiddenSeqs);
 320     }
 321     alignPanel = new AlignmentPanel(this, viewport);
 322     addAlignmentPanel(alignPanel, true);
 323     init();
 324   }
 325
 326   /**
 327    * Make a new AlignFrame from existing alignmentPanels
 328    *
 329    * @param ap
 330    *          AlignmentPanel
 331    * @param av
 332    *          AlignViewport
 333    */
 334   public AlignFrame(AlignmentPanel ap)
 335   {
 336     viewport = ap.av;
 337     alignPanel = ap;
 338     addAlignmentPanel(ap, false);
 339     init();
 340   }
 341
 342   /**
 343    * initalise the alignframe from the underlying viewport data and the
 344    * configurations
 345    */
 346   void init()
 347   {
 348 //        setBackground(Color.white); // BH 2019
 349
 350     if (!Jalview.isHeadlessMode())
 351     {
 352       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 353     }
 354
 355     avc = new jalview.controller.AlignViewController(this, viewport,
 356             alignPanel);
 357     if (viewport.getAlignmentConservationAnnotation() == null)
 358     {
 359       // BLOSUM62Colour.setEnabled(false);
 360       conservationMenuItem.setEnabled(false);
 361       modifyConservation.setEnabled(false);
 362       // PIDColour.setEnabled(false);
 363       // abovePIDThreshold.setEnabled(false);
 364       // modifyPID.setEnabled(false);
 365     }
 366
 367     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 368             "No sort");
 369
 370     if (sortby.equals("Id"))
 371     {
 372       sortIDMenuItem_actionPerformed(null);
 373     }
 374     else if (sortby.equals("Pairwise Identity"))
 375     {
 376       sortPairwiseMenuItem_actionPerformed(null);
 377     }
 378
 379     this.alignPanel.av
 380             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 381
 382     setMenusFromViewport(viewport);
 383     buildSortByAnnotationScoresMenu();
 384     calculateTree.addActionListener(new ActionListener()
 385     {
 386
 387       @Override
 388       public void actionPerformed(ActionEvent e)
 389       {
 390         openTreePcaDialog();
 391       }
 392     });
 393     buildColourMenu();
 394
 395     if (Desktop.desktop != null)
 396     {
 397       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 398       if (!Platform.isJS())
 399       {
 400         addServiceListeners();
 401       }
 402       setGUINucleotide();
 403     }
 404
 405     if (viewport.getWrapAlignment())
 406     {
 407       wrapMenuItem_actionPerformed(null);
 408     }
 409
 410     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 411     {
 412       this.overviewMenuItem_actionPerformed(null);
 413     }
 414
 415     addKeyListener();
 416
 417     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 418     final List<AlignmentPanel> origview = new ArrayList<>();
 419     final String menuLabel = MessageManager
 420             .getString("label.copy_format_from");
 421     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 422             new ViewSetProvider()
 423             {
 424
 425               @Override
 426               public AlignmentPanel[] getAllAlignmentPanels()
 427               {
 428                 origview.clear();
 429                 origview.add(alignPanel);
 430                 // make an array of all alignment panels except for this one
 431                 List<AlignmentPanel> aps = new ArrayList<>(
 432                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 433                 aps.remove(AlignFrame.this.alignPanel);
 434                 return aps.toArray(new AlignmentPanel[aps.size()]);
 435               }
 436             }, selviews, new ItemListener()
 437             {
 438
 439               @Override
 440               public void itemStateChanged(ItemEvent e)
 441               {
 442                 if (origview.size() > 0)
 443                 {
 444                   final AlignmentPanel ap = origview.get(0);
 445
 446                   /*
 447                    * Copy the ViewStyle of the selected panel to 'this one'.
 448                    * Don't change value of 'scaleProteinAsCdna' unless copying
 449                    * from a SplitFrame.
 450                    */
 451                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 452                           .getViewStyle();
 453                   boolean fromSplitFrame = selviews.get(0)
 454                           .getAlignViewport().getCodingComplement() != null;
 455                   if (!fromSplitFrame)
 456                   {
 457                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 458                             .getViewStyle().isScaleProteinAsCdna());
 459                   }
 460                   ap.getAlignViewport().setViewStyle(vs);
 461
 462                   /*
 463                    * Also rescale ViewStyle of SplitFrame complement if there is
 464                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 465                    * the whole ViewStyle (allow cDNA protein to have different
 466                    * fonts)
 467                    */
 468                   AlignViewportI complement = ap.getAlignViewport()
 469                           .getCodingComplement();
 470                   if (complement != null && vs.isScaleProteinAsCdna())
 471                   {
 472                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 473                     ((SplitFrame) af.getSplitViewContainer())
 474                             .adjustLayout();
 475                     af.setMenusForViewport();
 476                   }
 477
 478                   ap.updateLayout();
 479                   ap.setSelected(true);
 480                   ap.alignFrame.setMenusForViewport();
 481
 482                 }
 483               }
 484             });
 485     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 486             .indexOf("devel") > -1
 487             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 488                     .indexOf("test") > -1)
 489     {
 490       formatMenu.add(vsel);
 491     }
 492     addFocusListener(new FocusAdapter()
 493     {
 494       @Override
 495       public void focusGained(FocusEvent e)
 496       {
 497         Jalview.setCurrentAlignFrame(AlignFrame.this);
 498       }
 499     });
 500
 501   }
 502
 503   /**
 504    * Change the filename and format for the alignment, and enable the 'reload'
 505    * button functionality.
 506    *
 507    * @param file
 508    *          valid filename
 509    * @param format
 510    *          format of file
 511    */
 512   public void setFileName(String file, FileFormatI format)
 513   {
 514     fileName = file;
 515     setFileFormat(format);
 516     reload.setEnabled(true);
 517   }
 518
 519   /**
 520    * JavaScript will have this, maybe others. More dependable than a file name
 521    * and maintains a reference to the actual bytes loaded.
 522    *
 523    * @param file
 524    */
 525   public void setFileObject(File file)
 526   {
 527     this.fileObject = file;
 528   }
 529
 530   /**
 531    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 532    * events
 533    */
 534   void addKeyListener()
 535   {
 536     addKeyListener(new KeyAdapter()
 537     {
 538       @Override
 539       public void keyPressed(KeyEvent evt)
 540       {
 541         if (viewport.cursorMode
 542                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 543                         && evt.getKeyCode() <= KeyEvent.VK_9)
 544                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 545                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 546                 && Character.isDigit(evt.getKeyChar()))
 547         {
 548           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 549         }
 550
 551         switch (evt.getKeyCode())
 552         {
 553
 554         case 27: // escape key
 555           deselectAllSequenceMenuItem_actionPerformed(null);
 556
 557           break;
 558
 559         case KeyEvent.VK_DOWN:
 560           if (evt.isAltDown() || !viewport.cursorMode)
 561           {
 562             moveSelectedSequences(false);
 563           }
 564           if (viewport.cursorMode)
 565           {
 566             alignPanel.getSeqPanel().moveCursor(0, 1);
 567           }
 568           break;
 569
 570         case KeyEvent.VK_UP:
 571           if (evt.isAltDown() || !viewport.cursorMode)
 572           {
 573             moveSelectedSequences(true);
 574           }
 575           if (viewport.cursorMode)
 576           {
 577             alignPanel.getSeqPanel().moveCursor(0, -1);
 578           }
 579
 580           break;
 581
 582         case KeyEvent.VK_LEFT:
 583           if (evt.isAltDown() || !viewport.cursorMode)
 584           {
 585             slideSequences(false,
 586                     alignPanel.getSeqPanel().getKeyboardNo1());
 587           }
 588           else
 589           {
 590             alignPanel.getSeqPanel().moveCursor(-1, 0);
 591           }
 592
 593           break;
 594
 595         case KeyEvent.VK_RIGHT:
 596           if (evt.isAltDown() || !viewport.cursorMode)
 597           {
 598             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 599           }
 600           else
 601           {
 602             alignPanel.getSeqPanel().moveCursor(1, 0);
 603           }
 604           break;
 605
 606         case KeyEvent.VK_SPACE:
 607           if (viewport.cursorMode)
 608           {
 609             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 610                     || evt.isShiftDown() || evt.isAltDown());
 611           }
 612           break;
 613
 614         // case KeyEvent.VK_A:
 615         // if (viewport.cursorMode)
 616         // {
 617         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 618         // //System.out.println("A");
 619         // }
 620         // break;
 621         /*
 622          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 623          * System.out.println("closing bracket"); } break;
 624          */
 625         case KeyEvent.VK_DELETE:
 626         case KeyEvent.VK_BACK_SPACE:
 627           if (!viewport.cursorMode)
 628           {
 629             cut_actionPerformed();
 630           }
 631           else
 632           {
 633             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 634                     || evt.isShiftDown() || evt.isAltDown());
 635           }
 636
 637           break;
 638
 639         case KeyEvent.VK_S:
 640           if (viewport.cursorMode)
 641           {
 642             alignPanel.getSeqPanel().setCursorRow();
 643           }
 644           break;
 645         case KeyEvent.VK_C:
 646           if (viewport.cursorMode && !evt.isControlDown())
 647           {
 648             alignPanel.getSeqPanel().setCursorColumn();
 649           }
 650           break;
 651         case KeyEvent.VK_P:
 652           if (viewport.cursorMode)
 653           {
 654             alignPanel.getSeqPanel().setCursorPosition();
 655           }
 656           break;
 657
 658         case KeyEvent.VK_ENTER:
 659         case KeyEvent.VK_COMMA:
 660           if (viewport.cursorMode)
 661           {
 662             alignPanel.getSeqPanel().setCursorRowAndColumn();
 663           }
 664           break;
 665
 666         case KeyEvent.VK_Q:
 667           if (viewport.cursorMode)
 668           {
 669             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 670           }
 671           break;
 672         case KeyEvent.VK_M:
 673           if (viewport.cursorMode)
 674           {
 675             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 676           }
 677           break;
 678
 679         case KeyEvent.VK_F2:
 680           viewport.cursorMode = !viewport.cursorMode;
 681           setStatus(MessageManager
 682                   .formatMessage("label.keyboard_editing_mode", new String[]
 683                   { (viewport.cursorMode ? "on" : "off") }));
 684           if (viewport.cursorMode)
 685           {
 686             ViewportRanges ranges = viewport.getRanges();
 687             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 688                     .getStartRes();
 689             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 690                     .getStartSeq();
 691           }
 692           alignPanel.getSeqPanel().seqCanvas.repaint();
 693           break;
 694
 695         case KeyEvent.VK_F1:
 696           try
 697           {
 698             Help.showHelpWindow();
 699           } catch (Exception ex)
 700           {
 701             ex.printStackTrace();
 702           }
 703           break;
 704         case KeyEvent.VK_H:
 705         {
 706           boolean toggleSeqs = !evt.isControlDown();
 707           boolean toggleCols = !evt.isShiftDown();
 708           toggleHiddenRegions(toggleSeqs, toggleCols);
 709           break;
 710         }
 711         case KeyEvent.VK_B:
 712         {
 713           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 714           boolean modifyExisting = true; // always modify, don't clear
 715                                          // evt.isShiftDown();
 716           boolean invertHighlighted = evt.isAltDown();
 717           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 718                   toggleSel);
 719           break;
 720         }
 721         case KeyEvent.VK_PAGE_UP:
 722           viewport.getRanges().pageUp();
 723           break;
 724         case KeyEvent.VK_PAGE_DOWN:
 725           viewport.getRanges().pageDown();
 726           break;
 727         }
 728       }
 729
 730       @Override
 731       public void keyReleased(KeyEvent evt)
 732       {
 733         switch (evt.getKeyCode())
 734         {
 735         case KeyEvent.VK_LEFT:
 736           if (evt.isAltDown() || !viewport.cursorMode)
 737           {
 738             viewport.firePropertyChange("alignment", null,
 739                     viewport.getAlignment().getSequences());
 740           }
 741           break;
 742
 743         case KeyEvent.VK_RIGHT:
 744           if (evt.isAltDown() || !viewport.cursorMode)
 745           {
 746             viewport.firePropertyChange("alignment", null,
 747                     viewport.getAlignment().getSequences());
 748           }
 749           break;
 750         }
 751       }
 752     });
 753   }
 754
 755   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 756   {
 757     ap.alignFrame = this;
 758     avc = new jalview.controller.AlignViewController(this, viewport,
 759             alignPanel);
 760
 761     alignPanels.add(ap);
 762
 763     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 764
 765     int aSize = alignPanels.size();
 766
 767     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 768
 769     if (aSize == 1 && ap.av.getViewName() == null)
 770     {
 771       this.getContentPane().add(ap, BorderLayout.CENTER);
 772     }
 773     else
 774     {
 775       if (aSize == 2)
 776       {
 777         setInitialTabVisible();
 778       }
 779
 780       expandViews.setEnabled(true);
 781       gatherViews.setEnabled(true);
 782       tabbedPane.addTab(ap.av.getViewName(), ap);
 783
 784       ap.setVisible(false);
 785     }
 786
 787     if (newPanel)
 788     {
 789       if (ap.av.isPadGaps())
 790       {
 791         ap.av.getAlignment().padGaps();
 792       }
 793       ap.av.updateConservation(ap);
 794       ap.av.updateConsensus(ap);
 795       ap.av.updateStrucConsensus(ap);
 796     }
 797   }
 798
 799   public void setInitialTabVisible()
 800   {
 801     expandViews.setEnabled(true);
 802     gatherViews.setEnabled(true);
 803     tabbedPane.setVisible(true);
 804     AlignmentPanel first = alignPanels.get(0);
 805     tabbedPane.addTab(first.av.getViewName(), first);
 806     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 807   }
 808
 809   public AlignViewport getViewport()
 810   {
 811     return viewport;
 812   }
 813
 814   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 815   private void addServiceListeners()
 816   {
 817     final java.beans.PropertyChangeListener thisListener;
 818     Desktop.instance.addJalviewPropertyChangeListener("services",
 819             thisListener = new java.beans.PropertyChangeListener()
 820             {
 821               @Override
 822               public void propertyChange(PropertyChangeEvent evt)
 823               {
 824                 // // System.out.println("Discoverer property change.");
 825                 // if (evt.getPropertyName().equals("services"))
 826                 {
 827                   SwingUtilities.invokeLater(new Runnable()
 828                   {
 829
 830                     @Override
 831                     public void run()
 832                     {
 833                       System.err.println(
 834                               "Rebuild WS Menu for service change");
 835                       BuildWebServiceMenu();
 836                     }
 837
 838                   });
 839                 }
 840               }
 841             });
 842     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 843     {
 844       @Override
 845       public void internalFrameClosed(
 846               javax.swing.event.InternalFrameEvent evt)
 847       {
 848         // System.out.println("deregistering discoverer listener");
 849         Desktop.instance.removeJalviewPropertyChangeListener("services",
 850                 thisListener);
 851         closeMenuItem_actionPerformed(true);
 852       }
 853     });
 854     // Finally, build the menu once to get current service state
 855     new Thread(new Runnable()
 856     {
 857       @Override
 858       public void run()
 859       {
 860         BuildWebServiceMenu();
 861       }
 862     }).start();
 863   }
 864
 865   /**
 866    * Configure menu items that vary according to whether the alignment is
 867    * nucleotide or protein
 868    */
 869   public void setGUINucleotide()
 870   {
 871     AlignmentI al = getViewport().getAlignment();
 872     boolean nucleotide = al.isNucleotide();
 873
 874     loadVcf.setVisible(nucleotide);
 875     showTranslation.setVisible(nucleotide);
 876     showReverse.setVisible(nucleotide);
 877     showReverseComplement.setVisible(nucleotide);
 878     conservationMenuItem.setEnabled(!nucleotide);
 879     modifyConservation
 880             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 881     showGroupConservation.setEnabled(!nucleotide);
 882
 883     showComplementMenuItem
 884             .setText(nucleotide ? MessageManager.getString("label.protein")
 885                     : MessageManager.getString("label.nucleotide"));
 886   }
 887
 888   /**
 889    * set up menus for the current viewport. This may be called after any
 890    * operation that affects the data in the current view (selection changed,
 891    * etc) to update the menus to reflect the new state.
 892    */
 893   @Override
 894   public void setMenusForViewport()
 895   {
 896     setMenusFromViewport(viewport);
 897   }
 898
 899   /**
 900    * Need to call this method when tabs are selected for multiple views, or when
 901    * loading from Jalview2XML.java
 902    *
 903    * @param av
 904    *          AlignViewport
 905    */
 906   public void setMenusFromViewport(AlignViewport av)
 907   {
 908     padGapsMenuitem.setSelected(av.isPadGaps());
 909     colourTextMenuItem.setSelected(av.isShowColourText());
 910     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 911     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 912     conservationMenuItem.setSelected(av.getConservationSelected());
 913     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 914     seqLimits.setSelected(av.getShowJVSuffix());
 915     idRightAlign.setSelected(av.isRightAlignIds());
 916     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 917     renderGapsMenuItem.setSelected(av.isRenderGaps());
 918     wrapMenuItem.setSelected(av.getWrapAlignment());
 919     scaleAbove.setVisible(av.getWrapAlignment());
 920     scaleLeft.setVisible(av.getWrapAlignment());
 921     scaleRight.setVisible(av.getWrapAlignment());
 922     annotationPanelMenuItem.setState(av.isShowAnnotation());
 923     /*
 924      * Show/hide annotations only enabled if annotation panel is shown
 925      */
 926     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 927     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 928     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 929     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 930     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 931     viewTextMenuItem.setSelected(av.getShowText());
 932     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 933     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 934     showGroupConservation.setSelected(av.isShowGroupConservation());
 935     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 936     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 937     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 938
 939     ColourMenuHelper.setColourSelected(colourMenu,
 940             av.getGlobalColourScheme());
 941
 942     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 943     hiddenMarkers.setState(av.getShowHiddenMarkers());
 944     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 945     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 946     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 947     autoCalculate.setSelected(av.autoCalculateConsensus);
 948     sortByTree.setSelected(av.sortByTree);
 949     listenToViewSelections.setSelected(av.followSelection);
 950
 951     showProducts.setEnabled(canShowProducts());
 952     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 953
 954     updateEditMenuBar();
 955   }
 956
 957   /**
 958    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 959    *
 960    * @param b
 961    */
 962   public void setGroovyEnabled(boolean b)
 963   {
 964     runGroovy.setEnabled(b);
 965   }
 966
 967   private IProgressIndicator progressBar;
 968
 969   /*
 970    * (non-Javadoc)
 971    *
 972    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 973    */
 974   @Override
 975   public void setProgressBar(String message, long id)
 976   {
 977     progressBar.setProgressBar(message, id);
 978   }
 979
 980   @Override
 981   public void registerHandler(final long id,
 982           final IProgressIndicatorHandler handler)
 983   {
 984     progressBar.registerHandler(id, handler);
 985   }
 986
 987   /**
 988    *
 989    * @return true if any progress bars are still active
 990    */
 991   @Override
 992   public boolean operationInProgress()
 993   {
 994     return progressBar.operationInProgress();
 995   }
 996
 997   /**
 998    * Sets the text of the status bar. Note that setting a null or empty value
 999    * will cause the status bar to be hidden, with possibly undesirable flicker
1000    * of the screen layout.
1001    */
1002   @Override
1003   public void setStatus(String text)
1004   {
1005     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1006   }
1007
1008   /*
1009    * Added so Castor Mapping file can obtain Jalview Version
1010    */
1011   public String getVersion()
1012   {
1013     return jalview.bin.Cache.getProperty("VERSION");
1014   }
1015
1016   public FeatureRenderer getFeatureRenderer()
1017   {
1018     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1019   }
1020
1021   @Override
1022   public void fetchSequence_actionPerformed()
1023   {
1024     new SequenceFetcher(this);
1025   }
1026
1027   @Override
1028   public void addFromFile_actionPerformed(ActionEvent e)
1029   {
1030     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1031   }
1032
1033   @Override
1034   public void reload_actionPerformed(ActionEvent e)
1035   {
1036     if (fileName != null)
1037     {
1038       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1039       // originating file's format
1040       // TODO: work out how to recover feature settings for correct view(s) when
1041       // file is reloaded.
1042       if (FileFormat.Jalview.equals(currentFileFormat))
1043       {
1044         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1045         for (int i = 0; i < frames.length; i++)
1046         {
1047           if (frames[i] instanceof AlignFrame && frames[i] != this
1048                   && ((AlignFrame) frames[i]).fileName != null
1049                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1050           {
1051             try
1052             {
1053               frames[i].setSelected(true);
1054               Desktop.instance.closeAssociatedWindows();
1055             } catch (java.beans.PropertyVetoException ex)
1056             {
1057             }
1058           }
1059
1060         }
1061         Desktop.instance.closeAssociatedWindows();
1062
1063         FileLoader loader = new FileLoader();
1064         DataSourceType protocol = fileName.startsWith("http:")
1065                 ? DataSourceType.URL
1066                 : DataSourceType.FILE;
1067         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1068       }
1069       else
1070       {
1071         Rectangle bounds = this.getBounds();
1072
1073         FileLoader loader = new FileLoader();
1074
1075         AlignFrame newframe = null;
1076
1077         if (fileObject == null)
1078         {
1079
1080           DataSourceType protocol = (fileName.startsWith("http:")
1081                   ? DataSourceType.URL
1082                   : DataSourceType.FILE);
1083           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1084                   currentFileFormat);
1085         }
1086         else
1087         {
1088           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1089                   DataSourceType.FILE, currentFileFormat);
1090         }
1091
1092         newframe.setBounds(bounds);
1093         if (featureSettings != null && featureSettings.isShowing())
1094         {
1095           final Rectangle fspos = featureSettings.frame.getBounds();
1096           // TODO: need a 'show feature settings' function that takes bounds -
1097           // need to refactor Desktop.addFrame
1098           newframe.featureSettings_actionPerformed(null);
1099           final FeatureSettings nfs = newframe.featureSettings;
1100           SwingUtilities.invokeLater(new Runnable()
1101           {
1102             @Override
1103             public void run()
1104             {
1105               nfs.frame.setBounds(fspos);
1106             }
1107           });
1108           this.featureSettings.close();
1109           this.featureSettings = null;
1110         }
1111         this.closeMenuItem_actionPerformed(true);
1112       }
1113     }
1114   }
1115
1116   @Override
1117   public void addFromText_actionPerformed(ActionEvent e)
1118   {
1119     Desktop.instance
1120             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1121   }
1122
1123   @Override
1124   public void addFromURL_actionPerformed(ActionEvent e)
1125   {
1126     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1127   }
1128
1129   @Override
1130   public void save_actionPerformed(ActionEvent e)
1131   {
1132     if (fileName == null || (currentFileFormat == null)
1133             || fileName.startsWith("http"))
1134     {
1135       saveAs_actionPerformed();
1136     }
1137     else
1138     {
1139       saveAlignment(fileName, currentFileFormat);
1140     }
1141   }
1142
1143   /**
1144    * Saves the alignment to a file with a name chosen by the user, if necessary
1145    * warning if a file would be overwritten
1146    */
1147   @Override
1148   public void saveAs_actionPerformed()
1149   {
1150     String format = currentFileFormat == null ? null
1151             : currentFileFormat.getName();
1152     JalviewFileChooser chooser = JalviewFileChooser
1153             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1154
1155     chooser.setFileView(new JalviewFileView());
1156     chooser.setDialogTitle(
1157             MessageManager.getString("label.save_alignment_to_file"));
1158     chooser.setToolTipText(MessageManager.getString("action.save"));
1159
1160     int value = chooser.showSaveDialog(this);
1161
1162     if (value != JalviewFileChooser.APPROVE_OPTION)
1163     {
1164       return;
1165     }
1166     currentFileFormat = chooser.getSelectedFormat();
1167     // todo is this (2005) test now obsolete - value is never null?
1168     while (currentFileFormat == null)
1169     {
1170       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1171               MessageManager
1172                       .getString("label.select_file_format_before_saving"),
1173               MessageManager.getString("label.file_format_not_specified"),
1174               JvOptionPane.WARNING_MESSAGE);
1175       currentFileFormat = chooser.getSelectedFormat();
1176       value = chooser.showSaveDialog(this);
1177       if (value != JalviewFileChooser.APPROVE_OPTION)
1178       {
1179         return;
1180       }
1181     }
1182
1183     fileName = chooser.getSelectedFile().getPath();
1184
1185     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1186     Cache.setProperty("LAST_DIRECTORY", fileName);
1187     saveAlignment(fileName, currentFileFormat);
1188   }
1189
1190   boolean lastSaveSuccessful = false;
1191
1192   FileFormatI lastFormatSaved;
1193
1194   String lastFilenameSaved;
1195
1196   /**
1197    * Raise a dialog or status message for the last call to saveAlignment.
1198    *
1199    * @return true if last call to saveAlignment(file, format) was successful.
1200    */
1201   public boolean isSaveAlignmentSuccessful()
1202   {
1203
1204     if (!lastSaveSuccessful)
1205     {
1206       JvOptionPane.showInternalMessageDialog(this, MessageManager
1207               .formatMessage("label.couldnt_save_file", new Object[]
1208               { lastFilenameSaved }),
1209               MessageManager.getString("label.error_saving_file"),
1210               JvOptionPane.WARNING_MESSAGE);
1211     }
1212     else
1213     {
1214
1215       setStatus(MessageManager.formatMessage(
1216               "label.successfully_saved_to_file_in_format", new Object[]
1217               { lastFilenameSaved, lastFormatSaved }));
1218
1219     }
1220     return lastSaveSuccessful;
1221   }
1222
1223   /**
1224    * Saves the alignment to the specified file path, in the specified format,
1225    * which may be an alignment format, or Jalview project format. If the
1226    * alignment has hidden regions, or the format is one capable of including
1227    * non-sequence data (features, annotations, groups), then the user may be
1228    * prompted to specify what to include in the output.
1229    *
1230    * @param file
1231    * @param format
1232    */
1233   public void saveAlignment(String file, FileFormatI format)
1234   {
1235     lastSaveSuccessful = true;
1236     lastFilenameSaved = file;
1237     lastFormatSaved = format;
1238
1239     if (FileFormat.Jalview.equals(format))
1240     {
1241       String shortName = title;
1242       if (shortName.indexOf(File.separatorChar) > -1)
1243       {
1244         shortName = shortName.substring(
1245                 shortName.lastIndexOf(File.separatorChar) + 1);
1246       }
1247       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
1248
1249       statusBar.setText(MessageManager.formatMessage(
1250               "label.successfully_saved_to_file_in_format", new Object[]
1251               { fileName, format }));
1252
1253       return;
1254     }
1255
1256     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1257     Runnable cancelAction = new Runnable()
1258     {
1259       @Override
1260       public void run()
1261       {
1262         lastSaveSuccessful = false;
1263       }
1264     };
1265     Runnable outputAction = new Runnable()
1266     {
1267       @Override
1268       public void run()
1269       {
1270         // todo defer this to inside formatSequences (or later)
1271         AlignmentExportData exportData = viewport
1272                 .getAlignExportData(options);
1273         String output = new FormatAdapter(alignPanel, options)
1274                 .formatSequences(format, exportData.getAlignment(),
1275                         exportData.getOmitHidden(),
1276                         exportData.getStartEndPostions(),
1277                         viewport.getAlignment().getHiddenColumns());
1278         if (output == null)
1279         {
1280           lastSaveSuccessful = false;
1281         }
1282         else
1283         {
1284           // create backupfiles object and get new temp filename destination
1285           boolean doBackup = BackupFiles.getEnabled();
1286           BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1287           try
1288           {
1289             String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
1290                         PrintWriter out = new PrintWriter(
1291                     new FileWriter(tempFilePath));
1292
1293             out.print(output);
1294             out.close();
1295             AlignFrame.this.setTitle(file);
1296             statusBar.setText(MessageManager.formatMessage(
1297                   "label.successfully_saved_to_file_in_format", new Object[]
1298                   { fileName, format.getName() }));
1299             lastSaveSuccessful = true;
1300           } catch (Exception ex)
1301           {
1302             lastSaveSuccessful = false;
1303             ex.printStackTrace();
1304           }
1305
1306           if (doBackup)
1307           {
1308             backupfiles.setWriteSuccess(lastSaveSuccessful);
1309             // do the backup file roll and rename the temp file to actual file
1310             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1311           }
1312         }
1313       }
1314     };
1315
1316     /*
1317      * show dialog with export options if applicable; else just do it
1318      */
1319     if (AlignExportOptions.isNeeded(viewport, format))
1320     {
1321       AlignExportOptions choices = new AlignExportOptions(
1322               alignPanel.getAlignViewport(), format, options);
1323       choices.setResponseAction(0, outputAction);
1324       choices.setResponseAction(1, cancelAction);
1325       choices.showDialog();
1326     }
1327     else
1328     {
1329       outputAction.run();
1330     }
1331   }
1332
1333   /**
1334    * Outputs the alignment to textbox in the requested format, if necessary
1335    * first prompting the user for whether to include hidden regions or
1336    * non-sequence data
1337    *
1338    * @param fileFormatName
1339    */
1340   @Override
1341   protected void outputText_actionPerformed(String fileFormatName)
1342   {
1343     FileFormatI fileFormat = FileFormats.getInstance()
1344             .forName(fileFormatName);
1345     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1346     Runnable outputAction = new Runnable()
1347     {
1348       @Override
1349       public void run()
1350       {
1351         // todo defer this to inside formatSequences (or later)
1352         AlignmentExportData exportData = viewport
1353                 .getAlignExportData(options);
1354         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1355         cap.setForInput(null);
1356         try
1357         {
1358           FileFormatI format = fileFormat;
1359           cap.setText(new FormatAdapter(alignPanel, options)
1360                   .formatSequences(format, exportData.getAlignment(),
1361                           exportData.getOmitHidden(),
1362                           exportData.getStartEndPostions(),
1363                           viewport.getAlignment().getHiddenColumns()));
1364           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1365                   "label.alignment_output_command", new Object[]
1366                   { fileFormat.getName() }), 600, 500);
1367         } catch (OutOfMemoryError oom)
1368         {
1369           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1370                   oom);
1371           cap.dispose();
1372         }
1373       }
1374     };
1375
1376     /*
1377      * show dialog with export options if applicable; else just do it
1378      */
1379     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1380     {
1381       AlignExportOptions choices = new AlignExportOptions(
1382               alignPanel.getAlignViewport(), fileFormat, options);
1383       choices.setResponseAction(0, outputAction);
1384       choices.showDialog();
1385     }
1386     else
1387     {
1388       outputAction.run();
1389     }
1390   }
1391
1392   /**
1393    * DOCUMENT ME!
1394    *
1395    * @param e
1396    *          DOCUMENT ME!
1397    */
1398   @Override
1399   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1400   {
1401     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1402     htmlSVG.exportHTML(null);
1403   }
1404
1405   @Override
1406   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1407   {
1408     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1409     bjs.exportHTML(null);
1410   }
1411
1412   public void createImageMap(File file, String image)
1413   {
1414     alignPanel.makePNGImageMap(file, image);
1415   }
1416
1417   /**
1418    * Creates a PNG image of the alignment and writes it to the given file. If
1419    * the file is null, the user is prompted to choose a file.
1420    *
1421    * @param f
1422    */
1423   @Override
1424   public void createPNG(File f)
1425   {
1426     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1427   }
1428
1429   /**
1430    * Creates an EPS image of the alignment and writes it to the given file. If
1431    * the file is null, the user is prompted to choose a file.
1432    *
1433    * @param f
1434    */
1435   @Override
1436   public void createEPS(File f)
1437   {
1438     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1439   }
1440
1441   /**
1442    * Creates an SVG image of the alignment and writes it to the given file. If
1443    * the file is null, the user is prompted to choose a file.
1444    *
1445    * @param f
1446    */
1447   @Override
1448   public void createSVG(File f)
1449   {
1450     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1451   }
1452
1453   @Override
1454   public void pageSetup_actionPerformed(ActionEvent e)
1455   {
1456     PrinterJob printJob = PrinterJob.getPrinterJob();
1457     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1458   }
1459
1460   /**
1461    * DOCUMENT ME!
1462    *
1463    * @param e
1464    *          DOCUMENT ME!
1465    */
1466   @Override
1467   public void printMenuItem_actionPerformed(ActionEvent e)
1468   {
1469     // Putting in a thread avoids Swing painting problems
1470     PrintThread thread = new PrintThread(alignPanel);
1471     thread.start();
1472   }
1473
1474   @Override
1475   public void exportFeatures_actionPerformed(ActionEvent e)
1476   {
1477     new AnnotationExporter(alignPanel).exportFeatures();
1478   }
1479
1480   @Override
1481   public void exportAnnotations_actionPerformed(ActionEvent e)
1482   {
1483     new AnnotationExporter(alignPanel).exportAnnotations();
1484   }
1485
1486   @Override
1487   public void associatedData_actionPerformed(ActionEvent e)
1488   {
1489     final JalviewFileChooser chooser = new JalviewFileChooser(
1490             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1491     chooser.setFileView(new JalviewFileView());
1492     String tooltip = MessageManager.getString("label.load_jalview_annotations");
1493     chooser.setDialogTitle(tooltip);
1494     chooser.setToolTipText(tooltip);
1495     chooser.setResponseHandler(0, new Runnable()
1496     {
1497       @Override
1498       public void run()
1499       {
1500         String choice = chooser.getSelectedFile().getPath();
1501         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1502         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1503       }
1504     });
1505
1506     chooser.showOpenDialog(this);
1507   }
1508
1509   /**
1510    * Close the current view or all views in the alignment frame. If the frame
1511    * only contains one view then the alignment will be removed from memory.
1512    *
1513    * @param closeAllTabs
1514    */
1515   @Override
1516   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1517   {
1518     if (alignPanels != null && alignPanels.size() < 2)
1519     {
1520       closeAllTabs = true;
1521     }
1522
1523     try
1524     {
1525       if (alignPanels != null)
1526       {
1527         if (closeAllTabs)
1528         {
1529           if (this.isClosed())
1530           {
1531             // really close all the windows - otherwise wait till
1532             // setClosed(true) is called
1533             for (int i = 0; i < alignPanels.size(); i++)
1534             {
1535               AlignmentPanel ap = alignPanels.get(i);
1536               ap.closePanel();
1537             }
1538           }
1539         }
1540         else
1541         {
1542           closeView(alignPanel);
1543         }
1544       }
1545       if (closeAllTabs)
1546       {
1547         if (featureSettings != null && featureSettings.isOpen())
1548         {
1549           featureSettings.close();
1550           featureSettings = null;
1551         }
1552         /*
1553          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1554          * be called recursively, with the frame now in 'closed' state
1555          */
1556         this.setClosed(true);
1557       }
1558     } catch (Exception ex)
1559     {
1560       ex.printStackTrace();
1561     }
1562   }
1563
1564   /**
1565    * Close the specified panel and close up tabs appropriately.
1566    *
1567    * @param panelToClose
1568    */
1569   public void closeView(AlignmentPanel panelToClose)
1570   {
1571     int index = tabbedPane.getSelectedIndex();
1572     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1573     alignPanels.remove(panelToClose);
1574     panelToClose.closePanel();
1575     panelToClose = null;
1576
1577     tabbedPane.removeTabAt(closedindex);
1578     tabbedPane.validate();
1579
1580     if (index > closedindex || index == tabbedPane.getTabCount())
1581     {
1582       // modify currently selected tab index if necessary.
1583       index--;
1584     }
1585
1586     this.tabSelectionChanged(index);
1587   }
1588
1589   /**
1590    * DOCUMENT ME!
1591    */
1592   void updateEditMenuBar()
1593   {
1594
1595     if (viewport.getHistoryList().size() > 0)
1596     {
1597       undoMenuItem.setEnabled(true);
1598       CommandI command = viewport.getHistoryList().peek();
1599       undoMenuItem.setText(MessageManager
1600               .formatMessage("label.undo_command", new Object[]
1601               { command.getDescription() }));
1602     }
1603     else
1604     {
1605       undoMenuItem.setEnabled(false);
1606       undoMenuItem.setText(MessageManager.getString("action.undo"));
1607     }
1608
1609     if (viewport.getRedoList().size() > 0)
1610     {
1611       redoMenuItem.setEnabled(true);
1612
1613       CommandI command = viewport.getRedoList().peek();
1614       redoMenuItem.setText(MessageManager
1615               .formatMessage("label.redo_command", new Object[]
1616               { command.getDescription() }));
1617     }
1618     else
1619     {
1620       redoMenuItem.setEnabled(false);
1621       redoMenuItem.setText(MessageManager.getString("action.redo"));
1622     }
1623   }
1624
1625   @Override
1626   public void addHistoryItem(CommandI command)
1627   {
1628     if (command.getSize() > 0)
1629     {
1630       viewport.addToHistoryList(command);
1631       viewport.clearRedoList();
1632       updateEditMenuBar();
1633       viewport.updateHiddenColumns();
1634       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1635       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1636       // viewport.getColumnSelection()
1637       // .getHiddenColumns().size() > 0);
1638     }
1639   }
1640
1641   /**
1642    *
1643    * @return alignment objects for all views
1644    */
1645   AlignmentI[] getViewAlignments()
1646   {
1647     if (alignPanels != null)
1648     {
1649       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1650       int i = 0;
1651       for (AlignmentPanel ap : alignPanels)
1652       {
1653         als[i++] = ap.av.getAlignment();
1654       }
1655       return als;
1656     }
1657     if (viewport != null)
1658     {
1659       return new AlignmentI[] { viewport.getAlignment() };
1660     }
1661     return null;
1662   }
1663
1664   /**
1665    * DOCUMENT ME!
1666    *
1667    * @param e
1668    *          DOCUMENT ME!
1669    */
1670   @Override
1671   protected void undoMenuItem_actionPerformed(ActionEvent e)
1672   {
1673     if (viewport.getHistoryList().isEmpty())
1674     {
1675       return;
1676     }
1677     CommandI command = viewport.getHistoryList().pop();
1678     viewport.addToRedoList(command);
1679     command.undoCommand(getViewAlignments());
1680
1681     AlignmentViewport originalSource = getOriginatingSource(command);
1682     updateEditMenuBar();
1683
1684     if (originalSource != null)
1685     {
1686       if (originalSource != viewport)
1687       {
1688         Cache.log.warn(
1689                 "Implementation worry: mismatch of viewport origin for undo");
1690       }
1691       originalSource.updateHiddenColumns();
1692       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1693       // null
1694       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1695       // viewport.getColumnSelection()
1696       // .getHiddenColumns().size() > 0);
1697       originalSource.firePropertyChange("alignment", null,
1698               originalSource.getAlignment().getSequences());
1699     }
1700   }
1701
1702   /**
1703    * DOCUMENT ME!
1704    *
1705    * @param e
1706    *          DOCUMENT ME!
1707    */
1708   @Override
1709   protected void redoMenuItem_actionPerformed(ActionEvent e)
1710   {
1711     if (viewport.getRedoList().size() < 1)
1712     {
1713       return;
1714     }
1715
1716     CommandI command = viewport.getRedoList().pop();
1717     viewport.addToHistoryList(command);
1718     command.doCommand(getViewAlignments());
1719
1720     AlignmentViewport originalSource = getOriginatingSource(command);
1721     updateEditMenuBar();
1722
1723     if (originalSource != null)
1724     {
1725
1726       if (originalSource != viewport)
1727       {
1728         Cache.log.warn(
1729                 "Implementation worry: mismatch of viewport origin for redo");
1730       }
1731       originalSource.updateHiddenColumns();
1732       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1733       // null
1734       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1735       // viewport.getColumnSelection()
1736       // .getHiddenColumns().size() > 0);
1737       originalSource.firePropertyChange("alignment", null,
1738               originalSource.getAlignment().getSequences());
1739     }
1740   }
1741
1742   AlignmentViewport getOriginatingSource(CommandI command)
1743   {
1744     AlignmentViewport originalSource = null;
1745     // For sequence removal and addition, we need to fire
1746     // the property change event FROM the viewport where the
1747     // original alignment was altered
1748     AlignmentI al = null;
1749     if (command instanceof EditCommand)
1750     {
1751       EditCommand editCommand = (EditCommand) command;
1752       al = editCommand.getAlignment();
1753       List<Component> comps = PaintRefresher.components
1754               .get(viewport.getSequenceSetId());
1755
1756       for (Component comp : comps)
1757       {
1758         if (comp instanceof AlignmentPanel)
1759         {
1760           if (al == ((AlignmentPanel) comp).av.getAlignment())
1761           {
1762             originalSource = ((AlignmentPanel) comp).av;
1763             break;
1764           }
1765         }
1766       }
1767     }
1768
1769     if (originalSource == null)
1770     {
1771       // The original view is closed, we must validate
1772       // the current view against the closed view first
1773       if (al != null)
1774       {
1775         PaintRefresher.validateSequences(al, viewport.getAlignment());
1776       }
1777
1778       originalSource = viewport;
1779     }
1780
1781     return originalSource;
1782   }
1783
1784   /**
1785    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode
1786    *
1787    * @param up
1788    *          or down (if !up)
1789    */
1790   public void moveSelectedSequences(boolean up)
1791   {
1792     SequenceGroup sg = viewport.getSelectionGroup();
1793
1794     if (sg == null)
1795     {
1796       if (viewport.cursorMode)
1797       {
1798         sg = new SequenceGroup();
1799         sg.addSequence(viewport.getAlignment()
1800                 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
1801       } else {
1802         return;
1803       }
1804     }
1805
1806     if (sg.getSize() < 1)
1807     {
1808         return;
1809     }
1810
1811     // TODO: JAL-3733 - add an event to the undo buffer for this !
1812
1813     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1814             viewport.getHiddenRepSequences(), up);
1815     alignPanel.paintAlignment(true, false);
1816   }
1817
1818   synchronized void slideSequences(boolean right, int size)
1819   {
1820     List<SequenceI> sg = new ArrayList<>();
1821     if (viewport.cursorMode)
1822     {
1823       sg.add(viewport.getAlignment()
1824               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1825     }
1826     else if (viewport.getSelectionGroup() != null
1827             && viewport.getSelectionGroup().getSize() != viewport
1828                     .getAlignment().getHeight())
1829     {
1830       sg = viewport.getSelectionGroup()
1831               .getSequences(viewport.getHiddenRepSequences());
1832     }
1833
1834     if (sg.size() < 1)
1835     {
1836       return;
1837     }
1838
1839     List<SequenceI> invertGroup = new ArrayList<>();
1840
1841     for (SequenceI seq : viewport.getAlignment().getSequences())
1842     {
1843       if (!sg.contains(seq))
1844       {
1845         invertGroup.add(seq);
1846       }
1847     }
1848
1849     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1850
1851     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1852     for (int i = 0; i < invertGroup.size(); i++)
1853     {
1854       seqs2[i] = invertGroup.get(i);
1855     }
1856
1857     SlideSequencesCommand ssc;
1858     if (right)
1859     {
1860       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1861               viewport.getGapCharacter());
1862     }
1863     else
1864     {
1865       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1866               viewport.getGapCharacter());
1867     }
1868
1869     int groupAdjustment = 0;
1870     if (ssc.getGapsInsertedBegin() && right)
1871     {
1872       if (viewport.cursorMode)
1873       {
1874         alignPanel.getSeqPanel().moveCursor(size, 0);
1875       }
1876       else
1877       {
1878         groupAdjustment = size;
1879       }
1880     }
1881     else if (!ssc.getGapsInsertedBegin() && !right)
1882     {
1883       if (viewport.cursorMode)
1884       {
1885         alignPanel.getSeqPanel().moveCursor(-size, 0);
1886       }
1887       else
1888       {
1889         groupAdjustment = -size;
1890       }
1891     }
1892
1893     if (groupAdjustment != 0)
1894     {
1895       viewport.getSelectionGroup().setStartRes(
1896               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1897       viewport.getSelectionGroup().setEndRes(
1898               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1899     }
1900
1901     /*
1902      * just extend the last slide command if compatible; but not if in
1903      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1904      */
1905     boolean appendHistoryItem = false;
1906     Deque<CommandI> historyList = viewport.getHistoryList();
1907     boolean inSplitFrame = getSplitViewContainer() != null;
1908     if (!inSplitFrame && historyList != null && historyList.size() > 0
1909             && historyList.peek() instanceof SlideSequencesCommand)
1910     {
1911       appendHistoryItem = ssc.appendSlideCommand(
1912               (SlideSequencesCommand) historyList.peek());
1913     }
1914
1915     if (!appendHistoryItem)
1916     {
1917       addHistoryItem(ssc);
1918     }
1919
1920     repaint();
1921   }
1922
1923   /**
1924    * DOCUMENT ME!
1925    *
1926    * @param e
1927    *          DOCUMENT ME!
1928    */
1929   @Override
1930   protected void copy_actionPerformed()
1931   {
1932     if (viewport.getSelectionGroup() == null)
1933     {
1934       return;
1935     }
1936     // TODO: preserve the ordering of displayed alignment annotation in any
1937     // internal paste (particularly sequence associated annotation)
1938     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1939     String[] omitHidden = null;
1940
1941     if (viewport.hasHiddenColumns())
1942     {
1943       omitHidden = viewport.getViewAsString(true);
1944     }
1945
1946     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1947             seqs, omitHidden, null);
1948
1949     StringSelection ss = new StringSelection(output);
1950
1951     try
1952     {
1953       jalview.gui.Desktop.internalCopy = true;
1954       // Its really worth setting the clipboard contents
1955       // to empty before setting the large StringSelection!!
1956       Toolkit.getDefaultToolkit().getSystemClipboard()
1957               .setContents(new StringSelection(""), null);
1958
1959       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1960               Desktop.instance);
1961     } catch (OutOfMemoryError er)
1962     {
1963       new OOMWarning("copying region", er);
1964       return;
1965     }
1966
1967     HiddenColumns hiddenColumns = null;
1968     if (viewport.hasHiddenColumns())
1969     {
1970       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1971       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1972
1973       // create new HiddenColumns object with copy of hidden regions
1974       // between startRes and endRes, offset by startRes
1975       hiddenColumns = new HiddenColumns(
1976               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1977               hiddenCutoff, hiddenOffset);
1978     }
1979
1980     Desktop.jalviewClipboard = new Object[] { seqs,
1981         viewport.getAlignment().getDataset(), hiddenColumns };
1982     setStatus(MessageManager.formatMessage(
1983             "label.copied_sequences_to_clipboard", new Object[]
1984             { Integer.valueOf(seqs.length).toString() }));
1985   }
1986
1987   /**
1988    * DOCUMENT ME!
1989    *
1990    * @param e
1991    *          DOCUMENT ME!
1992    */
1993   @Override
1994   protected void pasteNew_actionPerformed(ActionEvent e)
1995   {
1996     paste(true);
1997   }
1998
1999   /**
2000    * DOCUMENT ME!
2001    *
2002    * @param e
2003    *          DOCUMENT ME!
2004    */
2005   @Override
2006   protected void pasteThis_actionPerformed(ActionEvent e)
2007   {
2008     paste(false);
2009   }
2010
2011   /**
2012    * Paste contents of Jalview clipboard
2013    *
2014    * @param newAlignment
2015    *          true to paste to a new alignment, otherwise add to this.
2016    */
2017   void paste(boolean newAlignment)
2018   {
2019     boolean externalPaste = true;
2020     try
2021     {
2022       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2023       Transferable contents = c.getContents(this);
2024
2025       if (contents == null)
2026       {
2027         return;
2028       }
2029
2030       String str;
2031       FileFormatI format;
2032       try
2033       {
2034         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2035         if (str.length() < 1)
2036         {
2037           return;
2038         }
2039
2040         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2041
2042       } catch (OutOfMemoryError er)
2043       {
2044         new OOMWarning("Out of memory pasting sequences!!", er);
2045         return;
2046       }
2047
2048       SequenceI[] sequences;
2049       boolean annotationAdded = false;
2050       AlignmentI alignment = null;
2051
2052       if (Desktop.jalviewClipboard != null)
2053       {
2054         // The clipboard was filled from within Jalview, we must use the
2055         // sequences
2056         // And dataset from the copied alignment
2057         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2058         // be doubly sure that we create *new* sequence objects.
2059         sequences = new SequenceI[newseq.length];
2060         for (int i = 0; i < newseq.length; i++)
2061         {
2062           sequences[i] = new Sequence(newseq[i]);
2063         }
2064         alignment = new Alignment(sequences);
2065         externalPaste = false;
2066       }
2067       else
2068       {
2069         // parse the clipboard as an alignment.
2070         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2071                 format);
2072         sequences = alignment.getSequencesArray();
2073       }
2074
2075       int alwidth = 0;
2076       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2077       int fgroup = -1;
2078
2079       if (newAlignment)
2080       {
2081
2082         if (Desktop.jalviewClipboard != null)
2083         {
2084           // dataset is inherited
2085           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2086         }
2087         else
2088         {
2089           // new dataset is constructed
2090           alignment.setDataset(null);
2091         }
2092         alwidth = alignment.getWidth() + 1;
2093       }
2094       else
2095       {
2096         AlignmentI pastedal = alignment; // preserve pasted alignment object
2097         // Add pasted sequences and dataset into existing alignment.
2098         alignment = viewport.getAlignment();
2099         alwidth = alignment.getWidth() + 1;
2100         // decide if we need to import sequences from an existing dataset
2101         boolean importDs = Desktop.jalviewClipboard != null
2102                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2103         // importDs==true instructs us to copy over new dataset sequences from
2104         // an existing alignment
2105         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2106                                                                       // create
2107         // minimum dataset set
2108
2109         for (int i = 0; i < sequences.length; i++)
2110         {
2111           if (importDs)
2112           {
2113             newDs.addElement(null);
2114           }
2115           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2116           // paste
2117           if (importDs && ds != null)
2118           {
2119             if (!newDs.contains(ds))
2120             {
2121               newDs.setElementAt(ds, i);
2122               ds = new Sequence(ds);
2123               // update with new dataset sequence
2124               sequences[i].setDatasetSequence(ds);
2125             }
2126             else
2127             {
2128               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2129             }
2130           }
2131           else
2132           {
2133             // copy and derive new dataset sequence
2134             sequences[i] = sequences[i].deriveSequence();
2135             alignment.getDataset()
2136                     .addSequence(sequences[i].getDatasetSequence());
2137             // TODO: avoid creation of duplicate dataset sequences with a
2138             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2139           }
2140           alignment.addSequence(sequences[i]); // merges dataset
2141         }
2142         if (newDs != null)
2143         {
2144           newDs.clear(); // tidy up
2145         }
2146         if (alignment.getAlignmentAnnotation() != null)
2147         {
2148           for (AlignmentAnnotation alan : alignment
2149                   .getAlignmentAnnotation())
2150           {
2151             if (alan.graphGroup > fgroup)
2152             {
2153               fgroup = alan.graphGroup;
2154             }
2155           }
2156         }
2157         if (pastedal.getAlignmentAnnotation() != null)
2158         {
2159           // Add any annotation attached to alignment.
2160           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2161           for (int i = 0; i < alann.length; i++)
2162           {
2163             annotationAdded = true;
2164             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2165             {
2166               AlignmentAnnotation newann = new AlignmentAnnotation(
2167                       alann[i]);
2168               if (newann.graphGroup > -1)
2169               {
2170                 if (newGraphGroups.size() <= newann.graphGroup
2171                         || newGraphGroups.get(newann.graphGroup) == null)
2172                 {
2173                   for (int q = newGraphGroups
2174                           .size(); q <= newann.graphGroup; q++)
2175                   {
2176                     newGraphGroups.add(q, null);
2177                   }
2178                   newGraphGroups.set(newann.graphGroup,
2179                           Integer.valueOf(++fgroup));
2180                 }
2181                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2182                         .intValue();
2183               }
2184
2185               newann.padAnnotation(alwidth);
2186               alignment.addAnnotation(newann);
2187             }
2188           }
2189         }
2190       }
2191       if (!newAlignment)
2192       {
2193         // /////
2194         // ADD HISTORY ITEM
2195         //
2196         addHistoryItem(new EditCommand(
2197                 MessageManager.getString("label.add_sequences"),
2198                 Action.PASTE, sequences, 0, alignment.getWidth(),
2199                 alignment));
2200       }
2201       // Add any annotations attached to sequences
2202       for (int i = 0; i < sequences.length; i++)
2203       {
2204         if (sequences[i].getAnnotation() != null)
2205         {
2206           AlignmentAnnotation newann;
2207           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2208           {
2209             annotationAdded = true;
2210             newann = sequences[i].getAnnotation()[a];
2211             newann.adjustForAlignment();
2212             newann.padAnnotation(alwidth);
2213             if (newann.graphGroup > -1)
2214             {
2215               if (newann.graphGroup > -1)
2216               {
2217                 if (newGraphGroups.size() <= newann.graphGroup
2218                         || newGraphGroups.get(newann.graphGroup) == null)
2219                 {
2220                   for (int q = newGraphGroups
2221                           .size(); q <= newann.graphGroup; q++)
2222                   {
2223                     newGraphGroups.add(q, null);
2224                   }
2225                   newGraphGroups.set(newann.graphGroup,
2226                           Integer.valueOf(++fgroup));
2227                 }
2228                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2229                         .intValue();
2230               }
2231             }
2232             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2233             // was
2234             // duplicated
2235             // earlier
2236             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2237                     a);
2238           }
2239         }
2240       }
2241       if (!newAlignment)
2242       {
2243
2244         // propagate alignment changed.
2245         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2246         if (annotationAdded)
2247         {
2248           // Duplicate sequence annotation in all views.
2249           AlignmentI[] alview = this.getViewAlignments();
2250           for (int i = 0; i < sequences.length; i++)
2251           {
2252             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2253             if (sann == null)
2254             {
2255               continue;
2256             }
2257             for (int avnum = 0; avnum < alview.length; avnum++)
2258             {
2259               if (alview[avnum] != alignment)
2260               {
2261                 // duplicate in a view other than the one with input focus
2262                 int avwidth = alview[avnum].getWidth() + 1;
2263                 // this relies on sann being preserved after we
2264                 // modify the sequence's annotation array for each duplication
2265                 for (int a = 0; a < sann.length; a++)
2266                 {
2267                   AlignmentAnnotation newann = new AlignmentAnnotation(
2268                           sann[a]);
2269                   sequences[i].addAlignmentAnnotation(newann);
2270                   newann.padAnnotation(avwidth);
2271                   alview[avnum].addAnnotation(newann); // annotation was
2272                   // duplicated earlier
2273                   // TODO JAL-1145 graphGroups are not updated for sequence
2274                   // annotation added to several views. This may cause
2275                   // strangeness
2276                   alview[avnum].setAnnotationIndex(newann, a);
2277                 }
2278               }
2279             }
2280           }
2281           buildSortByAnnotationScoresMenu();
2282         }
2283         viewport.firePropertyChange("alignment", null,
2284                 alignment.getSequences());
2285         if (alignPanels != null)
2286         {
2287           for (AlignmentPanel ap : alignPanels)
2288           {
2289             ap.validateAnnotationDimensions(false);
2290           }
2291         }
2292         else
2293         {
2294           alignPanel.validateAnnotationDimensions(false);
2295         }
2296
2297       }
2298       else
2299       {
2300         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2301                 DEFAULT_HEIGHT);
2302         String newtitle = new String("Copied sequences");
2303
2304         if (Desktop.jalviewClipboard != null
2305                 && Desktop.jalviewClipboard[2] != null)
2306         {
2307           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2308           af.viewport.setHiddenColumns(hc);
2309         }
2310
2311         // >>>This is a fix for the moment, until a better solution is
2312         // found!!<<<
2313         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2314                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2315                         .getFeatureRenderer());
2316
2317         // TODO: maintain provenance of an alignment, rather than just make the
2318         // title a concatenation of operations.
2319         if (!externalPaste)
2320         {
2321           if (title.startsWith("Copied sequences"))
2322           {
2323             newtitle = title;
2324           }
2325           else
2326           {
2327             newtitle = newtitle.concat("- from " + title);
2328           }
2329         }
2330         else
2331         {
2332           newtitle = new String("Pasted sequences");
2333         }
2334
2335         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2336                 DEFAULT_HEIGHT);
2337
2338       }
2339
2340     } catch (Exception ex)
2341     {
2342       ex.printStackTrace();
2343       System.out.println("Exception whilst pasting: " + ex);
2344       // could be anything being pasted in here
2345     }
2346
2347   }
2348
2349   @Override
2350   protected void expand_newalign(ActionEvent e)
2351   {
2352     try
2353     {
2354       AlignmentI alignment = AlignmentUtils
2355               .expandContext(getViewport().getAlignment(), -1);
2356       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2357               DEFAULT_HEIGHT);
2358       String newtitle = new String("Flanking alignment");
2359
2360       if (Desktop.jalviewClipboard != null
2361               && Desktop.jalviewClipboard[2] != null)
2362       {
2363         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2364         af.viewport.setHiddenColumns(hc);
2365       }
2366
2367       // >>>This is a fix for the moment, until a better solution is
2368       // found!!<<<
2369       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2370               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2371                       .getFeatureRenderer());
2372
2373       // TODO: maintain provenance of an alignment, rather than just make the
2374       // title a concatenation of operations.
2375       {
2376         if (title.startsWith("Copied sequences"))
2377         {
2378           newtitle = title;
2379         }
2380         else
2381         {
2382           newtitle = newtitle.concat("- from " + title);
2383         }
2384       }
2385
2386       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2387
2388     } catch (Exception ex)
2389     {
2390       ex.printStackTrace();
2391       System.out.println("Exception whilst pasting: " + ex);
2392       // could be anything being pasted in here
2393     } catch (OutOfMemoryError oom)
2394     {
2395       new OOMWarning("Viewing flanking region of alignment", oom);
2396     }
2397   }
2398
2399   /**
2400    * Action Cut (delete and copy) the selected region
2401    */
2402   @Override
2403   protected void cut_actionPerformed()
2404   {
2405     copy_actionPerformed();
2406     delete_actionPerformed();
2407   }
2408
2409   /**
2410    * Performs menu option to Delete the currently selected region
2411    */
2412   @Override
2413   protected void delete_actionPerformed()
2414   {
2415
2416     SequenceGroup sg = viewport.getSelectionGroup();
2417     if (sg == null)
2418     {
2419       return;
2420     }
2421
2422     Runnable okAction = new Runnable()
2423     {
2424                 @Override
2425                 public void run()
2426                 {
2427                     SequenceI[] cut = sg.getSequences()
2428                             .toArray(new SequenceI[sg.getSize()]);
2429
2430                     addHistoryItem(new EditCommand(
2431                             MessageManager.getString("label.cut_sequences"), Action.CUT,
2432                             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2433                             viewport.getAlignment()));
2434
2435                     viewport.setSelectionGroup(null);
2436                     viewport.sendSelection();
2437                     viewport.getAlignment().deleteGroup(sg);
2438
2439                     viewport.firePropertyChange("alignment", null,
2440                             viewport.getAlignment().getSequences());
2441                     if (viewport.getAlignment().getHeight() < 1)
2442                     {
2443                       try
2444                       {
2445                         AlignFrame.this.setClosed(true);
2446                       } catch (Exception ex)
2447                       {
2448                       }
2449                     }
2450                 }};
2451
2452     /*
2453      * If the cut affects all sequences, prompt for confirmation
2454      */
2455     boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2456     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2457             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2458         if (wholeHeight && wholeWidth)
2459         {
2460             JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2461                 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2462             Object[] options = new Object[] { MessageManager.getString("action.ok"),
2463                     MessageManager.getString("action.cancel") };
2464                 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2465                     MessageManager.getString("label.delete_all"),
2466                     JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2467                     options, options[0]);
2468         } else
2469         {
2470                 okAction.run();
2471         }
2472   }
2473
2474   /**
2475    * DOCUMENT ME!
2476    *
2477    * @param e
2478    *          DOCUMENT ME!
2479    */
2480   @Override
2481   protected void deleteGroups_actionPerformed(ActionEvent e)
2482   {
2483     if (avc.deleteGroups())
2484     {
2485       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2486       alignPanel.updateAnnotation();
2487       alignPanel.paintAlignment(true, true);
2488     }
2489   }
2490
2491   /**
2492    * DOCUMENT ME!
2493    *
2494    * @param e
2495    *          DOCUMENT ME!
2496    */
2497   @Override
2498   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2499   {
2500     SequenceGroup sg = new SequenceGroup(
2501             viewport.getAlignment().getSequences());
2502
2503     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2504     viewport.setSelectionGroup(sg);
2505     viewport.isSelectionGroupChanged(true);
2506     viewport.sendSelection();
2507     // JAL-2034 - should delegate to
2508     // alignPanel to decide if overview needs
2509     // updating.
2510     alignPanel.paintAlignment(false, false);
2511     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2512   }
2513
2514   /**
2515    * DOCUMENT ME!
2516    *
2517    * @param e
2518    *          DOCUMENT ME!
2519    */
2520   @Override
2521   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2522   {
2523     if (viewport.cursorMode)
2524     {
2525       alignPanel.getSeqPanel().keyboardNo1 = null;
2526       alignPanel.getSeqPanel().keyboardNo2 = null;
2527     }
2528     viewport.setSelectionGroup(null);
2529     viewport.getColumnSelection().clear();
2530     viewport.setSearchResults(null);
2531     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2532     // JAL-2034 - should delegate to
2533     // alignPanel to decide if overview needs
2534     // updating.
2535     alignPanel.paintAlignment(false, false);
2536     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2537     viewport.sendSelection();
2538   }
2539
2540   /**
2541    * DOCUMENT ME!
2542    *
2543    * @param e
2544    *          DOCUMENT ME!
2545    */
2546   @Override
2547   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2548   {
2549     SequenceGroup sg = viewport.getSelectionGroup();
2550
2551     if (sg == null)
2552     {
2553       selectAllSequenceMenuItem_actionPerformed(null);
2554
2555       return;
2556     }
2557
2558     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2559     {
2560       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2561     }
2562     // JAL-2034 - should delegate to
2563     // alignPanel to decide if overview needs
2564     // updating.
2565
2566     alignPanel.paintAlignment(true, false);
2567     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2568     viewport.sendSelection();
2569   }
2570
2571   @Override
2572   public void invertColSel_actionPerformed(ActionEvent e)
2573   {
2574     viewport.invertColumnSelection();
2575     alignPanel.paintAlignment(true, false);
2576     viewport.sendSelection();
2577   }
2578
2579   /**
2580    * DOCUMENT ME!
2581    *
2582    * @param e
2583    *          DOCUMENT ME!
2584    */
2585   @Override
2586   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2587   {
2588     trimAlignment(true);
2589   }
2590
2591   /**
2592    * DOCUMENT ME!
2593    *
2594    * @param e
2595    *          DOCUMENT ME!
2596    */
2597   @Override
2598   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2599   {
2600     trimAlignment(false);
2601   }
2602
2603   void trimAlignment(boolean trimLeft)
2604   {
2605     ColumnSelection colSel = viewport.getColumnSelection();
2606     int column;
2607
2608     if (!colSel.isEmpty())
2609     {
2610       if (trimLeft)
2611       {
2612         column = colSel.getMin();
2613       }
2614       else
2615       {
2616         column = colSel.getMax();
2617       }
2618
2619       SequenceI[] seqs;
2620       if (viewport.getSelectionGroup() != null)
2621       {
2622         seqs = viewport.getSelectionGroup()
2623                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2624       }
2625       else
2626       {
2627         seqs = viewport.getAlignment().getSequencesArray();
2628       }
2629
2630       TrimRegionCommand trimRegion;
2631       if (trimLeft)
2632       {
2633         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2634                 column, viewport.getAlignment());
2635         viewport.getRanges().setStartRes(0);
2636       }
2637       else
2638       {
2639         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2640                 column, viewport.getAlignment());
2641       }
2642
2643       setStatus(MessageManager
2644               .formatMessage("label.removed_columns", new String[]
2645               { Integer.valueOf(trimRegion.getSize()).toString() }));
2646
2647       addHistoryItem(trimRegion);
2648
2649       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2650       {
2651         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2652                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2653         {
2654           viewport.getAlignment().deleteGroup(sg);
2655         }
2656       }
2657
2658       viewport.firePropertyChange("alignment", null,
2659               viewport.getAlignment().getSequences());
2660     }
2661   }
2662
2663   /**
2664    * DOCUMENT ME!
2665    *
2666    * @param e
2667    *          DOCUMENT ME!
2668    */
2669   @Override
2670   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2671   {
2672     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2673
2674     SequenceI[] seqs;
2675     if (viewport.getSelectionGroup() != null)
2676     {
2677       seqs = viewport.getSelectionGroup()
2678               .getSequencesAsArray(viewport.getHiddenRepSequences());
2679       start = viewport.getSelectionGroup().getStartRes();
2680       end = viewport.getSelectionGroup().getEndRes();
2681     }
2682     else
2683     {
2684       seqs = viewport.getAlignment().getSequencesArray();
2685     }
2686
2687     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2688             "Remove Gapped Columns", seqs, start, end,
2689             viewport.getAlignment());
2690
2691     addHistoryItem(removeGapCols);
2692
2693     setStatus(MessageManager
2694             .formatMessage("label.removed_empty_columns", new Object[]
2695             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2696
2697     // This is to maintain viewport position on first residue
2698     // of first sequence
2699     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2700     ViewportRanges ranges = viewport.getRanges();
2701     int startRes = seq.findPosition(ranges.getStartRes());
2702     // ShiftList shifts;
2703     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2704     // edit.alColumnChanges=shifts.getInverse();
2705     // if (viewport.hasHiddenColumns)
2706     // viewport.getColumnSelection().compensateForEdits(shifts);
2707     ranges.setStartRes(seq.findIndex(startRes) - 1);
2708     viewport.firePropertyChange("alignment", null,
2709             viewport.getAlignment().getSequences());
2710
2711   }
2712
2713   /**
2714    * DOCUMENT ME!
2715    *
2716    * @param e
2717    *          DOCUMENT ME!
2718    */
2719   @Override
2720   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2721   {
2722     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2723
2724     SequenceI[] seqs;
2725     if (viewport.getSelectionGroup() != null)
2726     {
2727       seqs = viewport.getSelectionGroup()
2728               .getSequencesAsArray(viewport.getHiddenRepSequences());
2729       start = viewport.getSelectionGroup().getStartRes();
2730       end = viewport.getSelectionGroup().getEndRes();
2731     }
2732     else
2733     {
2734       seqs = viewport.getAlignment().getSequencesArray();
2735     }
2736
2737     // This is to maintain viewport position on first residue
2738     // of first sequence
2739     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2740     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2741
2742     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2743             viewport.getAlignment()));
2744
2745     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2746
2747     viewport.firePropertyChange("alignment", null,
2748             viewport.getAlignment().getSequences());
2749
2750   }
2751
2752   /**
2753    * DOCUMENT ME!
2754    *
2755    * @param e
2756    *          DOCUMENT ME!
2757    */
2758   @Override
2759   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2760   {
2761     viewport.setPadGaps(padGapsMenuitem.isSelected());
2762     viewport.firePropertyChange("alignment", null,
2763             viewport.getAlignment().getSequences());
2764   }
2765
2766   /**
2767    * Opens a Finder dialog
2768    *
2769    * @param e
2770    */
2771   @Override
2772   public void findMenuItem_actionPerformed(ActionEvent e)
2773   {
2774     new Finder(alignPanel);
2775   }
2776
2777   /**
2778    * Create a new view of the current alignment.
2779    */
2780   @Override
2781   public void newView_actionPerformed(ActionEvent e)
2782   {
2783     newView(null, true);
2784   }
2785
2786   /**
2787    * Creates and shows a new view of the current alignment.
2788    *
2789    * @param viewTitle
2790    *          title of newly created view; if null, one will be generated
2791    * @param copyAnnotation
2792    *          if true then duplicate all annnotation, groups and settings
2793    * @return new alignment panel, already displayed.
2794    */
2795   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2796   {
2797     /*
2798      * Create a new AlignmentPanel (with its own, new Viewport)
2799      */
2800     AlignmentPanel newap = new jalview.project.Jalview2XML()
2801             .copyAlignPanel(alignPanel);
2802     if (!copyAnnotation)
2803     {
2804       /*
2805        * remove all groups and annotation except for the automatic stuff
2806        */
2807       newap.av.getAlignment().deleteAllGroups();
2808       newap.av.getAlignment().deleteAllAnnotations(false);
2809     }
2810
2811     newap.av.setGatherViewsHere(false);
2812
2813     if (viewport.getViewName() == null)
2814     {
2815       viewport.setViewName(MessageManager
2816               .getString("label.view_name_original"));
2817     }
2818
2819     /*
2820      * Views share the same edits undo and redo stacks
2821      */
2822     newap.av.setHistoryList(viewport.getHistoryList());
2823     newap.av.setRedoList(viewport.getRedoList());
2824
2825     /*
2826      * copy any visualisation settings that are not saved in the project
2827      */
2828     newap.av.setColourAppliesToAllGroups(
2829             viewport.getColourAppliesToAllGroups());
2830
2831     /*
2832      * Views share the same mappings; need to deregister any new mappings
2833      * created by copyAlignPanel, and register the new reference to the shared
2834      * mappings
2835      */
2836     newap.av.replaceMappings(viewport.getAlignment());
2837
2838     /*
2839      * start up cDNA consensus (if applicable) now mappings are in place
2840      */
2841     if (newap.av.initComplementConsensus())
2842     {
2843       newap.refresh(true); // adjust layout of annotations
2844     }
2845
2846     newap.av.setViewName(getNewViewName(viewTitle));
2847
2848     addAlignmentPanel(newap, true);
2849     newap.alignmentChanged();
2850
2851     if (alignPanels.size() == 2)
2852     {
2853       viewport.setGatherViewsHere(true);
2854     }
2855     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2856     return newap;
2857   }
2858
2859   /**
2860    * Make a new name for the view, ensuring it is unique within the current
2861    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2862    * these now use viewId. Unique view names are still desirable for usability.)
2863    *
2864    * @param viewTitle
2865    * @return
2866    */
2867   protected String getNewViewName(String viewTitle)
2868   {
2869     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2870     boolean addFirstIndex = false;
2871     if (viewTitle == null || viewTitle.trim().length() == 0)
2872     {
2873       viewTitle = MessageManager.getString("action.view");
2874       addFirstIndex = true;
2875     }
2876     else
2877     {
2878       index = 1;// we count from 1 if given a specific name
2879     }
2880     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2881
2882     List<Component> comps = PaintRefresher.components
2883             .get(viewport.getSequenceSetId());
2884
2885     List<String> existingNames = getExistingViewNames(comps);
2886
2887     while (existingNames.contains(newViewName))
2888     {
2889       newViewName = viewTitle + " " + (++index);
2890     }
2891     return newViewName;
2892   }
2893
2894   /**
2895    * Returns a list of distinct view names found in the given list of
2896    * components. View names are held on the viewport of an AlignmentPanel.
2897    *
2898    * @param comps
2899    * @return
2900    */
2901   protected List<String> getExistingViewNames(List<Component> comps)
2902   {
2903     List<String> existingNames = new ArrayList<>();
2904     for (Component comp : comps)
2905     {
2906       if (comp instanceof AlignmentPanel)
2907       {
2908         AlignmentPanel ap = (AlignmentPanel) comp;
2909         if (!existingNames.contains(ap.av.getViewName()))
2910         {
2911           existingNames.add(ap.av.getViewName());
2912         }
2913       }
2914     }
2915     return existingNames;
2916   }
2917
2918   /**
2919    * Explode tabbed views into separate windows.
2920    */
2921   @Override
2922   public void expandViews_actionPerformed(ActionEvent e)
2923   {
2924     Desktop.explodeViews(this);
2925   }
2926
2927   /**
2928    * Gather views in separate windows back into a tabbed presentation.
2929    */
2930   @Override
2931   public void gatherViews_actionPerformed(ActionEvent e)
2932   {
2933     Desktop.instance.gatherViews(this);
2934   }
2935
2936   /**
2937    * DOCUMENT ME!
2938    *
2939    * @param e
2940    *          DOCUMENT ME!
2941    */
2942   @Override
2943   public void font_actionPerformed(ActionEvent e)
2944   {
2945     new FontChooser(alignPanel);
2946   }
2947
2948   /**
2949    * DOCUMENT ME!
2950    *
2951    * @param e
2952    *          DOCUMENT ME!
2953    */
2954   @Override
2955   protected void seqLimit_actionPerformed(ActionEvent e)
2956   {
2957     viewport.setShowJVSuffix(seqLimits.isSelected());
2958
2959     alignPanel.getIdPanel().getIdCanvas()
2960             .setPreferredSize(alignPanel.calculateIdWidth());
2961     alignPanel.paintAlignment(true, false);
2962   }
2963
2964   @Override
2965   public void idRightAlign_actionPerformed(ActionEvent e)
2966   {
2967     viewport.setRightAlignIds(idRightAlign.isSelected());
2968     alignPanel.paintAlignment(false, false);
2969   }
2970
2971   @Override
2972   public void centreColumnLabels_actionPerformed(ActionEvent e)
2973   {
2974     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2975     alignPanel.paintAlignment(false, false);
2976   }
2977
2978   /*
2979    * (non-Javadoc)
2980    *
2981    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2982    */
2983   @Override
2984   protected void followHighlight_actionPerformed()
2985   {
2986     /*
2987      * Set the 'follow' flag on the Viewport (and scroll to position if now
2988      * true).
2989      */
2990     final boolean state = this.followHighlightMenuItem.getState();
2991     viewport.setFollowHighlight(state);
2992     if (state)
2993     {
2994       alignPanel.scrollToPosition(viewport.getSearchResults());
2995     }
2996   }
2997
2998   /**
2999    * DOCUMENT ME!
3000    *
3001    * @param e
3002    *          DOCUMENT ME!
3003    */
3004   @Override
3005   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3006   {
3007     viewport.setColourText(colourTextMenuItem.isSelected());
3008     alignPanel.paintAlignment(false, false);
3009   }
3010
3011   /**
3012    * DOCUMENT ME!
3013    *
3014    * @param e
3015    *          DOCUMENT ME!
3016    */
3017   @Override
3018   public void wrapMenuItem_actionPerformed(ActionEvent e)
3019   {
3020     scaleAbove.setVisible(wrapMenuItem.isSelected());
3021     scaleLeft.setVisible(wrapMenuItem.isSelected());
3022     scaleRight.setVisible(wrapMenuItem.isSelected());
3023     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3024     alignPanel.updateLayout();
3025   }
3026
3027   @Override
3028   public void showAllSeqs_actionPerformed(ActionEvent e)
3029   {
3030     viewport.showAllHiddenSeqs();
3031   }
3032
3033   @Override
3034   public void showAllColumns_actionPerformed(ActionEvent e)
3035   {
3036     viewport.showAllHiddenColumns();
3037     alignPanel.paintAlignment(true, true);
3038     viewport.sendSelection();
3039   }
3040
3041   @Override
3042   public void hideSelSequences_actionPerformed(ActionEvent e)
3043   {
3044     viewport.hideAllSelectedSeqs();
3045   }
3046
3047   /**
3048    * called by key handler and the hide all/show all menu items
3049    *
3050    * @param toggleSeqs
3051    * @param toggleCols
3052    */
3053   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3054   {
3055
3056     boolean hide = false;
3057     SequenceGroup sg = viewport.getSelectionGroup();
3058     if (!toggleSeqs && !toggleCols)
3059     {
3060       // Hide everything by the current selection - this is a hack - we do the
3061       // invert and then hide
3062       // first check that there will be visible columns after the invert.
3063       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3064               && sg.getStartRes() <= sg.getEndRes()))
3065       {
3066         // now invert the sequence set, if required - empty selection implies
3067         // that no hiding is required.
3068         if (sg != null)
3069         {
3070           invertSequenceMenuItem_actionPerformed(null);
3071           sg = viewport.getSelectionGroup();
3072           toggleSeqs = true;
3073
3074         }
3075         viewport.expandColSelection(sg, true);
3076         // finally invert the column selection and get the new sequence
3077         // selection.
3078         invertColSel_actionPerformed(null);
3079         toggleCols = true;
3080       }
3081     }
3082
3083     if (toggleSeqs)
3084     {
3085       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3086       {
3087         hideSelSequences_actionPerformed(null);
3088         hide = true;
3089       }
3090       else if (!(toggleCols && viewport.hasSelectedColumns()))
3091       {
3092         showAllSeqs_actionPerformed(null);
3093       }
3094     }
3095
3096     if (toggleCols)
3097     {
3098       if (viewport.hasSelectedColumns())
3099       {
3100         hideSelColumns_actionPerformed(null);
3101         if (!toggleSeqs)
3102         {
3103           viewport.setSelectionGroup(sg);
3104         }
3105       }
3106       else if (!hide)
3107       {
3108         showAllColumns_actionPerformed(null);
3109       }
3110     }
3111   }
3112
3113   /*
3114    * (non-Javadoc)
3115    *
3116    * @see
3117    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3118    * event.ActionEvent)
3119    */
3120   @Override
3121   public void hideAllButSelection_actionPerformed(ActionEvent e)
3122   {
3123     toggleHiddenRegions(false, false);
3124     viewport.sendSelection();
3125   }
3126
3127   /*
3128    * (non-Javadoc)
3129    *
3130    * @see
3131    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3132    * .ActionEvent)
3133    */
3134   @Override
3135   public void hideAllSelection_actionPerformed(ActionEvent e)
3136   {
3137     SequenceGroup sg = viewport.getSelectionGroup();
3138     viewport.expandColSelection(sg, false);
3139     viewport.hideAllSelectedSeqs();
3140     viewport.hideSelectedColumns();
3141     alignPanel.updateLayout();
3142     alignPanel.paintAlignment(true, true);
3143     viewport.sendSelection();
3144   }
3145
3146   /*
3147    * (non-Javadoc)
3148    *
3149    * @see
3150    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3151    * ActionEvent)
3152    */
3153   @Override
3154   public void showAllhidden_actionPerformed(ActionEvent e)
3155   {
3156     viewport.showAllHiddenColumns();
3157     viewport.showAllHiddenSeqs();
3158     alignPanel.paintAlignment(true, true);
3159     viewport.sendSelection();
3160   }
3161
3162   @Override
3163   public void hideSelColumns_actionPerformed(ActionEvent e)
3164   {
3165     viewport.hideSelectedColumns();
3166     alignPanel.updateLayout();
3167     alignPanel.paintAlignment(true, true);
3168     viewport.sendSelection();
3169   }
3170
3171   @Override
3172   public void hiddenMarkers_actionPerformed(ActionEvent e)
3173   {
3174     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3175     repaint();
3176   }
3177
3178   /**
3179    * DOCUMENT ME!
3180    *
3181    * @param e
3182    *          DOCUMENT ME!
3183    */
3184   @Override
3185   protected void scaleAbove_actionPerformed(ActionEvent e)
3186   {
3187     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3188     alignPanel.updateLayout();
3189     alignPanel.paintAlignment(true, false);
3190   }
3191
3192   /**
3193    * DOCUMENT ME!
3194    *
3195    * @param e
3196    *          DOCUMENT ME!
3197    */
3198   @Override
3199   protected void scaleLeft_actionPerformed(ActionEvent e)
3200   {
3201     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3202     alignPanel.updateLayout();
3203     alignPanel.paintAlignment(true, false);
3204   }
3205
3206   /**
3207    * DOCUMENT ME!
3208    *
3209    * @param e
3210    *          DOCUMENT ME!
3211    */
3212   @Override
3213   protected void scaleRight_actionPerformed(ActionEvent e)
3214   {
3215     viewport.setScaleRightWrapped(scaleRight.isSelected());
3216     alignPanel.updateLayout();
3217     alignPanel.paintAlignment(true, false);
3218   }
3219
3220   /**
3221    * DOCUMENT ME!
3222    *
3223    * @param e
3224    *          DOCUMENT ME!
3225    */
3226   @Override
3227   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3228   {
3229     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3230     alignPanel.paintAlignment(false, false);
3231   }
3232
3233   /**
3234    * DOCUMENT ME!
3235    *
3236    * @param e
3237    *          DOCUMENT ME!
3238    */
3239   @Override
3240   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3241   {
3242     viewport.setShowText(viewTextMenuItem.isSelected());
3243     alignPanel.paintAlignment(false, false);
3244   }
3245
3246   /**
3247    * DOCUMENT ME!
3248    *
3249    * @param e
3250    *          DOCUMENT ME!
3251    */
3252   @Override
3253   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3254   {
3255     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3256     alignPanel.paintAlignment(false, false);
3257   }
3258
3259   public FeatureSettings featureSettings;
3260
3261   @Override
3262   public FeatureSettingsControllerI getFeatureSettingsUI()
3263   {
3264     return featureSettings;
3265   }
3266
3267   @Override
3268   public void featureSettings_actionPerformed(ActionEvent e)
3269   {
3270     showFeatureSettingsUI();
3271   }
3272
3273   @Override
3274   public FeatureSettingsControllerI showFeatureSettingsUI()
3275   {
3276     if (featureSettings != null)
3277     {
3278       featureSettings.closeOldSettings();
3279       featureSettings = null;
3280     }
3281     if (!showSeqFeatures.isSelected())
3282     {
3283       // make sure features are actually displayed
3284       showSeqFeatures.setSelected(true);
3285       showSeqFeatures_actionPerformed(null);
3286     }
3287     featureSettings = new FeatureSettings(this);
3288     return featureSettings;
3289   }
3290
3291   /**
3292    * Set or clear 'Show Sequence Features'
3293    *
3294    * @param evt
3295    *          DOCUMENT ME!
3296    */
3297   @Override
3298   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3299   {
3300     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3301     alignPanel.paintAlignment(true, true);
3302   }
3303
3304   /**
3305    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3306    * the annotations panel as a whole.
3307    *
3308    * The options to show/hide all annotations should be enabled when the panel
3309    * is shown, and disabled when the panel is hidden.
3310    *
3311    * @param e
3312    */
3313   @Override
3314   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3315   {
3316     final boolean setVisible = annotationPanelMenuItem.isSelected();
3317     viewport.setShowAnnotation(setVisible);
3318     this.showAllSeqAnnotations.setEnabled(setVisible);
3319     this.hideAllSeqAnnotations.setEnabled(setVisible);
3320     this.showAllAlAnnotations.setEnabled(setVisible);
3321     this.hideAllAlAnnotations.setEnabled(setVisible);
3322     alignPanel.updateLayout();
3323   }
3324
3325   @Override
3326   public void alignmentProperties()
3327   {
3328     JComponent pane;
3329     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3330
3331             .formatAsHtml();
3332     String content = MessageManager.formatMessage("label.html_content",
3333             new Object[]
3334             { contents.toString() });
3335     contents = null;
3336
3337     if (Platform.isJS())
3338     {
3339       JLabel textLabel = new JLabel();
3340       textLabel.setText(content);
3341       textLabel.setBackground(Color.WHITE);
3342
3343       pane = new JPanel(new BorderLayout());
3344       ((JPanel) pane).setOpaque(true);
3345       pane.setBackground(Color.WHITE);
3346       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3347     }
3348     else
3349     /**
3350      * Java only
3351      *
3352      * @j2sIgnore
3353      */
3354     {
3355       JEditorPane editPane = new JEditorPane("text/html", "");
3356       editPane.setEditable(false);
3357       editPane.setText(content);
3358       pane = editPane;
3359     }
3360
3361     JInternalFrame frame = new JInternalFrame();
3362
3363     frame.getContentPane().add(new JScrollPane(pane));
3364
3365     Desktop.addInternalFrame(frame, MessageManager
3366             .formatMessage("label.alignment_properties", new Object[]
3367             { getTitle() }), 500, 400);
3368   }
3369
3370   /**
3371    * Opens an Overview panel for the alignment, unless one is open already
3372    *
3373    * @param e
3374    */
3375   @Override
3376   public void overviewMenuItem_actionPerformed(ActionEvent e)
3377   {
3378     if (alignPanel.overviewPanel != null)
3379     {
3380       return;
3381     }
3382
3383     boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
3384                 false);
3385     openOverviewPanel(showHiddenRegions);
3386   }
3387
3388   public OverviewPanel openOverviewPanel(boolean showHidden)
3389   {
3390     JInternalFrame frame = new JInternalFrame();
3391     final OverviewPanel overview = new OverviewPanel(alignPanel, showHidden);
3392     frame.setContentPane(overview);
3393     String overviewTitle = MessageManager
3394             .formatMessage("label.overview_params", new Object[]
3395             { this.getTitle() });
3396     String viewName = alignPanel.getViewName();
3397     if (viewName != null)
3398     {
3399       overviewTitle += (" " + viewName);
3400     }
3401     Desktop.addInternalFrame(frame, overviewTitle, true, frame.getWidth(), frame.getHeight(),
3402             true, true);
3403     frame.pack();
3404     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3405     frame.addInternalFrameListener(
3406             new javax.swing.event.InternalFrameAdapter()
3407             {
3408               @Override
3409               public void internalFrameClosed(
3410                       javax.swing.event.InternalFrameEvent evt)
3411               {
3412                 overview.dispose();
3413                 alignPanel.setOverviewPanel(null);
3414               }
3415             });
3416     if (getKeyListeners().length > 0)
3417     {
3418       frame.addKeyListener(getKeyListeners()[0]);
3419     }
3420
3421     alignPanel.setOverviewPanel(overview);
3422
3423     return overview;
3424   }
3425
3426   @Override
3427   public void textColour_actionPerformed()
3428   {
3429     new TextColourChooser().chooseColour(alignPanel, null);
3430   }
3431
3432   /*
3433    * public void covariationColour_actionPerformed() {
3434    * changeColour(new
3435    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3436    * ()[0])); }
3437    */
3438   @Override
3439   public void annotationColour_actionPerformed()
3440   {
3441     new AnnotationColourChooser(viewport, alignPanel);
3442   }
3443
3444   @Override
3445   public void annotationColumn_actionPerformed(ActionEvent e)
3446   {
3447     new AnnotationColumnChooser(viewport, alignPanel);
3448   }
3449
3450   /**
3451    * Action on the user checking or unchecking the option to apply the selected
3452    * colour scheme to all groups. If unchecked, groups may have their own
3453    * independent colour schemes.
3454    *
3455    * @param selected
3456    */
3457   @Override
3458   public void applyToAllGroups_actionPerformed(boolean selected)
3459   {
3460     viewport.setColourAppliesToAllGroups(selected);
3461   }
3462
3463   /**
3464    * Action on user selecting a colour from the colour menu
3465    *
3466    * @param name
3467    *          the name (not the menu item label!) of the colour scheme
3468    */
3469   @Override
3470   public void changeColour_actionPerformed(String name)
3471   {
3472     /*
3473      * 'User Defined' opens a panel to configure or load a
3474      * user-defined colour scheme
3475      */
3476     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3477     {
3478       new UserDefinedColours(alignPanel);
3479       return;
3480     }
3481
3482     /*
3483      * otherwise set the chosen colour scheme (or null for 'None')
3484      */
3485     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3486             viewport,
3487             viewport.getAlignment(), viewport.getHiddenRepSequences());
3488     changeColour(cs);
3489   }
3490
3491   /**
3492    * Actions on setting or changing the alignment colour scheme
3493    *
3494    * @param cs
3495    */
3496   @Override
3497   public void changeColour(ColourSchemeI cs)
3498   {
3499     // TODO: pull up to controller method
3500     ColourMenuHelper.setColourSelected(colourMenu, cs);
3501
3502     viewport.setGlobalColourScheme(cs);
3503
3504     alignPanel.paintAlignment(true, true);
3505   }
3506
3507   /**
3508    * Show the PID threshold slider panel
3509    */
3510   @Override
3511   protected void modifyPID_actionPerformed()
3512   {
3513     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3514             alignPanel.getViewName());
3515     SliderPanel.showPIDSlider();
3516   }
3517
3518   /**
3519    * Show the Conservation slider panel
3520    */
3521   @Override
3522   protected void modifyConservation_actionPerformed()
3523   {
3524     SliderPanel.setConservationSlider(alignPanel,
3525             viewport.getResidueShading(), alignPanel.getViewName());
3526     SliderPanel.showConservationSlider();
3527   }
3528
3529   /**
3530    * Action on selecting or deselecting (Colour) By Conservation
3531    */
3532   @Override
3533   public void conservationMenuItem_actionPerformed(boolean selected)
3534   {
3535     modifyConservation.setEnabled(selected);
3536     viewport.setConservationSelected(selected);
3537     viewport.getResidueShading().setConservationApplied(selected);
3538
3539     changeColour(viewport.getGlobalColourScheme());
3540     if (selected)
3541     {
3542       modifyConservation_actionPerformed();
3543     }
3544     else
3545     {
3546       SliderPanel.hideConservationSlider();
3547     }
3548   }
3549
3550   /**
3551    * Action on selecting or deselecting (Colour) Above PID Threshold
3552    */
3553   @Override
3554   public void abovePIDThreshold_actionPerformed(boolean selected)
3555   {
3556     modifyPID.setEnabled(selected);
3557     viewport.setAbovePIDThreshold(selected);
3558     if (!selected)
3559     {
3560       viewport.getResidueShading().setThreshold(0,
3561               viewport.isIgnoreGapsConsensus());
3562     }
3563
3564     changeColour(viewport.getGlobalColourScheme());
3565     if (selected)
3566     {
3567       modifyPID_actionPerformed();
3568     }
3569     else
3570     {
3571       SliderPanel.hidePIDSlider();
3572     }
3573   }
3574
3575   /**
3576    * DOCUMENT ME!
3577    *
3578    * @param e
3579    *          DOCUMENT ME!
3580    */
3581   @Override
3582   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3583   {
3584     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3585     AlignmentSorter.sortByPID(viewport.getAlignment(),
3586             viewport.getAlignment().getSequenceAt(0));
3587     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3588             viewport.getAlignment()));
3589     alignPanel.paintAlignment(true, false);
3590   }
3591
3592   /**
3593    * DOCUMENT ME!
3594    *
3595    * @param e
3596    *          DOCUMENT ME!
3597    */
3598   @Override
3599   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3600   {
3601     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3602     AlignmentSorter.sortByID(viewport.getAlignment());
3603     addHistoryItem(
3604             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3605     alignPanel.paintAlignment(true, false);
3606   }
3607
3608   /**
3609    * DOCUMENT ME!
3610    *
3611    * @param e
3612    *          DOCUMENT ME!
3613    */
3614   @Override
3615   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3616   {
3617     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3618     AlignmentSorter.sortByLength(viewport.getAlignment());
3619     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3620             viewport.getAlignment()));
3621     alignPanel.paintAlignment(true, false);
3622   }
3623
3624   /**
3625    * DOCUMENT ME!
3626    *
3627    * @param e
3628    *          DOCUMENT ME!
3629    */
3630   @Override
3631   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3632   {
3633     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3634     AlignmentSorter.sortByGroup(viewport.getAlignment());
3635     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3636             viewport.getAlignment()));
3637
3638     alignPanel.paintAlignment(true, false);
3639   }
3640
3641   /**
3642    * DOCUMENT ME!
3643    *
3644    * @param e
3645    *          DOCUMENT ME!
3646    */
3647   @Override
3648   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3649   {
3650     new RedundancyPanel(alignPanel, this);
3651   }
3652
3653   /**
3654    * DOCUMENT ME!
3655    *
3656    * @param e
3657    *          DOCUMENT ME!
3658    */
3659   @Override
3660   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3661   {
3662     if ((viewport.getSelectionGroup() == null)
3663             || (viewport.getSelectionGroup().getSize() < 2))
3664     {
3665       JvOptionPane.showInternalMessageDialog(this,
3666               MessageManager.getString(
3667                       "label.you_must_select_least_two_sequences"),
3668               MessageManager.getString("label.invalid_selection"),
3669               JvOptionPane.WARNING_MESSAGE);
3670     }
3671     else
3672     {
3673       JInternalFrame frame = new JInternalFrame();
3674       frame.setContentPane(new PairwiseAlignPanel(viewport));
3675       Desktop.addInternalFrame(frame,
3676               MessageManager.getString("action.pairwise_alignment"), 600,
3677               500);
3678     }
3679   }
3680
3681   @Override
3682   public void autoCalculate_actionPerformed(ActionEvent e)
3683   {
3684     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3685     if (viewport.autoCalculateConsensus)
3686     {
3687       viewport.firePropertyChange("alignment", null,
3688               viewport.getAlignment().getSequences());
3689     }
3690   }
3691
3692   @Override
3693   public void sortByTreeOption_actionPerformed(ActionEvent e)
3694   {
3695     viewport.sortByTree = sortByTree.isSelected();
3696   }
3697
3698   @Override
3699   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3700   {
3701     viewport.followSelection = listenToViewSelections.isSelected();
3702   }
3703
3704   /**
3705    * Constructs a tree panel and adds it to the desktop
3706    *
3707    * @param type
3708    *          tree type (NJ or AV)
3709    * @param modelName
3710    *          name of score model used to compute the tree
3711    * @param options
3712    *          parameters for the distance or similarity calculation
3713    */
3714   void newTreePanel(String type, String modelName,
3715           SimilarityParamsI options)
3716   {
3717     String frameTitle = "";
3718     TreePanel tp;
3719
3720     boolean onSelection = false;
3721     if (viewport.getSelectionGroup() != null
3722             && viewport.getSelectionGroup().getSize() > 0)
3723     {
3724       SequenceGroup sg = viewport.getSelectionGroup();
3725
3726       /* Decide if the selection is a column region */
3727       for (SequenceI _s : sg.getSequences())
3728       {
3729         if (_s.getLength() < sg.getEndRes())
3730         {
3731           JvOptionPane.showMessageDialog(Desktop.desktop,
3732                   MessageManager.getString(
3733                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3734                   MessageManager.getString(
3735                           "label.sequences_selection_not_aligned"),
3736                   JvOptionPane.WARNING_MESSAGE);
3737
3738           return;
3739         }
3740       }
3741       onSelection = true;
3742     }
3743     else
3744     {
3745       if (viewport.getAlignment().getHeight() < 2)
3746       {
3747         return;
3748       }
3749     }
3750
3751     tp = new TreePanel(alignPanel, type, modelName, options);
3752     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3753
3754     frameTitle += " from ";
3755
3756     if (viewport.getViewName() != null)
3757     {
3758       frameTitle += viewport.getViewName() + " of ";
3759     }
3760
3761     frameTitle += this.title;
3762
3763     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3764   }
3765
3766   /**
3767    * DOCUMENT ME!
3768    *
3769    * @param title
3770    *          DOCUMENT ME!
3771    * @param order
3772    *          DOCUMENT ME!
3773    */
3774   public void addSortByOrderMenuItem(String title,
3775           final AlignmentOrder order)
3776   {
3777     final JMenuItem item = new JMenuItem(MessageManager
3778             .formatMessage("action.by_title_param", new Object[]
3779             { title }));
3780     sort.add(item);
3781     item.addActionListener(new java.awt.event.ActionListener()
3782     {
3783       @Override
3784       public void actionPerformed(ActionEvent e)
3785       {
3786         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3787
3788         // TODO: JBPNote - have to map order entries to curent SequenceI
3789         // pointers
3790         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3791
3792         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3793                 viewport.getAlignment()));
3794
3795         alignPanel.paintAlignment(true, false);
3796       }
3797     });
3798   }
3799
3800   /**
3801    * Add a new sort by annotation score menu item
3802    *
3803    * @param sort
3804    *          the menu to add the option to
3805    * @param scoreLabel
3806    *          the label used to retrieve scores for each sequence on the
3807    *          alignment
3808    */
3809   public void addSortByAnnotScoreMenuItem(JMenu sort,
3810           final String scoreLabel)
3811   {
3812     final JMenuItem item = new JMenuItem(scoreLabel);
3813     sort.add(item);
3814     item.addActionListener(new java.awt.event.ActionListener()
3815     {
3816       @Override
3817       public void actionPerformed(ActionEvent e)
3818       {
3819         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3820         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3821                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3822         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3823                 viewport.getAlignment()));
3824         alignPanel.paintAlignment(true, false);
3825       }
3826     });
3827   }
3828
3829   /**
3830    * last hash for alignment's annotation array - used to minimise cost of
3831    * rebuild.
3832    */
3833   protected int _annotationScoreVectorHash;
3834
3835   /**
3836    * search the alignment and rebuild the sort by annotation score submenu the
3837    * last alignment annotation vector hash is stored to minimize cost of
3838    * rebuilding in subsequence calls.
3839    *
3840    */
3841   @Override
3842   public void buildSortByAnnotationScoresMenu()
3843   {
3844     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3845     {
3846       return;
3847     }
3848
3849     if (viewport.getAlignment().getAlignmentAnnotation()
3850             .hashCode() != _annotationScoreVectorHash)
3851     {
3852       sortByAnnotScore.removeAll();
3853       // almost certainly a quicker way to do this - but we keep it simple
3854       Hashtable<String, String> scoreSorts = new Hashtable<>();
3855       AlignmentAnnotation aann[];
3856       for (SequenceI sqa : viewport.getAlignment().getSequences())
3857       {
3858         aann = sqa.getAnnotation();
3859         for (int i = 0; aann != null && i < aann.length; i++)
3860         {
3861           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3862           {
3863             scoreSorts.put(aann[i].label, aann[i].label);
3864           }
3865         }
3866       }
3867       Enumeration<String> labels = scoreSorts.keys();
3868       while (labels.hasMoreElements())
3869       {
3870         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3871                 labels.nextElement());
3872       }
3873       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3874       scoreSorts.clear();
3875
3876       _annotationScoreVectorHash = viewport.getAlignment()
3877               .getAlignmentAnnotation().hashCode();
3878     }
3879   }
3880
3881   /**
3882    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3883    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3884    * call. Listeners are added to remove the menu item when the treePanel is
3885    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3886    * modified.
3887    */
3888   @Override
3889   public void buildTreeSortMenu()
3890   {
3891     sortByTreeMenu.removeAll();
3892
3893     List<Component> comps = PaintRefresher.components
3894             .get(viewport.getSequenceSetId());
3895     List<TreePanel> treePanels = new ArrayList<>();
3896     for (Component comp : comps)
3897     {
3898       if (comp instanceof TreePanel)
3899       {
3900         treePanels.add((TreePanel) comp);
3901       }
3902     }
3903
3904     if (treePanels.size() < 1)
3905     {
3906       sortByTreeMenu.setVisible(false);
3907       return;
3908     }
3909
3910     sortByTreeMenu.setVisible(true);
3911
3912     for (final TreePanel tp : treePanels)
3913     {
3914       final JMenuItem item = new JMenuItem(tp.getTitle());
3915       item.addActionListener(new java.awt.event.ActionListener()
3916       {
3917         @Override
3918         public void actionPerformed(ActionEvent e)
3919         {
3920           tp.sortByTree_actionPerformed();
3921           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3922
3923         }
3924       });
3925
3926       sortByTreeMenu.add(item);
3927     }
3928   }
3929
3930   public boolean sortBy(AlignmentOrder alorder, String undoname)
3931   {
3932     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3933     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3934     if (undoname != null)
3935     {
3936       addHistoryItem(new OrderCommand(undoname, oldOrder,
3937               viewport.getAlignment()));
3938     }
3939     alignPanel.paintAlignment(true, false);
3940     return true;
3941   }
3942
3943   /**
3944    * Work out whether the whole set of sequences or just the selected set will
3945    * be submitted for multiple alignment.
3946    *
3947    */
3948   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3949   {
3950     // Now, check we have enough sequences
3951     AlignmentView msa = null;
3952
3953     if ((viewport.getSelectionGroup() != null)
3954             && (viewport.getSelectionGroup().getSize() > 1))
3955     {
3956       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3957       // some common interface!
3958       /*
3959        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3960        * SequenceI[sz = seqs.getSize(false)];
3961        *
3962        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3963        * seqs.getSequenceAt(i); }
3964        */
3965       msa = viewport.getAlignmentView(true);
3966     }
3967     else if (viewport.getSelectionGroup() != null
3968             && viewport.getSelectionGroup().getSize() == 1)
3969     {
3970       int option = JvOptionPane.showConfirmDialog(this,
3971               MessageManager.getString("warn.oneseq_msainput_selection"),
3972               MessageManager.getString("label.invalid_selection"),
3973               JvOptionPane.OK_CANCEL_OPTION);
3974       if (option == JvOptionPane.OK_OPTION)
3975       {
3976         msa = viewport.getAlignmentView(false);
3977       }
3978     }
3979     else
3980     {
3981       msa = viewport.getAlignmentView(false);
3982     }
3983     return msa;
3984   }
3985
3986   /**
3987    * Decides what is submitted to a secondary structure prediction service: the
3988    * first sequence in the alignment, or in the current selection, or, if the
3989    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3990    * region or the whole alignment. (where the first sequence in the set is the
3991    * one that the prediction will be for).
3992    */
3993   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3994   {
3995     AlignmentView seqs = null;
3996
3997     if ((viewport.getSelectionGroup() != null)
3998             && (viewport.getSelectionGroup().getSize() > 0))
3999     {
4000       seqs = viewport.getAlignmentView(true);
4001     }
4002     else
4003     {
4004       seqs = viewport.getAlignmentView(false);
4005     }
4006     // limit sequences - JBPNote in future - could spawn multiple prediction
4007     // jobs
4008     // TODO: viewport.getAlignment().isAligned is a global state - the local
4009     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4010     if (!viewport.getAlignment().isAligned(false))
4011     {
4012       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4013       // TODO: if seqs.getSequences().length>1 then should really have warned
4014       // user!
4015
4016     }
4017     return seqs;
4018   }
4019
4020   /**
4021    * DOCUMENT ME!
4022    *
4023    * @param e
4024    *          DOCUMENT ME!
4025    */
4026   @Override
4027   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4028   {
4029     // Pick the tree file
4030     JalviewFileChooser chooser = new JalviewFileChooser(
4031             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4032     chooser.setFileView(new JalviewFileView());
4033     chooser.setDialogTitle(
4034             MessageManager.getString("label.select_newick_like_tree_file"));
4035     chooser.setToolTipText(
4036             MessageManager.getString("label.load_tree_file"));
4037
4038     chooser.setResponseHandler(0,new Runnable()
4039     {
4040       @Override
4041       public void run()
4042       {
4043         String filePath = chooser.getSelectedFile().getPath();
4044         Cache.setProperty("LAST_DIRECTORY", filePath);
4045         NewickFile fin = null;
4046         try
4047         {
4048           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4049                   DataSourceType.FILE));
4050           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4051         } catch (Exception ex)
4052         {
4053           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4054                   MessageManager
4055                           .getString("label.problem_reading_tree_file"),
4056                   JvOptionPane.WARNING_MESSAGE);
4057           ex.printStackTrace();
4058         }
4059         if (fin != null && fin.hasWarningMessage())
4060         {
4061           JvOptionPane.showMessageDialog(Desktop.desktop,
4062                   fin.getWarningMessage(),
4063                   MessageManager.getString(
4064                           "label.possible_problem_with_tree_file"),
4065                   JvOptionPane.WARNING_MESSAGE);
4066         }
4067       }
4068     });
4069     chooser.showOpenDialog(this);
4070   }
4071
4072   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4073   {
4074     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4075   }
4076
4077   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4078           int h, int x, int y)
4079   {
4080     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4081   }
4082
4083   /**
4084    * Add a treeviewer for the tree extracted from a Newick file object to the
4085    * current alignment view
4086    *
4087    * @param nf
4088    *          the tree
4089    * @param title
4090    *          tree viewer title
4091    * @param input
4092    *          Associated alignment input data (or null)
4093    * @param w
4094    *          width
4095    * @param h
4096    *          height
4097    * @param x
4098    *          position
4099    * @param y
4100    *          position
4101    * @return TreePanel handle
4102    */
4103   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4104           AlignmentView input, int w, int h, int x, int y)
4105   {
4106     TreePanel tp = null;
4107
4108     try
4109     {
4110       nf.parse();
4111
4112       if (nf.getTree() != null)
4113       {
4114         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4115
4116         tp.setSize(w, h);
4117
4118         if (x > 0 && y > 0)
4119         {
4120           tp.setLocation(x, y);
4121         }
4122
4123         Desktop.addInternalFrame(tp, treeTitle, w, h);
4124       }
4125     } catch (Exception ex)
4126     {
4127       ex.printStackTrace();
4128     }
4129
4130     return tp;
4131   }
4132
4133   private boolean buildingMenu = false;
4134
4135   /**
4136    * Generates menu items and listener event actions for web service clients
4137    *
4138    */
4139   public void BuildWebServiceMenu()
4140   {
4141     while (buildingMenu)
4142     {
4143       try
4144       {
4145         System.err.println("Waiting for building menu to finish.");
4146         Thread.sleep(10);
4147       } catch (Exception e)
4148       {
4149       }
4150     }
4151     final AlignFrame me = this;
4152     buildingMenu = true;
4153     new Thread(new Runnable()
4154     {
4155       @Override
4156       public void run()
4157       {
4158         final List<JMenuItem> legacyItems = new ArrayList<>();
4159         try
4160         {
4161           // System.err.println("Building ws menu again "
4162           // + Thread.currentThread());
4163           // TODO: add support for context dependent disabling of services based
4164           // on
4165           // alignment and current selection
4166           // TODO: add additional serviceHandle parameter to specify abstract
4167           // handler
4168           // class independently of AbstractName
4169           // TODO: add in rediscovery GUI function to restart discoverer
4170           // TODO: group services by location as well as function and/or
4171           // introduce
4172           // object broker mechanism.
4173           final Vector<JMenu> wsmenu = new Vector<>();
4174           final IProgressIndicator af = me;
4175
4176           /*
4177            * do not i18n these strings - they are hard-coded in class
4178            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4179            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4180            */
4181           final JMenu msawsmenu = new JMenu("Alignment");
4182           final JMenu secstrmenu = new JMenu(
4183                   "Secondary Structure Prediction");
4184           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4185           final JMenu analymenu = new JMenu("Analysis");
4186           final JMenu dismenu = new JMenu("Protein Disorder");
4187           // JAL-940 - only show secondary structure prediction services from
4188           // the legacy server
4189           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4190               // &&
4191           Discoverer.services != null && (Discoverer.services.size() > 0))
4192           {
4193             // TODO: refactor to allow list of AbstractName/Handler bindings to
4194             // be
4195             // stored or retrieved from elsewhere
4196             // No MSAWS used any more:
4197             // Vector msaws = null; // (Vector)
4198             // Discoverer.services.get("MsaWS");
4199             Vector<ServiceHandle> secstrpr = Discoverer.services
4200                     .get("SecStrPred");
4201             if (secstrpr != null)
4202             {
4203               // Add any secondary structure prediction services
4204               for (int i = 0, j = secstrpr.size(); i < j; i++)
4205               {
4206                 final ext.vamsas.ServiceHandle sh = secstrpr
4207                         .get(i);
4208                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4209                         .getServiceClient(sh);
4210                 int p = secstrmenu.getItemCount();
4211                 impl.attachWSMenuEntry(secstrmenu, me);
4212                 int q = secstrmenu.getItemCount();
4213                 for (int litm = p; litm < q; litm++)
4214                 {
4215                   legacyItems.add(secstrmenu.getItem(litm));
4216                 }
4217               }
4218             }
4219           }
4220
4221           // Add all submenus in the order they should appear on the web
4222           // services menu
4223           wsmenu.add(msawsmenu);
4224           wsmenu.add(secstrmenu);
4225           wsmenu.add(dismenu);
4226           wsmenu.add(analymenu);
4227           // No search services yet
4228           // wsmenu.add(seqsrchmenu);
4229
4230           javax.swing.SwingUtilities.invokeLater(new Runnable()
4231           {
4232             @Override
4233             public void run()
4234             {
4235               try
4236               {
4237                 webService.removeAll();
4238                 // first, add discovered services onto the webservices menu
4239                 if (wsmenu.size() > 0)
4240                 {
4241                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4242                   {
4243                     webService.add(wsmenu.get(i));
4244                   }
4245                 }
4246                 else
4247                 {
4248                   webService.add(me.webServiceNoServices);
4249                 }
4250                 // TODO: move into separate menu builder class.
4251                 boolean new_sspred = false;
4252                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4253                 {
4254                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4255                   if (jws2servs != null)
4256                   {
4257                     if (jws2servs.hasServices())
4258                     {
4259                       jws2servs.attachWSMenuEntry(webService, me);
4260                       for (Jws2Instance sv : jws2servs.getServices())
4261                       {
4262                         if (sv.description.toLowerCase().contains("jpred"))
4263                         {
4264                           for (JMenuItem jmi : legacyItems)
4265                           {
4266                             jmi.setVisible(false);
4267                           }
4268                         }
4269                       }
4270
4271                     }
4272                     if (jws2servs.isRunning())
4273                     {
4274                       JMenuItem tm = new JMenuItem(
4275                               "Still discovering JABA Services");
4276                       tm.setEnabled(false);
4277                       webService.add(tm);
4278                     }
4279                   }
4280                 }
4281                 build_urlServiceMenu(me.webService);
4282                 build_fetchdbmenu(webService);
4283                 for (JMenu item : wsmenu)
4284                 {
4285                   if (item.getItemCount() == 0)
4286                   {
4287                     item.setEnabled(false);
4288                   }
4289                   else
4290                   {
4291                     item.setEnabled(true);
4292                   }
4293                 }
4294               } catch (Exception e)
4295               {
4296                 Cache.log.debug(
4297                         "Exception during web service menu building process.",
4298                         e);
4299               }
4300             }
4301           });
4302         } catch (Exception e)
4303         {
4304         }
4305         buildingMenu = false;
4306       }
4307     }).start();
4308
4309   }
4310
4311   /**
4312    * construct any groupURL type service menu entries.
4313    *
4314    * @param webService
4315    */
4316   protected void build_urlServiceMenu(JMenu webService)
4317   {
4318     // TODO: remove this code when 2.7 is released
4319     // DEBUG - alignmentView
4320     /*
4321      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4322      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4323      *
4324      * @Override public void actionPerformed(ActionEvent e) {
4325      * jalview.datamodel.AlignmentView
4326      * .testSelectionViews(af.viewport.getAlignment(),
4327      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4328      *
4329      * }); webService.add(testAlView);
4330      */
4331     // TODO: refactor to RestClient discoverer and merge menu entries for
4332     // rest-style services with other types of analysis/calculation service
4333     // SHmmr test client - still being implemented.
4334     // DEBUG - alignmentView
4335
4336     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4337             .getRestClients())
4338     {
4339       client.attachWSMenuEntry(
4340               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4341               this);
4342     }
4343   }
4344
4345   /**
4346    * Searches the alignment sequences for xRefs and builds the Show
4347    * Cross-References menu (formerly called Show Products), with database
4348    * sources for which cross-references are found (protein sources for a
4349    * nucleotide alignment and vice versa)
4350    *
4351    * @return true if Show Cross-references menu should be enabled
4352    */
4353   public boolean canShowProducts()
4354   {
4355     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4356     AlignmentI dataset = viewport.getAlignment().getDataset();
4357
4358     showProducts.removeAll();
4359     final boolean dna = viewport.getAlignment().isNucleotide();
4360
4361     if (seqs == null || seqs.length == 0)
4362     {
4363       // nothing to see here.
4364       return false;
4365     }
4366
4367     boolean showp = false;
4368     try
4369     {
4370       List<String> ptypes = new CrossRef(seqs, dataset)
4371               .findXrefSourcesForSequences(dna);
4372
4373       for (final String source : ptypes)
4374       {
4375         showp = true;
4376         final AlignFrame af = this;
4377         JMenuItem xtype = new JMenuItem(source);
4378         xtype.addActionListener(new ActionListener()
4379         {
4380           @Override
4381           public void actionPerformed(ActionEvent e)
4382           {
4383             showProductsFor(af.viewport.getSequenceSelection(), dna,
4384                     source);
4385           }
4386         });
4387         showProducts.add(xtype);
4388       }
4389       showProducts.setVisible(showp);
4390       showProducts.setEnabled(showp);
4391     } catch (Exception e)
4392     {
4393       Cache.log.warn(
4394               "canShowProducts threw an exception - please report to help@jalview.org",
4395               e);
4396       return false;
4397     }
4398     return showp;
4399   }
4400
4401   /**
4402    * Finds and displays cross-references for the selected sequences (protein
4403    * products for nucleotide sequences, dna coding sequences for peptides).
4404    *
4405    * @param sel
4406    *          the sequences to show cross-references for
4407    * @param dna
4408    *          true if from a nucleotide alignment (so showing proteins)
4409    * @param source
4410    *          the database to show cross-references for
4411    */
4412   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4413           final String source)
4414   {
4415     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4416             .start();
4417   }
4418
4419   /**
4420    * Construct and display a new frame containing the translation of this
4421    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4422    */
4423   @Override
4424   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4425   {
4426     AlignmentI al = null;
4427     try
4428     {
4429       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4430
4431       al = dna.translateCdna(codeTable);
4432     } catch (Exception ex)
4433     {
4434       jalview.bin.Cache.log.error(
4435               "Exception during translation. Please report this !", ex);
4436       final String msg = MessageManager.getString(
4437               "label.error_when_translating_sequences_submit_bug_report");
4438       final String errorTitle = MessageManager
4439               .getString("label.implementation_error")
4440               + MessageManager.getString("label.translation_failed");
4441       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4442               JvOptionPane.ERROR_MESSAGE);
4443       return;
4444     }
4445     if (al == null || al.getHeight() == 0)
4446     {
4447       final String msg = MessageManager.getString(
4448               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4449       final String errorTitle = MessageManager
4450               .getString("label.translation_failed");
4451       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4452               JvOptionPane.WARNING_MESSAGE);
4453     }
4454     else
4455     {
4456       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4457       af.setFileFormat(this.currentFileFormat);
4458       final String newTitle = MessageManager
4459               .formatMessage("label.translation_of_params", new Object[]
4460               { this.getTitle(), codeTable.getId() });
4461       af.setTitle(newTitle);
4462       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4463       {
4464         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4465         viewport.openSplitFrame(af, new Alignment(seqs));
4466       }
4467       else
4468       {
4469         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4470                 DEFAULT_HEIGHT);
4471       }
4472     }
4473   }
4474
4475   /**
4476    * Set the file format
4477    *
4478    * @param format
4479    */
4480   public void setFileFormat(FileFormatI format)
4481   {
4482     this.currentFileFormat = format;
4483   }
4484
4485   /**
4486    * Try to load a features file onto the alignment.
4487    *
4488    * @param file
4489    *          contents or path to retrieve file or a File object
4490    * @param sourceType
4491    *          access mode of file (see jalview.io.AlignFile)
4492    * @return true if features file was parsed correctly.
4493    */
4494   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4495   {
4496     // BH 2018
4497     return avc.parseFeaturesFile(file, sourceType,
4498             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4499
4500   }
4501
4502   @Override
4503   public void refreshFeatureUI(boolean enableIfNecessary)
4504   {
4505     // note - currently this is only still here rather than in the controller
4506     // because of the featureSettings hard reference that is yet to be
4507     // abstracted
4508     if (enableIfNecessary)
4509     {
4510       viewport.setShowSequenceFeatures(true);
4511       showSeqFeatures.setSelected(true);
4512     }
4513
4514   }
4515
4516   @Override
4517   public void dragEnter(DropTargetDragEvent evt)
4518   {
4519   }
4520
4521   @Override
4522   public void dragExit(DropTargetEvent evt)
4523   {
4524   }
4525
4526   @Override
4527   public void dragOver(DropTargetDragEvent evt)
4528   {
4529   }
4530
4531   @Override
4532   public void dropActionChanged(DropTargetDragEvent evt)
4533   {
4534   }
4535
4536   @Override
4537   public void drop(DropTargetDropEvent evt)
4538   {
4539     // JAL-1552 - acceptDrop required before getTransferable call for
4540     // Java's Transferable for native dnd
4541     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4542     Transferable t = evt.getTransferable();
4543
4544     final AlignFrame thisaf = this;
4545     final List<Object> files = new ArrayList<>();
4546     List<DataSourceType> protocols = new ArrayList<>();
4547
4548     try
4549     {
4550       Desktop.transferFromDropTarget(files, protocols, evt, t);
4551     } catch (Exception e)
4552     {
4553       e.printStackTrace();
4554     }
4555     if (files != null)
4556     {
4557       new Thread(new Runnable()
4558       {
4559         @Override
4560         public void run()
4561         {
4562           try
4563           {
4564             // check to see if any of these files have names matching sequences
4565             // in
4566             // the alignment
4567             SequenceIdMatcher idm = new SequenceIdMatcher(
4568                     viewport.getAlignment().getSequencesArray());
4569             /**
4570              * Object[] { String,SequenceI}
4571              */
4572             ArrayList<Object[]> filesmatched = new ArrayList<>();
4573             ArrayList<Object> filesnotmatched = new ArrayList<>();
4574             for (int i = 0; i < files.size(); i++)
4575             {
4576               // BH 2018
4577               Object file = files.get(i);
4578               String fileName = file.toString();
4579               String pdbfn = "";
4580               DataSourceType protocol = (file instanceof File
4581                       ? DataSourceType.FILE
4582                       : FormatAdapter.checkProtocol(fileName));
4583               if (protocol == DataSourceType.FILE)
4584               {
4585                 File fl;
4586                 if (file instanceof File) {
4587                   fl = (File) file;
4588                   Platform.cacheFileData(fl);
4589                 } else {
4590                   fl = new File(fileName);
4591                 }
4592                 pdbfn = fl.getName();
4593               }
4594               else if (protocol == DataSourceType.URL)
4595               {
4596                 URL url = new URL(fileName);
4597                 pdbfn = url.getFile();
4598               }
4599               if (pdbfn.length() > 0)
4600               {
4601                 // attempt to find a match in the alignment
4602                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4603                 int l = 0, c = pdbfn.indexOf(".");
4604                 while (mtch == null && c != -1)
4605                 {
4606                   do
4607                   {
4608                     l = c;
4609                   } while ((c = pdbfn.indexOf(".", l)) > l);
4610                   if (l > -1)
4611                   {
4612                     pdbfn = pdbfn.substring(0, l);
4613                   }
4614                   mtch = idm.findAllIdMatches(pdbfn);
4615                 }
4616                 if (mtch != null)
4617                 {
4618                   FileFormatI type;
4619                   try
4620                   {
4621                     type = new IdentifyFile().identify(file, protocol);
4622                   } catch (Exception ex)
4623                   {
4624                     type = null;
4625                   }
4626                   if (type != null && type.isStructureFile())
4627                   {
4628                     filesmatched.add(new Object[] { file, protocol, mtch });
4629                     continue;
4630                   }
4631                 }
4632                 // File wasn't named like one of the sequences or wasn't a PDB
4633                 // file.
4634                 filesnotmatched.add(file);
4635               }
4636             }
4637             int assocfiles = 0;
4638             if (filesmatched.size() > 0)
4639             {
4640               boolean autoAssociate = Cache
4641                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4642               if (!autoAssociate)
4643               {
4644                 String msg = MessageManager.formatMessage(
4645                         "label.automatically_associate_structure_files_with_sequences_same_name",
4646                         new Object[]
4647                         { Integer.valueOf(filesmatched.size())
4648                                 .toString() });
4649                 String ttl = MessageManager.getString(
4650                         "label.automatically_associate_structure_files_by_name");
4651                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4652                         ttl, JvOptionPane.YES_NO_OPTION);
4653                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4654               }
4655               if (autoAssociate)
4656               {
4657                 for (Object[] fm : filesmatched)
4658                 {
4659                   // try and associate
4660                   // TODO: may want to set a standard ID naming formalism for
4661                   // associating PDB files which have no IDs.
4662                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4663                   {
4664                     PDBEntry pe = new AssociatePdbFileWithSeq()
4665                             .associatePdbWithSeq(fm[0].toString(),
4666                                     (DataSourceType) fm[1], toassoc, false,
4667                                     Desktop.instance);
4668                     if (pe != null)
4669                     {
4670                       System.err.println("Associated file : "
4671                               + (fm[0].toString()) + " with "
4672                               + toassoc.getDisplayId(true));
4673                       assocfiles++;
4674                     }
4675                   }
4676                   // TODO: do we need to update overview ? only if features are
4677                   // shown I guess
4678                   alignPanel.paintAlignment(true, false);
4679                 }
4680               }
4681               else
4682               {
4683                 /*
4684                  * add declined structures as sequences
4685                  */
4686                 for (Object[] o : filesmatched)
4687                 {
4688                   filesnotmatched.add(o[0]);
4689                 }
4690               }
4691             }
4692             if (filesnotmatched.size() > 0)
4693             {
4694               if (assocfiles > 0 && (Cache.getDefault(
4695                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4696                       || JvOptionPane.showConfirmDialog(thisaf,
4697                               "<html>" + MessageManager.formatMessage(
4698                                       "label.ignore_unmatched_dropped_files_info",
4699                                       new Object[]
4700                                       { Integer.valueOf(
4701                                               filesnotmatched.size())
4702                                               .toString() })
4703                                       + "</html>",
4704                               MessageManager.getString(
4705                                       "label.ignore_unmatched_dropped_files"),
4706                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4707               {
4708                 return;
4709               }
4710               for (Object fn : filesnotmatched)
4711               {
4712                 loadJalviewDataFile(fn, null, null, null);
4713               }
4714
4715             }
4716           } catch (Exception ex)
4717           {
4718             ex.printStackTrace();
4719           }
4720         }
4721       }).start();
4722     }
4723   }
4724
4725   /**
4726    * Attempt to load a "dropped" file or URL string, by testing in turn for
4727    * <ul>
4728    * <li>an Annotation file</li>
4729    * <li>a JNet file</li>
4730    * <li>a features file</li>
4731    * <li>else try to interpret as an alignment file</li>
4732    * </ul>
4733    *
4734    * @param file
4735    *          either a filename or a URL string.
4736    */
4737   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4738           FileFormatI format, SequenceI assocSeq)
4739   {
4740     // BH 2018 was String file
4741     try
4742     {
4743       if (sourceType == null)
4744       {
4745         sourceType = FormatAdapter.checkProtocol(file);
4746       }
4747       // if the file isn't identified, or not positively identified as some
4748       // other filetype (PFAM is default unidentified alignment file type) then
4749       // try to parse as annotation.
4750       boolean isAnnotation = (format == null
4751               || FileFormat.Pfam.equals(format))
4752                       ? new AnnotationFile().annotateAlignmentView(viewport,
4753                               file, sourceType)
4754                       : false;
4755
4756       if (!isAnnotation)
4757       {
4758         // first see if its a T-COFFEE score file
4759         TCoffeeScoreFile tcf = null;
4760         try
4761         {
4762           tcf = new TCoffeeScoreFile(file, sourceType);
4763           if (tcf.isValid())
4764           {
4765             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4766             {
4767               buildColourMenu();
4768               changeColour(
4769                       new TCoffeeColourScheme(viewport.getAlignment()));
4770               isAnnotation = true;
4771               setStatus(MessageManager.getString(
4772                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4773             }
4774             else
4775             {
4776               // some problem - if no warning its probable that the ID matching
4777               // process didn't work
4778               JvOptionPane.showMessageDialog(Desktop.desktop,
4779                       tcf.getWarningMessage() == null
4780                               ? MessageManager.getString(
4781                                       "label.check_file_matches_sequence_ids_alignment")
4782                               : tcf.getWarningMessage(),
4783                       MessageManager.getString(
4784                               "label.problem_reading_tcoffee_score_file"),
4785                       JvOptionPane.WARNING_MESSAGE);
4786             }
4787           }
4788           else
4789           {
4790             tcf = null;
4791           }
4792         } catch (Exception x)
4793         {
4794           Cache.log.debug(
4795                   "Exception when processing data source as T-COFFEE score file",
4796                   x);
4797           tcf = null;
4798         }
4799         if (tcf == null)
4800         {
4801           // try to see if its a JNet 'concise' style annotation file *before*
4802           // we
4803           // try to parse it as a features file
4804           if (format == null)
4805           {
4806             format = new IdentifyFile().identify(file, sourceType);
4807           }
4808           if (FileFormat.ScoreMatrix == format)
4809           {
4810             ScoreMatrixFile sm = new ScoreMatrixFile(
4811                     new FileParse(file, sourceType));
4812             sm.parse();
4813             // todo: i18n this message
4814             setStatus(MessageManager.formatMessage(
4815                     "label.successfully_loaded_matrix",
4816                     sm.getMatrixName()));
4817           }
4818           else if (FileFormat.Jnet.equals(format))
4819           {
4820             JPredFile predictions = new JPredFile(file, sourceType);
4821             new JnetAnnotationMaker();
4822             JnetAnnotationMaker.add_annotation(predictions,
4823                     viewport.getAlignment(), 0, false);
4824             viewport.getAlignment().setupJPredAlignment();
4825             isAnnotation = true;
4826           }
4827           // else if (IdentifyFile.FeaturesFile.equals(format))
4828           else if (FileFormat.Features.equals(format))
4829           {
4830             if (parseFeaturesFile(file, sourceType))
4831             {
4832               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4833               if (splitFrame != null)
4834               {
4835                 splitFrame.repaint();
4836               }
4837               else
4838               {
4839                 alignPanel.paintAlignment(true, true);
4840               }
4841             }
4842           }
4843           else
4844           {
4845             new FileLoader().LoadFile(viewport, file, sourceType, format);
4846           }
4847         }
4848       }
4849       if (isAnnotation)
4850       {
4851
4852         alignPanel.adjustAnnotationHeight();
4853         viewport.updateSequenceIdColours();
4854         buildSortByAnnotationScoresMenu();
4855         alignPanel.paintAlignment(true, true);
4856       }
4857     } catch (Exception ex)
4858     {
4859       ex.printStackTrace();
4860     } catch (OutOfMemoryError oom)
4861     {
4862       try
4863       {
4864         System.gc();
4865       } catch (Exception x)
4866       {
4867       }
4868       new OOMWarning(
4869               "loading data "
4870                       + (sourceType != null
4871                               ? (sourceType == DataSourceType.PASTE
4872                                       ? "from clipboard."
4873                                       : "using " + sourceType + " from "
4874                                               + file)
4875                               : ".")
4876                       + (format != null
4877                               ? "(parsing as '" + format + "' file)"
4878                               : ""),
4879               oom, Desktop.desktop);
4880     }
4881   }
4882
4883   /**
4884    * Method invoked by the ChangeListener on the tabbed pane, in other words
4885    * when a different tabbed pane is selected by the user or programmatically.
4886    */
4887   @Override
4888   public void tabSelectionChanged(int index)
4889   {
4890     if (index > -1)
4891     {
4892       alignPanel = alignPanels.get(index);
4893       viewport = alignPanel.av;
4894       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4895       setMenusFromViewport(viewport);
4896       if (featureSettings != null && featureSettings.isOpen()
4897               && featureSettings.fr.getViewport() != viewport)
4898       {
4899         if (viewport.isShowSequenceFeatures())
4900         {
4901           // refresh the featureSettings to reflect UI change
4902           showFeatureSettingsUI();
4903         }
4904         else
4905         {
4906           // close feature settings for this view.
4907           featureSettings.close();
4908         }
4909       }
4910
4911     }
4912
4913     /*
4914      * 'focus' any colour slider that is open to the selected viewport
4915      */
4916     if (viewport.getConservationSelected())
4917     {
4918       SliderPanel.setConservationSlider(alignPanel,
4919               viewport.getResidueShading(), alignPanel.getViewName());
4920     }
4921     else
4922     {
4923       SliderPanel.hideConservationSlider();
4924     }
4925     if (viewport.getAbovePIDThreshold())
4926     {
4927       SliderPanel.setPIDSliderSource(alignPanel,
4928               viewport.getResidueShading(), alignPanel.getViewName());
4929     }
4930     else
4931     {
4932       SliderPanel.hidePIDSlider();
4933     }
4934
4935     /*
4936      * If there is a frame linked to this one in a SplitPane, switch it to the
4937      * same view tab index. No infinite recursion of calls should happen, since
4938      * tabSelectionChanged() should not get invoked on setting the selected
4939      * index to an unchanged value. Guard against setting an invalid index
4940      * before the new view peer tab has been created.
4941      */
4942     final AlignViewportI peer = viewport.getCodingComplement();
4943     if (peer != null)
4944     {
4945       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4946               .getAlignPanel().alignFrame;
4947       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4948       {
4949         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4950       }
4951     }
4952   }
4953
4954   /**
4955    * On right mouse click on view tab, prompt for and set new view name.
4956    */
4957   @Override
4958   public void tabbedPane_mousePressed(MouseEvent e)
4959   {
4960     if (e.isPopupTrigger())
4961     {
4962       String msg = MessageManager.getString("label.enter_view_name");
4963       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4964       String reply = JvOptionPane.showInputDialog(msg, ttl);
4965
4966       if (reply != null)
4967       {
4968         viewport.setViewName(reply);
4969         // TODO warn if reply is in getExistingViewNames()?
4970         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4971       }
4972     }
4973   }
4974
4975   public AlignViewport getCurrentView()
4976   {
4977     return viewport;
4978   }
4979
4980   /**
4981    * Open the dialog for regex description parsing.
4982    */
4983   @Override
4984   protected void extractScores_actionPerformed(ActionEvent e)
4985   {
4986     ParseProperties pp = new jalview.analysis.ParseProperties(
4987             viewport.getAlignment());
4988     // TODO: verify regex and introduce GUI dialog for version 2.5
4989     // if (pp.getScoresFromDescription("col", "score column ",
4990     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4991     // true)>0)
4992     if (pp.getScoresFromDescription("description column",
4993             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4994     {
4995       buildSortByAnnotationScoresMenu();
4996     }
4997   }
4998
4999   /*
5000    * (non-Javadoc)
5001    *
5002    * @see
5003    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5004    * )
5005    */
5006   @Override
5007   protected void showDbRefs_actionPerformed(ActionEvent e)
5008   {
5009     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5010   }
5011
5012   /*
5013    * (non-Javadoc)
5014    *
5015    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5016    * ActionEvent)
5017    */
5018   @Override
5019   protected void showNpFeats_actionPerformed(ActionEvent e)
5020   {
5021     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5022   }
5023
5024   /**
5025    * find the viewport amongst the tabs in this alignment frame and close that
5026    * tab
5027    *
5028    * @param av
5029    */
5030   public boolean closeView(AlignViewportI av)
5031   {
5032     if (viewport == av)
5033     {
5034       this.closeMenuItem_actionPerformed(false);
5035       return true;
5036     }
5037     Component[] comp = tabbedPane.getComponents();
5038     for (int i = 0; comp != null && i < comp.length; i++)
5039     {
5040       if (comp[i] instanceof AlignmentPanel)
5041       {
5042         if (((AlignmentPanel) comp[i]).av == av)
5043         {
5044           // close the view.
5045           closeView((AlignmentPanel) comp[i]);
5046           return true;
5047         }
5048       }
5049     }
5050     return false;
5051   }
5052
5053   protected void build_fetchdbmenu(JMenu webService)
5054   {
5055     // Temporary hack - DBRef Fetcher always top level ws entry.
5056     // TODO We probably want to store a sequence database checklist in
5057     // preferences and have checkboxes.. rather than individual sources selected
5058     // here
5059     final JMenu rfetch = new JMenu(
5060             MessageManager.getString("action.fetch_db_references"));
5061     rfetch.setToolTipText(MessageManager.getString(
5062             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5063     webService.add(rfetch);
5064
5065     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5066             MessageManager.getString("option.trim_retrieved_seqs"));
5067     trimrs.setToolTipText(
5068             MessageManager.getString("label.trim_retrieved_sequences"));
5069     trimrs.setSelected(
5070             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5071     trimrs.addActionListener(new ActionListener()
5072     {
5073       @Override
5074       public void actionPerformed(ActionEvent e)
5075       {
5076         trimrs.setSelected(trimrs.isSelected());
5077         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5078                 Boolean.valueOf(trimrs.isSelected()).toString());
5079       }
5080     });
5081     rfetch.add(trimrs);
5082     JMenuItem fetchr = new JMenuItem(
5083             MessageManager.getString("label.standard_databases"));
5084     fetchr.setToolTipText(
5085             MessageManager.getString("label.fetch_embl_uniprot"));
5086     fetchr.addActionListener(new ActionListener()
5087     {
5088
5089       @Override
5090       public void actionPerformed(ActionEvent e)
5091       {
5092         new Thread(new Runnable()
5093         {
5094           @Override
5095           public void run()
5096           {
5097             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5098                     .getAlignment().isNucleotide();
5099             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5100                     alignPanel.av.getSequenceSelection(),
5101                     alignPanel.alignFrame, null,
5102                     alignPanel.alignFrame.featureSettings, isNucleotide);
5103             dbRefFetcher.addListener(new FetchFinishedListenerI()
5104             {
5105               @Override
5106               public void finished()
5107               {
5108
5109                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5110                         .getFeatureSettingsModels())
5111                 {
5112
5113                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5114                 }
5115                 AlignFrame.this.setMenusForViewport();
5116               }
5117             });
5118             dbRefFetcher.fetchDBRefs(false);
5119           }
5120         }).start();
5121
5122       }
5123
5124     });
5125     rfetch.add(fetchr);
5126     new Thread(new Runnable()
5127     {
5128       @Override
5129       public void run()
5130       {
5131         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5132                 .getSequenceFetcherSingleton();
5133         javax.swing.SwingUtilities.invokeLater(new Runnable()
5134         {
5135           @Override
5136           public void run()
5137           {
5138             String[] dbclasses = sf.getNonAlignmentSources();
5139             List<DbSourceProxy> otherdb;
5140             JMenu dfetch = new JMenu();
5141             JMenu ifetch = new JMenu();
5142             JMenuItem fetchr = null;
5143             int comp = 0, icomp = 0, mcomp = 15;
5144             String mname = null;
5145             int dbi = 0;
5146             for (String dbclass : dbclasses)
5147             {
5148               otherdb = sf.getSourceProxy(dbclass);
5149               // add a single entry for this class, or submenu allowing 'fetch
5150               // all' or pick one
5151               if (otherdb == null || otherdb.size() < 1)
5152               {
5153                 continue;
5154               }
5155               if (mname == null)
5156               {
5157                 mname = "From " + dbclass;
5158               }
5159               if (otherdb.size() == 1)
5160               {
5161                 final DbSourceProxy[] dassource = otherdb
5162                         .toArray(new DbSourceProxy[0]);
5163                 DbSourceProxy src = otherdb.get(0);
5164                 fetchr = new JMenuItem(src.getDbSource());
5165                 fetchr.addActionListener(new ActionListener()
5166                 {
5167
5168                   @Override
5169                   public void actionPerformed(ActionEvent e)
5170                   {
5171                     new Thread(new Runnable()
5172                     {
5173
5174                       @Override
5175                       public void run()
5176                       {
5177                         boolean isNucleotide = alignPanel.alignFrame
5178                                 .getViewport().getAlignment()
5179                                 .isNucleotide();
5180                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5181                                 alignPanel.av.getSequenceSelection(),
5182                                 alignPanel.alignFrame, dassource,
5183                                 alignPanel.alignFrame.featureSettings,
5184                                 isNucleotide);
5185                         dbRefFetcher
5186                                 .addListener(new FetchFinishedListenerI()
5187                                 {
5188                                   @Override
5189                                   public void finished()
5190                                   {
5191                                     FeatureSettingsModelI srcSettings = dassource[0]
5192                                             .getFeatureColourScheme();
5193                                     alignPanel.av.mergeFeaturesStyle(
5194                                             srcSettings);
5195                                     AlignFrame.this.setMenusForViewport();
5196                                   }
5197                                 });
5198                         dbRefFetcher.fetchDBRefs(false);
5199                       }
5200                     }).start();
5201                   }
5202
5203                 });
5204                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5205                         MessageManager.formatMessage(
5206                                 "label.fetch_retrieve_from", new Object[]
5207                                 { src.getDbName() })));
5208                 dfetch.add(fetchr);
5209                 comp++;
5210               }
5211               else
5212               {
5213                 final DbSourceProxy[] dassource = otherdb
5214                         .toArray(new DbSourceProxy[0]);
5215                 // fetch all entry
5216                 DbSourceProxy src = otherdb.get(0);
5217                 fetchr = new JMenuItem(MessageManager
5218                         .formatMessage("label.fetch_all_param", new Object[]
5219                         { src.getDbSource() }));
5220                 fetchr.addActionListener(new ActionListener()
5221                 {
5222                   @Override
5223                   public void actionPerformed(ActionEvent e)
5224                   {
5225                     new Thread(new Runnable()
5226                     {
5227
5228                       @Override
5229                       public void run()
5230                       {
5231                         boolean isNucleotide = alignPanel.alignFrame
5232                                 .getViewport().getAlignment()
5233                                 .isNucleotide();
5234                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5235                                 alignPanel.av.getSequenceSelection(),
5236                                 alignPanel.alignFrame, dassource,
5237                                 alignPanel.alignFrame.featureSettings,
5238                                 isNucleotide);
5239                         dbRefFetcher
5240                                 .addListener(new FetchFinishedListenerI()
5241                                 {
5242                                   @Override
5243                                   public void finished()
5244                                   {
5245                                     AlignFrame.this.setMenusForViewport();
5246                                   }
5247                                 });
5248                         dbRefFetcher.fetchDBRefs(false);
5249                       }
5250                     }).start();
5251                   }
5252                 });
5253
5254                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5255                         MessageManager.formatMessage(
5256                                 "label.fetch_retrieve_from_all_sources",
5257                                 new Object[]
5258                                 { Integer.valueOf(otherdb.size())
5259                                         .toString(),
5260                                     src.getDbSource(), src.getDbName() })));
5261                 dfetch.add(fetchr);
5262                 comp++;
5263                 // and then build the rest of the individual menus
5264                 ifetch = new JMenu(MessageManager.formatMessage(
5265                         "label.source_from_db_source", new Object[]
5266                         { src.getDbSource() }));
5267                 icomp = 0;
5268                 String imname = null;
5269                 int i = 0;
5270                 for (DbSourceProxy sproxy : otherdb)
5271                 {
5272                   String dbname = sproxy.getDbName();
5273                   String sname = dbname.length() > 5
5274                           ? dbname.substring(0, 5) + "..."
5275                           : dbname;
5276                   String msname = dbname.length() > 10
5277                           ? dbname.substring(0, 10) + "..."
5278                           : dbname;
5279                   if (imname == null)
5280                   {
5281                     imname = MessageManager
5282                             .formatMessage("label.from_msname", new Object[]
5283                             { sname });
5284                   }
5285                   fetchr = new JMenuItem(msname);
5286                   final DbSourceProxy[] dassrc = { sproxy };
5287                   fetchr.addActionListener(new ActionListener()
5288                   {
5289
5290                     @Override
5291                     public void actionPerformed(ActionEvent e)
5292                     {
5293                       new Thread(new Runnable()
5294                       {
5295
5296                         @Override
5297                         public void run()
5298                         {
5299                           boolean isNucleotide = alignPanel.alignFrame
5300                                   .getViewport().getAlignment()
5301                                   .isNucleotide();
5302                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5303                                   alignPanel.av.getSequenceSelection(),
5304                                   alignPanel.alignFrame, dassrc,
5305                                   alignPanel.alignFrame.featureSettings,
5306                                   isNucleotide);
5307                           dbRefFetcher
5308                                   .addListener(new FetchFinishedListenerI()
5309                                   {
5310                                     @Override
5311                                     public void finished()
5312                                     {
5313                                       AlignFrame.this.setMenusForViewport();
5314                                     }
5315                                   });
5316                           dbRefFetcher.fetchDBRefs(false);
5317                         }
5318                       }).start();
5319                     }
5320
5321                   });
5322                   fetchr.setToolTipText(
5323                           "<html>" + MessageManager.formatMessage(
5324                                   "label.fetch_retrieve_from", new Object[]
5325                                   { dbname }));
5326                   ifetch.add(fetchr);
5327                   ++i;
5328                   if (++icomp >= mcomp || i == (otherdb.size()))
5329                   {
5330                     ifetch.setText(MessageManager.formatMessage(
5331                             "label.source_to_target", imname, sname));
5332                     dfetch.add(ifetch);
5333                     ifetch = new JMenu();
5334                     imname = null;
5335                     icomp = 0;
5336                     comp++;
5337                   }
5338                 }
5339               }
5340               ++dbi;
5341               if (comp >= mcomp || dbi >= (dbclasses.length))
5342               {
5343                 dfetch.setText(MessageManager.formatMessage(
5344                         "label.source_to_target", mname, dbclass));
5345                 rfetch.add(dfetch);
5346                 dfetch = new JMenu();
5347                 mname = null;
5348                 comp = 0;
5349               }
5350             }
5351           }
5352         });
5353       }
5354     }).start();
5355
5356   }
5357
5358   /**
5359    * Left justify the whole alignment.
5360    */
5361   @Override
5362   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5363   {
5364     AlignmentI al = viewport.getAlignment();
5365     al.justify(false);
5366     viewport.firePropertyChange("alignment", null, al);
5367   }
5368
5369   /**
5370    * Right justify the whole alignment.
5371    */
5372   @Override
5373   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5374   {
5375     AlignmentI al = viewport.getAlignment();
5376     al.justify(true);
5377     viewport.firePropertyChange("alignment", null, al);
5378   }
5379
5380   @Override
5381   public void setShowSeqFeatures(boolean b)
5382   {
5383     showSeqFeatures.setSelected(b);
5384     viewport.setShowSequenceFeatures(b);
5385   }
5386
5387   /*
5388    * (non-Javadoc)
5389    *
5390    * @see
5391    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5392    * awt.event.ActionEvent)
5393    */
5394   @Override
5395   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5396   {
5397     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5398     alignPanel.paintAlignment(false, false);
5399   }
5400
5401   /*
5402    * (non-Javadoc)
5403    *
5404    * @see
5405    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5406    * .ActionEvent)
5407    */
5408   @Override
5409   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5410   {
5411     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5412     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5413
5414   }
5415
5416   /*
5417    * (non-Javadoc)
5418    *
5419    * @see
5420    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5421    * .event.ActionEvent)
5422    */
5423   @Override
5424   protected void showGroupConservation_actionPerformed(ActionEvent e)
5425   {
5426     viewport.setShowGroupConservation(showGroupConservation.getState());
5427     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5428   }
5429
5430   /*
5431    * (non-Javadoc)
5432    *
5433    * @see
5434    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5435    * .event.ActionEvent)
5436    */
5437   @Override
5438   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5439   {
5440     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5441     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5442   }
5443
5444   /*
5445    * (non-Javadoc)
5446    *
5447    * @see
5448    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5449    * .event.ActionEvent)
5450    */
5451   @Override
5452   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5453   {
5454     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5455     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5456   }
5457
5458   @Override
5459   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5460   {
5461     showSequenceLogo.setState(true);
5462     viewport.setShowSequenceLogo(true);
5463     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5464     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5465   }
5466
5467   @Override
5468   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5469   {
5470     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5471   }
5472
5473   /*
5474    * (non-Javadoc)
5475    *
5476    * @see
5477    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5478    * .event.ActionEvent)
5479    */
5480   @Override
5481   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5482   {
5483     if (avc.makeGroupsFromSelection())
5484     {
5485       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5486       alignPanel.updateAnnotation();
5487       alignPanel.paintAlignment(true,
5488               viewport.needToUpdateStructureViews());
5489     }
5490   }
5491
5492   public void clearAlignmentSeqRep()
5493   {
5494     // TODO refactor alignmentseqrep to controller
5495     if (viewport.getAlignment().hasSeqrep())
5496     {
5497       viewport.getAlignment().setSeqrep(null);
5498       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5499       alignPanel.updateAnnotation();
5500       alignPanel.paintAlignment(true, true);
5501     }
5502   }
5503
5504   @Override
5505   protected void createGroup_actionPerformed(ActionEvent e)
5506   {
5507     if (avc.createGroup())
5508     {
5509       if (applyAutoAnnotationSettings.isSelected())
5510       {
5511         alignPanel.updateAnnotation(true, false);
5512       }
5513       alignPanel.alignmentChanged();
5514     }
5515   }
5516
5517   @Override
5518   protected void unGroup_actionPerformed(ActionEvent e)
5519   {
5520     if (avc.unGroup())
5521     {
5522       alignPanel.alignmentChanged();
5523     }
5524   }
5525
5526   /**
5527    * make the given alignmentPanel the currently selected tab
5528    *
5529    * @param alignmentPanel
5530    */
5531   public void setDisplayedView(AlignmentPanel alignmentPanel)
5532   {
5533     if (!viewport.getSequenceSetId()
5534             .equals(alignmentPanel.av.getSequenceSetId()))
5535     {
5536       throw new Error(MessageManager.getString(
5537               "error.implementation_error_cannot_show_view_alignment_frame"));
5538     }
5539     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5540             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5541     {
5542       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5543     }
5544   }
5545
5546   /**
5547    * Action on selection of menu options to Show or Hide annotations.
5548    *
5549    * @param visible
5550    * @param forSequences
5551    *          update sequence-related annotations
5552    * @param forAlignment
5553    *          update non-sequence-related annotations
5554    */
5555   @Override
5556   protected void setAnnotationsVisibility(boolean visible,
5557           boolean forSequences, boolean forAlignment)
5558   {
5559     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5560             .getAlignmentAnnotation();
5561     if (anns == null)
5562     {
5563       return;
5564     }
5565     for (AlignmentAnnotation aa : anns)
5566     {
5567       /*
5568        * don't display non-positional annotations on an alignment
5569        */
5570       if (aa.annotations == null)
5571       {
5572         continue;
5573       }
5574       boolean apply = (aa.sequenceRef == null && forAlignment)
5575               || (aa.sequenceRef != null && forSequences);
5576       if (apply)
5577       {
5578         aa.visible = visible;
5579       }
5580     }
5581     alignPanel.validateAnnotationDimensions(true);
5582     alignPanel.alignmentChanged();
5583   }
5584
5585   /**
5586    * Store selected annotation sort order for the view and repaint.
5587    */
5588   @Override
5589   protected void sortAnnotations_actionPerformed()
5590   {
5591     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5592     this.alignPanel.av
5593             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5594     alignPanel.paintAlignment(false, false);
5595   }
5596
5597   /**
5598    *
5599    * @return alignment panels in this alignment frame
5600    */
5601   public List<? extends AlignmentViewPanel> getAlignPanels()
5602   {
5603     // alignPanels is never null
5604     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5605     return alignPanels;
5606   }
5607
5608   /**
5609    * Open a new alignment window, with the cDNA associated with this (protein)
5610    * alignment, aligned as is the protein.
5611    */
5612   protected void viewAsCdna_actionPerformed()
5613   {
5614     // TODO no longer a menu action - refactor as required
5615     final AlignmentI alignment = getViewport().getAlignment();
5616     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5617     if (mappings == null)
5618     {
5619       return;
5620     }
5621     List<SequenceI> cdnaSeqs = new ArrayList<>();
5622     for (SequenceI aaSeq : alignment.getSequences())
5623     {
5624       for (AlignedCodonFrame acf : mappings)
5625       {
5626         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5627         if (dnaSeq != null)
5628         {
5629           /*
5630            * There is a cDNA mapping for this protein sequence - add to new
5631            * alignment. It will share the same dataset sequence as other mapped
5632            * cDNA (no new mappings need to be created).
5633            */
5634           final Sequence newSeq = new Sequence(dnaSeq);
5635           newSeq.setDatasetSequence(dnaSeq);
5636           cdnaSeqs.add(newSeq);
5637         }
5638       }
5639     }
5640     if (cdnaSeqs.size() == 0)
5641     {
5642       // show a warning dialog no mapped cDNA
5643       return;
5644     }
5645     AlignmentI cdna = new Alignment(
5646             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5647     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5648             AlignFrame.DEFAULT_HEIGHT);
5649     cdna.alignAs(alignment);
5650     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5651             + this.title;
5652     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5653             AlignFrame.DEFAULT_HEIGHT);
5654   }
5655
5656   /**
5657    * Set visibility of dna/protein complement view (available when shown in a
5658    * split frame).
5659    *
5660    * @param show
5661    */
5662   @Override
5663   protected void showComplement_actionPerformed(boolean show)
5664   {
5665     SplitContainerI sf = getSplitViewContainer();
5666     if (sf != null)
5667     {
5668       sf.setComplementVisible(this, show);
5669     }
5670   }
5671
5672   /**
5673    * Generate the reverse (optionally complemented) of the selected sequences,
5674    * and add them to the alignment
5675    */
5676   @Override
5677   protected void showReverse_actionPerformed(boolean complement)
5678   {
5679     AlignmentI al = null;
5680     try
5681     {
5682       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5683       al = dna.reverseCdna(complement);
5684       viewport.addAlignment(al, "");
5685       addHistoryItem(new EditCommand(
5686               MessageManager.getString("label.add_sequences"), Action.PASTE,
5687               al.getSequencesArray(), 0, al.getWidth(),
5688               viewport.getAlignment()));
5689     } catch (Exception ex)
5690     {
5691       System.err.println(ex.getMessage());
5692       return;
5693     }
5694   }
5695
5696   /**
5697    * Try to run a script in the Groovy console, having first ensured that this
5698    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5699    * be targeted at this alignment.
5700    */
5701   @Override
5702   protected void runGroovy_actionPerformed()
5703   {
5704     Jalview.setCurrentAlignFrame(this);
5705     groovy.ui.Console console = Desktop.getGroovyConsole();
5706     if (console != null)
5707     {
5708       try
5709       {
5710         console.runScript();
5711       } catch (Exception ex)
5712       {
5713         System.err.println((ex.toString()));
5714         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5715                 MessageManager.getString("label.couldnt_run_groovy_script"),
5716                 MessageManager.getString("label.groovy_support_failed"),
5717                 JvOptionPane.ERROR_MESSAGE);
5718       }
5719     }
5720     else
5721     {
5722       System.err.println("Can't run Groovy script as console not found");
5723     }
5724   }
5725
5726   /**
5727    * Hides columns containing (or not containing) a specified feature, provided
5728    * that would not leave all columns hidden
5729    *
5730    * @param featureType
5731    * @param columnsContaining
5732    * @return
5733    */
5734   public boolean hideFeatureColumns(String featureType,
5735           boolean columnsContaining)
5736   {
5737     boolean notForHiding = avc.markColumnsContainingFeatures(
5738             columnsContaining, false, false, featureType);
5739     if (notForHiding)
5740     {
5741       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5742               false, featureType))
5743       {
5744         getViewport().hideSelectedColumns();
5745         return true;
5746       }
5747     }
5748     return false;
5749   }
5750
5751   @Override
5752   protected void selectHighlightedColumns_actionPerformed(
5753           ActionEvent actionEvent)
5754   {
5755     // include key modifier check in case user selects from menu
5756     avc.markHighlightedColumns(
5757             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5758             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5759                     | ActionEvent.CTRL_MASK)) != 0);
5760   }
5761
5762   /**
5763    * Rebuilds the Colour menu, including any user-defined colours which have
5764    * been loaded either on startup or during the session
5765    */
5766   public void buildColourMenu()
5767   {
5768     colourMenu.removeAll();
5769
5770     colourMenu.add(applyToAllGroups);
5771     colourMenu.add(textColour);
5772     colourMenu.addSeparator();
5773
5774     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5775             viewport.getAlignment(), false);
5776
5777     colourMenu.add(annotationColour);
5778     bg.add(annotationColour);
5779     colourMenu.addSeparator();
5780     colourMenu.add(conservationMenuItem);
5781     colourMenu.add(modifyConservation);
5782     colourMenu.add(abovePIDThreshold);
5783     colourMenu.add(modifyPID);
5784
5785     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5786     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5787   }
5788
5789   /**
5790    * Open a dialog (if not already open) that allows the user to select and
5791    * calculate PCA or Tree analysis
5792    */
5793   protected void openTreePcaDialog()
5794   {
5795     if (alignPanel.getCalculationDialog() == null)
5796     {
5797       new CalculationChooser(AlignFrame.this);
5798     }
5799   }
5800
5801   @Override
5802   protected void loadVcf_actionPerformed()
5803   {
5804     JalviewFileChooser chooser = new JalviewFileChooser(
5805             Cache.getProperty("LAST_DIRECTORY"));
5806     chooser.setFileView(new JalviewFileView());
5807     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5808     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5809     final AlignFrame us = this;
5810     chooser.setResponseHandler(0, new Runnable()
5811     {
5812       @Override
5813       public void run()
5814       {
5815         String choice = chooser.getSelectedFile().getPath();
5816         Cache.setProperty("LAST_DIRECTORY", choice);
5817         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5818         new VCFLoader(choice).loadVCF(seqs, us);
5819       }
5820     });
5821     chooser.showOpenDialog(null);
5822
5823   }
5824
5825   private Rectangle lastFeatureSettingsBounds = null;
5826   @Override
5827   public void setFeatureSettingsGeometry(Rectangle bounds)
5828   {
5829     lastFeatureSettingsBounds = bounds;
5830   }
5831
5832   @Override
5833   public Rectangle getFeatureSettingsGeometry()
5834   {
5835     return lastFeatureSettingsBounds;
5836   }
5837 }
5838
5839 class PrintThread extends Thread
5840 {
5841   AlignmentPanel ap;
5842
5843   public PrintThread(AlignmentPanel ap)
5844   {
5845     this.ap = ap;
5846   }
5847
5848   static PageFormat pf;
5849
5850   @Override
5851   public void run()
5852   {
5853     PrinterJob printJob = PrinterJob.getPrinterJob();
5854
5855     if (pf != null)
5856     {
5857       printJob.setPrintable(ap, pf);
5858     }
5859     else
5860     {
5861       printJob.setPrintable(ap);
5862     }
5863
5864     if (printJob.printDialog())
5865     {
5866       try
5867       {
5868         printJob.print();
5869       } catch (Exception PrintException)
5870       {
5871         PrintException.printStackTrace();
5872       }
5873     }
5874   }
5875 }