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 jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  64 import jalview.io.AlignmentProperties;
  65 import jalview.io.AnnotationFile;
  66 import jalview.io.BioJsHTMLOutput;
  67 import jalview.io.DataSourceType;
  68 import jalview.io.FileFormat;
  69 import jalview.io.FileFormatI;
  70 import jalview.io.FileFormats;
  71 import jalview.io.FileLoader;
  72 import jalview.io.FormatAdapter;
  73 import jalview.io.HtmlSvgOutput;
  74 import jalview.io.IdentifyFile;
  75 import jalview.io.JPredFile;
  76 import jalview.io.JalviewFileChooser;
  77 import jalview.io.JalviewFileView;
  78 import jalview.io.JnetAnnotationMaker;
  79 import jalview.io.NewickFile;
  80 import jalview.io.TCoffeeScoreFile;
  81 import jalview.jbgui.GAlignFrame;
  82 import jalview.schemes.ColourSchemeI;
  83 import jalview.schemes.ColourSchemes;
  84 import jalview.schemes.ResidueColourScheme;
  85 import jalview.schemes.ResidueProperties;
  86 import jalview.schemes.TCoffeeColourScheme;
  87 import jalview.util.MessageManager;
  88 import jalview.viewmodel.AlignmentViewport;
  89 import jalview.viewmodel.ViewportRanges;
  90 import jalview.ws.DBRefFetcher;
  91 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  92 import jalview.ws.jws1.Discoverer;
  93 import jalview.ws.jws2.Jws2Discoverer;
  94 import jalview.ws.jws2.jabaws2.Jws2Instance;
  95 import jalview.ws.seqfetcher.DbSourceProxy;
  96
  97 import java.awt.BorderLayout;
  98 import java.awt.Component;
  99 import java.awt.Rectangle;
 100 import java.awt.Toolkit;
 101 import java.awt.datatransfer.Clipboard;
 102 import java.awt.datatransfer.DataFlavor;
 103 import java.awt.datatransfer.StringSelection;
 104 import java.awt.datatransfer.Transferable;
 105 import java.awt.dnd.DnDConstants;
 106 import java.awt.dnd.DropTargetDragEvent;
 107 import java.awt.dnd.DropTargetDropEvent;
 108 import java.awt.dnd.DropTargetEvent;
 109 import java.awt.dnd.DropTargetListener;
 110 import java.awt.event.ActionEvent;
 111 import java.awt.event.ActionListener;
 112 import java.awt.event.FocusAdapter;
 113 import java.awt.event.FocusEvent;
 114 import java.awt.event.ItemEvent;
 115 import java.awt.event.ItemListener;
 116 import java.awt.event.KeyAdapter;
 117 import java.awt.event.KeyEvent;
 118 import java.awt.event.MouseEvent;
 119 import java.awt.print.PageFormat;
 120 import java.awt.print.PrinterJob;
 121 import java.beans.PropertyChangeEvent;
 122 import java.io.File;
 123 import java.io.FileWriter;
 124 import java.io.PrintWriter;
 125 import java.net.URL;
 126 import java.util.ArrayList;
 127 import java.util.Arrays;
 128 import java.util.Deque;
 129 import java.util.Enumeration;
 130 import java.util.Hashtable;
 131 import java.util.List;
 132 import java.util.Vector;
 133
 134 import javax.swing.JCheckBoxMenuItem;
 135 import javax.swing.JEditorPane;
 136 import javax.swing.JInternalFrame;
 137 import javax.swing.JLayeredPane;
 138 import javax.swing.JMenu;
 139 import javax.swing.JMenuItem;
 140 import javax.swing.JScrollPane;
 141 import javax.swing.SwingUtilities;
 142
 143 /**
 144  * DOCUMENT ME!
 145  *
 146  * @author $author$
 147  * @version $Revision$
 148  */
 149 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 150         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 151 {
 152
 153   public static final int DEFAULT_WIDTH = 700;
 154
 155   public static final int DEFAULT_HEIGHT = 500;
 156
 157   /*
 158    * The currently displayed panel (selected tabbed view if more than one)
 159    */
 160   public AlignmentPanel alignPanel;
 161
 162   AlignViewport viewport;
 163
 164   ViewportRanges vpRanges;
 165
 166   public AlignViewControllerI avc;
 167
 168   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 169
 170   /**
 171    * Last format used to load or save alignments in this window
 172    */
 173   FileFormatI currentFileFormat = null;
 174
 175   /**
 176    * Current filename for this alignment
 177    */
 178   String fileName = null;
 179
 180   /**
 181    * Creates a new AlignFrame object with specific width and height.
 182    *
 183    * @param al
 184    * @param width
 185    * @param height
 186    */
 187   public AlignFrame(AlignmentI al, int width, int height)
 188   {
 189     this(al, null, width, height);
 190   }
 191
 192   /**
 193    * Creates a new AlignFrame object with specific width, height and
 194    * sequenceSetId
 195    *
 196    * @param al
 197    * @param width
 198    * @param height
 199    * @param sequenceSetId
 200    */
 201   public AlignFrame(AlignmentI al, int width, int height,
 202           String sequenceSetId)
 203   {
 204     this(al, null, width, height, sequenceSetId);
 205   }
 206
 207   /**
 208    * Creates a new AlignFrame object with specific width, height and
 209    * sequenceSetId
 210    *
 211    * @param al
 212    * @param width
 213    * @param height
 214    * @param sequenceSetId
 215    * @param viewId
 216    */
 217   public AlignFrame(AlignmentI al, int width, int height,
 218           String sequenceSetId, String viewId)
 219   {
 220     this(al, null, width, height, sequenceSetId, viewId);
 221   }
 222
 223   /**
 224    * new alignment window with hidden columns
 225    *
 226    * @param al
 227    *          AlignmentI
 228    * @param hiddenColumns
 229    *          ColumnSelection or null
 230    * @param width
 231    *          Width of alignment frame
 232    * @param height
 233    *          height of frame.
 234    */
 235   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 236           int width, int height)
 237   {
 238     this(al, hiddenColumns, width, height, null);
 239   }
 240
 241   /**
 242    * Create alignment frame for al with hiddenColumns, a specific width and
 243    * height, and specific sequenceId
 244    *
 245    * @param al
 246    * @param hiddenColumns
 247    * @param width
 248    * @param height
 249    * @param sequenceSetId
 250    *          (may be null)
 251    */
 252   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 253           int width, int height, String sequenceSetId)
 254   {
 255     this(al, hiddenColumns, width, height, sequenceSetId, null);
 256   }
 257
 258   /**
 259    * Create alignment frame for al with hiddenColumns, a specific width and
 260    * height, and specific sequenceId
 261    *
 262    * @param al
 263    * @param hiddenColumns
 264    * @param width
 265    * @param height
 266    * @param sequenceSetId
 267    *          (may be null)
 268    * @param viewId
 269    *          (may be null)
 270    */
 271   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 272           int width, int height, String sequenceSetId, String viewId)
 273   {
 274     setSize(width, height);
 275
 276     if (al.getDataset() == null)
 277     {
 278       al.setDataset(null);
 279     }
 280
 281     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 282
 283     alignPanel = new AlignmentPanel(this, viewport);
 284
 285     addAlignmentPanel(alignPanel, true);
 286     init();
 287   }
 288
 289   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 290           ColumnSelection hiddenColumns, int width, int height)
 291   {
 292     setSize(width, height);
 293
 294     if (al.getDataset() == null)
 295     {
 296       al.setDataset(null);
 297     }
 298
 299     viewport = new AlignViewport(al, hiddenColumns);
 300
 301     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 302     {
 303       viewport.hideSequence(hiddenSeqs);
 304     }
 305     alignPanel = new AlignmentPanel(this, viewport);
 306     addAlignmentPanel(alignPanel, true);
 307     init();
 308   }
 309
 310   /**
 311    * Make a new AlignFrame from existing alignmentPanels
 312    *
 313    * @param ap
 314    *          AlignmentPanel
 315    * @param av
 316    *          AlignViewport
 317    */
 318   public AlignFrame(AlignmentPanel ap)
 319   {
 320     viewport = ap.av;
 321     alignPanel = ap;
 322     addAlignmentPanel(ap, false);
 323     init();
 324   }
 325
 326   /**
 327    * initalise the alignframe from the underlying viewport data and the
 328    * configurations
 329    */
 330   void init()
 331   {
 332     if (!Jalview.isHeadlessMode())
 333     {
 334       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 335     }
 336
 337     vpRanges = viewport.getRanges();
 338     avc = new jalview.controller.AlignViewController(this, viewport,
 339             alignPanel);
 340     if (viewport.getAlignmentConservationAnnotation() == null)
 341     {
 342       // BLOSUM62Colour.setEnabled(false);
 343       conservationMenuItem.setEnabled(false);
 344       modifyConservation.setEnabled(false);
 345       // PIDColour.setEnabled(false);
 346       // abovePIDThreshold.setEnabled(false);
 347       // modifyPID.setEnabled(false);
 348     }
 349
 350     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 351             "No sort");
 352
 353     if (sortby.equals("Id"))
 354     {
 355       sortIDMenuItem_actionPerformed(null);
 356     }
 357     else if (sortby.equals("Pairwise Identity"))
 358     {
 359       sortPairwiseMenuItem_actionPerformed(null);
 360     }
 361
 362     this.alignPanel.av
 363             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 364
 365     setMenusFromViewport(viewport);
 366     buildSortByAnnotationScoresMenu();
 367     buildTreeMenu();
 368     buildColourMenu();
 369
 370     if (Desktop.desktop != null)
 371     {
 372       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 373       addServiceListeners();
 374       setGUINucleotide();
 375     }
 376
 377     if (viewport.getWrapAlignment())
 378     {
 379       wrapMenuItem_actionPerformed(null);
 380     }
 381
 382     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 383     {
 384       this.overviewMenuItem_actionPerformed(null);
 385     }
 386
 387     addKeyListener();
 388
 389     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 390     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 391     final String menuLabel = MessageManager
 392             .getString("label.copy_format_from");
 393     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 394             new ViewSetProvider()
 395             {
 396
 397               @Override
 398               public AlignmentPanel[] getAllAlignmentPanels()
 399               {
 400                 origview.clear();
 401                 origview.add(alignPanel);
 402                 // make an array of all alignment panels except for this one
 403                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 404                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 405                 aps.remove(AlignFrame.this.alignPanel);
 406                 return aps.toArray(new AlignmentPanel[aps.size()]);
 407               }
 408             }, selviews, new ItemListener()
 409             {
 410
 411               @Override
 412               public void itemStateChanged(ItemEvent e)
 413               {
 414                 if (origview.size() > 0)
 415                 {
 416                   final AlignmentPanel ap = origview.get(0);
 417
 418                   /*
 419                    * Copy the ViewStyle of the selected panel to 'this one'.
 420                    * Don't change value of 'scaleProteinAsCdna' unless copying
 421                    * from a SplitFrame.
 422                    */
 423                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 424                           .getViewStyle();
 425                   boolean fromSplitFrame = selviews.get(0)
 426                           .getAlignViewport().getCodingComplement() != null;
 427                   if (!fromSplitFrame)
 428                   {
 429                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 430                             .getViewStyle().isScaleProteinAsCdna());
 431                   }
 432                   ap.getAlignViewport().setViewStyle(vs);
 433
 434                   /*
 435                    * Also rescale ViewStyle of SplitFrame complement if there is
 436                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 437                    * the whole ViewStyle (allow cDNA protein to have different
 438                    * fonts)
 439                    */
 440                   AlignViewportI complement = ap.getAlignViewport()
 441                           .getCodingComplement();
 442                   if (complement != null && vs.isScaleProteinAsCdna())
 443                   {
 444                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 445                     ((SplitFrame) af.getSplitViewContainer())
 446                             .adjustLayout();
 447                     af.setMenusForViewport();
 448                   }
 449
 450                   ap.updateLayout();
 451                   ap.setSelected(true);
 452                   ap.alignFrame.setMenusForViewport();
 453
 454                 }
 455               }
 456             });
 457     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 458             .indexOf("devel") > -1
 459             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 460                     .indexOf("test") > -1)
 461     {
 462       formatMenu.add(vsel);
 463     }
 464     addFocusListener(new FocusAdapter()
 465     {
 466       @Override
 467       public void focusGained(FocusEvent e)
 468       {
 469         Jalview.setCurrentAlignFrame(AlignFrame.this);
 470       }
 471     });
 472
 473   }
 474
 475   /**
 476    * Change the filename and format for the alignment, and enable the 'reload'
 477    * button functionality.
 478    *
 479    * @param file
 480    *          valid filename
 481    * @param format
 482    *          format of file
 483    */
 484   public void setFileName(String file, FileFormatI format)
 485   {
 486     fileName = file;
 487     setFileFormat(format);
 488     reload.setEnabled(true);
 489   }
 490
 491   /**
 492    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 493    * events
 494    */
 495   void addKeyListener()
 496   {
 497     addKeyListener(new KeyAdapter()
 498     {
 499       @Override
 500       public void keyPressed(KeyEvent evt)
 501       {
 502         if (viewport.cursorMode
 503                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 504                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 505                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 506                 && Character.isDigit(evt.getKeyChar()))
 507         {
 508           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 509         }
 510
 511         switch (evt.getKeyCode())
 512         {
 513
 514         case 27: // escape key
 515           deselectAllSequenceMenuItem_actionPerformed(null);
 516
 517           break;
 518
 519         case KeyEvent.VK_DOWN:
 520           if (evt.isAltDown() || !viewport.cursorMode)
 521           {
 522             moveSelectedSequences(false);
 523           }
 524           if (viewport.cursorMode)
 525           {
 526             alignPanel.getSeqPanel().moveCursor(0, 1);
 527           }
 528           break;
 529
 530         case KeyEvent.VK_UP:
 531           if (evt.isAltDown() || !viewport.cursorMode)
 532           {
 533             moveSelectedSequences(true);
 534           }
 535           if (viewport.cursorMode)
 536           {
 537             alignPanel.getSeqPanel().moveCursor(0, -1);
 538           }
 539
 540           break;
 541
 542         case KeyEvent.VK_LEFT:
 543           if (evt.isAltDown() || !viewport.cursorMode)
 544           {
 545             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 546           }
 547           else
 548           {
 549             alignPanel.getSeqPanel().moveCursor(-1, 0);
 550           }
 551
 552           break;
 553
 554         case KeyEvent.VK_RIGHT:
 555           if (evt.isAltDown() || !viewport.cursorMode)
 556           {
 557             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 558           }
 559           else
 560           {
 561             alignPanel.getSeqPanel().moveCursor(1, 0);
 562           }
 563           break;
 564
 565         case KeyEvent.VK_SPACE:
 566           if (viewport.cursorMode)
 567           {
 568             alignPanel.getSeqPanel().insertGapAtCursor(
 569                     evt.isControlDown() || evt.isShiftDown()
 570                             || evt.isAltDown());
 571           }
 572           break;
 573
 574         // case KeyEvent.VK_A:
 575         // if (viewport.cursorMode)
 576         // {
 577         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 578         // //System.out.println("A");
 579         // }
 580         // break;
 581         /*
 582          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 583          * System.out.println("closing bracket"); } break;
 584          */
 585         case KeyEvent.VK_DELETE:
 586         case KeyEvent.VK_BACK_SPACE:
 587           if (!viewport.cursorMode)
 588           {
 589             cut_actionPerformed(null);
 590           }
 591           else
 592           {
 593             alignPanel.getSeqPanel().deleteGapAtCursor(
 594                     evt.isControlDown() || evt.isShiftDown()
 595                             || evt.isAltDown());
 596           }
 597
 598           break;
 599
 600         case KeyEvent.VK_S:
 601           if (viewport.cursorMode)
 602           {
 603             alignPanel.getSeqPanel().setCursorRow();
 604           }
 605           break;
 606         case KeyEvent.VK_C:
 607           if (viewport.cursorMode && !evt.isControlDown())
 608           {
 609             alignPanel.getSeqPanel().setCursorColumn();
 610           }
 611           break;
 612         case KeyEvent.VK_P:
 613           if (viewport.cursorMode)
 614           {
 615             alignPanel.getSeqPanel().setCursorPosition();
 616           }
 617           break;
 618
 619         case KeyEvent.VK_ENTER:
 620         case KeyEvent.VK_COMMA:
 621           if (viewport.cursorMode)
 622           {
 623             alignPanel.getSeqPanel().setCursorRowAndColumn();
 624           }
 625           break;
 626
 627         case KeyEvent.VK_Q:
 628           if (viewport.cursorMode)
 629           {
 630             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 631           }
 632           break;
 633         case KeyEvent.VK_M:
 634           if (viewport.cursorMode)
 635           {
 636             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 637           }
 638           break;
 639
 640         case KeyEvent.VK_F2:
 641           viewport.cursorMode = !viewport.cursorMode;
 642           statusBar.setText(MessageManager.formatMessage(
 643                   "label.keyboard_editing_mode",
 644                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 645           if (viewport.cursorMode)
 646           {
 647             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 648                     .getStartRes();
 649             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 650                     .getStartSeq();
 651           }
 652           alignPanel.getSeqPanel().seqCanvas.repaint();
 653           break;
 654
 655         case KeyEvent.VK_F1:
 656           try
 657           {
 658             Help.showHelpWindow();
 659           } catch (Exception ex)
 660           {
 661             ex.printStackTrace();
 662           }
 663           break;
 664         case KeyEvent.VK_H:
 665         {
 666           boolean toggleSeqs = !evt.isControlDown();
 667           boolean toggleCols = !evt.isShiftDown();
 668           toggleHiddenRegions(toggleSeqs, toggleCols);
 669           break;
 670         }
 671         case KeyEvent.VK_B:
 672         {
 673           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 674           boolean modifyExisting = true; // always modify, don't clear
 675                                          // evt.isShiftDown();
 676           boolean invertHighlighted = evt.isAltDown();
 677           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 678                   toggleSel);
 679           break;
 680         }
 681         case KeyEvent.VK_PAGE_UP:
 682           if (viewport.getWrapAlignment())
 683           {
 684             vpRanges.scrollUp(true);
 685           }
 686           else
 687           {
 688             vpRanges.setStartSeq(2 * vpRanges.getStartSeq()
 689                     - vpRanges.getEndSeq());
 690           }
 691           break;
 692         case KeyEvent.VK_PAGE_DOWN:
 693           if (viewport.getWrapAlignment())
 694           {
 695             vpRanges.scrollUp(false);
 696           }
 697           else
 698           {
 699             vpRanges.setStartSeq(vpRanges.getEndSeq());
 700           }
 701           break;
 702         }
 703       }
 704
 705       @Override
 706       public void keyReleased(KeyEvent evt)
 707       {
 708         switch (evt.getKeyCode())
 709         {
 710         case KeyEvent.VK_LEFT:
 711           if (evt.isAltDown() || !viewport.cursorMode)
 712           {
 713             viewport.firePropertyChange("alignment", null, viewport
 714                     .getAlignment().getSequences());
 715           }
 716           break;
 717
 718         case KeyEvent.VK_RIGHT:
 719           if (evt.isAltDown() || !viewport.cursorMode)
 720           {
 721             viewport.firePropertyChange("alignment", null, viewport
 722                     .getAlignment().getSequences());
 723           }
 724           break;
 725         }
 726       }
 727     });
 728   }
 729
 730   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 731   {
 732     ap.alignFrame = this;
 733     avc = new jalview.controller.AlignViewController(this, viewport,
 734             alignPanel);
 735
 736     alignPanels.add(ap);
 737
 738     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 739
 740     int aSize = alignPanels.size();
 741
 742     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 743
 744     if (aSize == 1 && ap.av.viewName == null)
 745     {
 746       this.getContentPane().add(ap, BorderLayout.CENTER);
 747     }
 748     else
 749     {
 750       if (aSize == 2)
 751       {
 752         setInitialTabVisible();
 753       }
 754
 755       expandViews.setEnabled(true);
 756       gatherViews.setEnabled(true);
 757       tabbedPane.addTab(ap.av.viewName, ap);
 758
 759       ap.setVisible(false);
 760     }
 761
 762     if (newPanel)
 763     {
 764       if (ap.av.isPadGaps())
 765       {
 766         ap.av.getAlignment().padGaps();
 767       }
 768       ap.av.updateConservation(ap);
 769       ap.av.updateConsensus(ap);
 770       ap.av.updateStrucConsensus(ap);
 771     }
 772   }
 773
 774   public void setInitialTabVisible()
 775   {
 776     expandViews.setEnabled(true);
 777     gatherViews.setEnabled(true);
 778     tabbedPane.setVisible(true);
 779     AlignmentPanel first = alignPanels.get(0);
 780     tabbedPane.addTab(first.av.viewName, first);
 781     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 782   }
 783
 784   public AlignViewport getViewport()
 785   {
 786     return viewport;
 787   }
 788
 789   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 790   private void addServiceListeners()
 791   {
 792     final java.beans.PropertyChangeListener thisListener;
 793     Desktop.instance.addJalviewPropertyChangeListener("services",
 794             thisListener = new java.beans.PropertyChangeListener()
 795             {
 796               @Override
 797               public void propertyChange(PropertyChangeEvent evt)
 798               {
 799                 // // System.out.println("Discoverer property change.");
 800                 // if (evt.getPropertyName().equals("services"))
 801                 {
 802                   SwingUtilities.invokeLater(new Runnable()
 803                   {
 804
 805                     @Override
 806                     public void run()
 807                     {
 808                       System.err
 809                               .println("Rebuild WS Menu for service change");
 810                       BuildWebServiceMenu();
 811                     }
 812
 813                   });
 814                 }
 815               }
 816             });
 817     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 818     {
 819       @Override
 820       public void internalFrameClosed(
 821               javax.swing.event.InternalFrameEvent evt)
 822       {
 823         // System.out.println("deregistering discoverer listener");
 824         Desktop.instance.removeJalviewPropertyChangeListener("services",
 825                 thisListener);
 826         closeMenuItem_actionPerformed(true);
 827       };
 828     });
 829     // Finally, build the menu once to get current service state
 830     new Thread(new Runnable()
 831     {
 832       @Override
 833       public void run()
 834       {
 835         BuildWebServiceMenu();
 836       }
 837     }).start();
 838   }
 839
 840   /**
 841    * Configure menu items that vary according to whether the alignment is
 842    * nucleotide or protein
 843    */
 844   public void setGUINucleotide()
 845   {
 846     AlignmentI al = getViewport().getAlignment();
 847     boolean nucleotide = al.isNucleotide();
 848
 849     showTranslation.setVisible(nucleotide);
 850     showReverse.setVisible(nucleotide);
 851     showReverseComplement.setVisible(nucleotide);
 852     conservationMenuItem.setEnabled(!nucleotide);
 853     modifyConservation.setEnabled(!nucleotide
 854             && conservationMenuItem.isSelected());
 855     showGroupConservation.setEnabled(!nucleotide);
 856
 857     showComplementMenuItem.setText(nucleotide ? MessageManager
 858             .getString("label.protein") : MessageManager
 859             .getString("label.nucleotide"));
 860   }
 861
 862   /**
 863    * set up menus for the current viewport. This may be called after any
 864    * operation that affects the data in the current view (selection changed,
 865    * etc) to update the menus to reflect the new state.
 866    */
 867   @Override
 868   public void setMenusForViewport()
 869   {
 870     setMenusFromViewport(viewport);
 871   }
 872
 873   /**
 874    * Need to call this method when tabs are selected for multiple views, or when
 875    * loading from Jalview2XML.java
 876    *
 877    * @param av
 878    *          AlignViewport
 879    */
 880   void setMenusFromViewport(AlignViewport av)
 881   {
 882     padGapsMenuitem.setSelected(av.isPadGaps());
 883     colourTextMenuItem.setSelected(av.isShowColourText());
 884     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 885     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 886     conservationMenuItem.setSelected(av.getConservationSelected());
 887     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 888     seqLimits.setSelected(av.getShowJVSuffix());
 889     idRightAlign.setSelected(av.isRightAlignIds());
 890     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 891     renderGapsMenuItem.setSelected(av.isRenderGaps());
 892     wrapMenuItem.setSelected(av.getWrapAlignment());
 893     scaleAbove.setVisible(av.getWrapAlignment());
 894     scaleLeft.setVisible(av.getWrapAlignment());
 895     scaleRight.setVisible(av.getWrapAlignment());
 896     annotationPanelMenuItem.setState(av.isShowAnnotation());
 897     /*
 898      * Show/hide annotations only enabled if annotation panel is shown
 899      */
 900     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 901     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 902     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 904     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 905     viewTextMenuItem.setSelected(av.getShowText());
 906     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 907     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 908     showGroupConservation.setSelected(av.isShowGroupConservation());
 909     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 910     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 911     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 912
 913     ColourMenuHelper.setColourSelected(colourMenu,
 914             av.getGlobalColourScheme());
 915
 916     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 917     hiddenMarkers.setState(av.getShowHiddenMarkers());
 918     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 919     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 920     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 921     autoCalculate.setSelected(av.autoCalculateConsensus);
 922     sortByTree.setSelected(av.sortByTree);
 923     listenToViewSelections.setSelected(av.followSelection);
 924
 925     showProducts.setEnabled(canShowProducts());
 926     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 927
 928     updateEditMenuBar();
 929   }
 930
 931   /**
 932    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 933    *
 934    * @param b
 935    */
 936   public void setGroovyEnabled(boolean b)
 937   {
 938     runGroovy.setEnabled(b);
 939   }
 940
 941   private IProgressIndicator progressBar;
 942
 943   /*
 944    * (non-Javadoc)
 945    *
 946    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 947    */
 948   @Override
 949   public void setProgressBar(String message, long id)
 950   {
 951     progressBar.setProgressBar(message, id);
 952   }
 953
 954   @Override
 955   public void registerHandler(final long id,
 956           final IProgressIndicatorHandler handler)
 957   {
 958     progressBar.registerHandler(id, handler);
 959   }
 960
 961   /**
 962    *
 963    * @return true if any progress bars are still active
 964    */
 965   @Override
 966   public boolean operationInProgress()
 967   {
 968     return progressBar.operationInProgress();
 969   }
 970
 971   @Override
 972   public void setStatus(String text)
 973   {
 974     statusBar.setText(text);
 975   }
 976
 977   /*
 978    * Added so Castor Mapping file can obtain Jalview Version
 979    */
 980   public String getVersion()
 981   {
 982     return jalview.bin.Cache.getProperty("VERSION");
 983   }
 984
 985   public FeatureRenderer getFeatureRenderer()
 986   {
 987     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 988   }
 989
 990   @Override
 991   public void fetchSequence_actionPerformed(ActionEvent e)
 992   {
 993     new jalview.gui.SequenceFetcher(this);
 994   }
 995
 996   @Override
 997   public void addFromFile_actionPerformed(ActionEvent e)
 998   {
 999     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1000   }
1001
1002   @Override
1003   public void reload_actionPerformed(ActionEvent e)
1004   {
1005     if (fileName != null)
1006     {
1007       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1008       // originating file's format
1009       // TODO: work out how to recover feature settings for correct view(s) when
1010       // file is reloaded.
1011       if (FileFormat.Jalview.equals(currentFileFormat))
1012       {
1013         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1014         for (int i = 0; i < frames.length; i++)
1015         {
1016           if (frames[i] instanceof AlignFrame && frames[i] != this
1017                   && ((AlignFrame) frames[i]).fileName != null
1018                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1019           {
1020             try
1021             {
1022               frames[i].setSelected(true);
1023               Desktop.instance.closeAssociatedWindows();
1024             } catch (java.beans.PropertyVetoException ex)
1025             {
1026             }
1027           }
1028
1029         }
1030         Desktop.instance.closeAssociatedWindows();
1031
1032         FileLoader loader = new FileLoader();
1033         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1034                 : DataSourceType.FILE;
1035         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1036       }
1037       else
1038       {
1039         Rectangle bounds = this.getBounds();
1040
1041         FileLoader loader = new FileLoader();
1042         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1043                 : DataSourceType.FILE;
1044         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1045                 protocol, currentFileFormat);
1046
1047         newframe.setBounds(bounds);
1048         if (featureSettings != null && featureSettings.isShowing())
1049         {
1050           final Rectangle fspos = featureSettings.frame.getBounds();
1051           // TODO: need a 'show feature settings' function that takes bounds -
1052           // need to refactor Desktop.addFrame
1053           newframe.featureSettings_actionPerformed(null);
1054           final FeatureSettings nfs = newframe.featureSettings;
1055           SwingUtilities.invokeLater(new Runnable()
1056           {
1057             @Override
1058             public void run()
1059             {
1060               nfs.frame.setBounds(fspos);
1061             }
1062           });
1063           this.featureSettings.close();
1064           this.featureSettings = null;
1065         }
1066         this.closeMenuItem_actionPerformed(true);
1067       }
1068     }
1069   }
1070
1071   @Override
1072   public void addFromText_actionPerformed(ActionEvent e)
1073   {
1074     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1075             .getAlignPanel());
1076   }
1077
1078   @Override
1079   public void addFromURL_actionPerformed(ActionEvent e)
1080   {
1081     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1082   }
1083
1084   @Override
1085   public void save_actionPerformed(ActionEvent e)
1086   {
1087     if (fileName == null || (currentFileFormat == null)
1088             || fileName.startsWith("http"))
1089     {
1090       saveAs_actionPerformed(null);
1091     }
1092     else
1093     {
1094       saveAlignment(fileName, currentFileFormat);
1095     }
1096   }
1097
1098   /**
1099    * DOCUMENT ME!
1100    *
1101    * @param e
1102    *          DOCUMENT ME!
1103    */
1104   @Override
1105   public void saveAs_actionPerformed(ActionEvent e)
1106   {
1107     String format = currentFileFormat == null ? null : currentFileFormat
1108             .getName();
1109     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1110             Cache.getProperty("LAST_DIRECTORY"), format);
1111
1112     chooser.setFileView(new JalviewFileView());
1113     chooser.setDialogTitle(MessageManager
1114             .getString("label.save_alignment_to_file"));
1115     chooser.setToolTipText(MessageManager.getString("action.save"));
1116
1117     int value = chooser.showSaveDialog(this);
1118
1119     if (value == JalviewFileChooser.APPROVE_OPTION)
1120     {
1121       currentFileFormat = chooser.getSelectedFormat();
1122       while (currentFileFormat == null)
1123       {
1124         JvOptionPane
1125                 .showInternalMessageDialog(
1126                         Desktop.desktop,
1127                         MessageManager
1128                                 .getString("label.select_file_format_before_saving"),
1129                         MessageManager
1130                                 .getString("label.file_format_not_specified"),
1131                         JvOptionPane.WARNING_MESSAGE);
1132         currentFileFormat = chooser.getSelectedFormat();
1133         value = chooser.showSaveDialog(this);
1134         if (value != JalviewFileChooser.APPROVE_OPTION)
1135         {
1136           return;
1137         }
1138       }
1139
1140       fileName = chooser.getSelectedFile().getPath();
1141
1142       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1143
1144       Cache.setProperty("LAST_DIRECTORY", fileName);
1145       saveAlignment(fileName, currentFileFormat);
1146     }
1147   }
1148
1149   public boolean saveAlignment(String file, FileFormatI format)
1150   {
1151     boolean success = true;
1152
1153     if (FileFormat.Jalview.equals(format))
1154     {
1155       String shortName = title;
1156
1157       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1158       {
1159         shortName = shortName.substring(shortName
1160                 .lastIndexOf(java.io.File.separatorChar) + 1);
1161       }
1162
1163       success = new Jalview2XML().saveAlignment(this, file, shortName);
1164
1165       statusBar.setText(MessageManager.formatMessage(
1166               "label.successfully_saved_to_file_in_format", new Object[] {
1167                   fileName, format }));
1168
1169     }
1170     else
1171     {
1172       AlignmentExportData exportData = getAlignmentForExport(format,
1173               viewport, null);
1174       if (exportData.getSettings().isCancelled())
1175       {
1176         return false;
1177       }
1178       FormatAdapter f = new FormatAdapter(alignPanel,
1179               exportData.getSettings());
1180       String output = f.formatSequences(
1181               format,
1182               exportData.getAlignment(), // class cast exceptions will
1183               // occur in the distant future
1184               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1185               f.getCacheSuffixDefault(format),
1186               viewport.getColumnSelection());
1187
1188       if (output == null)
1189       {
1190         success = false;
1191       }
1192       else
1193       {
1194         try
1195         {
1196           PrintWriter out = new PrintWriter(new FileWriter(file));
1197
1198           out.print(output);
1199           out.close();
1200           this.setTitle(file);
1201           statusBar.setText(MessageManager.formatMessage(
1202                   "label.successfully_saved_to_file_in_format",
1203                   new Object[] { fileName, format.getName() }));
1204         } catch (Exception ex)
1205         {
1206           success = false;
1207           ex.printStackTrace();
1208         }
1209       }
1210     }
1211
1212     if (!success)
1213     {
1214       JvOptionPane.showInternalMessageDialog(this, MessageManager
1215               .formatMessage("label.couldnt_save_file",
1216                       new Object[] { fileName }), MessageManager
1217               .getString("label.error_saving_file"),
1218               JvOptionPane.WARNING_MESSAGE);
1219     }
1220
1221     return success;
1222   }
1223
1224   private void warningMessage(String warning, String title)
1225   {
1226     if (new jalview.util.Platform().isHeadless())
1227     {
1228       System.err.println("Warning: " + title + "\nWarning: " + warning);
1229
1230     }
1231     else
1232     {
1233       JvOptionPane.showInternalMessageDialog(this, warning, title,
1234               JvOptionPane.WARNING_MESSAGE);
1235     }
1236     return;
1237   }
1238
1239   /**
1240    * DOCUMENT ME!
1241    *
1242    * @param e
1243    *          DOCUMENT ME!
1244    */
1245   @Override
1246   protected void outputText_actionPerformed(ActionEvent e)
1247   {
1248     FileFormatI fileFormat = FileFormats.getInstance().forName(
1249             e.getActionCommand());
1250     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1251             viewport, null);
1252     if (exportData.getSettings().isCancelled())
1253     {
1254       return;
1255     }
1256     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1257     cap.setForInput(null);
1258     try
1259     {
1260       FileFormatI format = fileFormat;
1261       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1262               .formatSequences(format, exportData.getAlignment(),
1263                       exportData.getOmitHidden(),
1264                       exportData.getStartEndPostions(),
1265                       viewport.getColumnSelection()));
1266       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1267               "label.alignment_output_command",
1268               new Object[] { e.getActionCommand() }), 600, 500);
1269     } catch (OutOfMemoryError oom)
1270     {
1271       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1272       cap.dispose();
1273     }
1274
1275   }
1276
1277   public static AlignmentExportData getAlignmentForExport(
1278           FileFormatI format, AlignViewportI viewport,
1279           AlignExportSettingI exportSettings)
1280   {
1281     AlignmentI alignmentToExport = null;
1282     AlignExportSettingI settings = exportSettings;
1283     String[] omitHidden = null;
1284
1285     HiddenSequences hiddenSeqs = viewport.getAlignment()
1286             .getHiddenSequences();
1287
1288     alignmentToExport = viewport.getAlignment();
1289
1290     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1291     if (settings == null)
1292     {
1293       settings = new AlignExportSettings(hasHiddenSeqs,
1294               viewport.hasHiddenColumns(), format);
1295     }
1296     // settings.isExportAnnotations();
1297
1298     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1299     {
1300       omitHidden = viewport.getViewAsString(false,
1301               settings.isExportHiddenSequences());
1302     }
1303
1304     int[] alignmentStartEnd = new int[2];
1305     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1306     {
1307       alignmentToExport = hiddenSeqs.getFullAlignment();
1308     }
1309     else
1310     {
1311       alignmentToExport = viewport.getAlignment();
1312     }
1313     alignmentStartEnd = alignmentToExport
1314             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1315                     .getHiddenColumns());
1316     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1317             omitHidden, alignmentStartEnd, settings);
1318     return ed;
1319   }
1320
1321   /**
1322    * DOCUMENT ME!
1323    *
1324    * @param e
1325    *          DOCUMENT ME!
1326    */
1327   @Override
1328   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1329   {
1330     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1331     htmlSVG.exportHTML(null);
1332   }
1333
1334   @Override
1335   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1336   {
1337     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1338     bjs.exportHTML(null);
1339   }
1340
1341   public void createImageMap(File file, String image)
1342   {
1343     alignPanel.makePNGImageMap(file, image);
1344   }
1345
1346   /**
1347    * DOCUMENT ME!
1348    *
1349    * @param e
1350    *          DOCUMENT ME!
1351    */
1352   @Override
1353   public void createPNG(File f)
1354   {
1355     alignPanel.makePNG(f);
1356   }
1357
1358   /**
1359    * DOCUMENT ME!
1360    *
1361    * @param e
1362    *          DOCUMENT ME!
1363    */
1364   @Override
1365   public void createEPS(File f)
1366   {
1367     alignPanel.makeEPS(f);
1368   }
1369
1370   @Override
1371   public void createSVG(File f)
1372   {
1373     alignPanel.makeSVG(f);
1374   }
1375
1376   @Override
1377   public void pageSetup_actionPerformed(ActionEvent e)
1378   {
1379     PrinterJob printJob = PrinterJob.getPrinterJob();
1380     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1381   }
1382
1383   /**
1384    * DOCUMENT ME!
1385    *
1386    * @param e
1387    *          DOCUMENT ME!
1388    */
1389   @Override
1390   public void printMenuItem_actionPerformed(ActionEvent e)
1391   {
1392     // Putting in a thread avoids Swing painting problems
1393     PrintThread thread = new PrintThread(alignPanel);
1394     thread.start();
1395   }
1396
1397   @Override
1398   public void exportFeatures_actionPerformed(ActionEvent e)
1399   {
1400     new AnnotationExporter().exportFeatures(alignPanel);
1401   }
1402
1403   @Override
1404   public void exportAnnotations_actionPerformed(ActionEvent e)
1405   {
1406     new AnnotationExporter().exportAnnotations(alignPanel);
1407   }
1408
1409   @Override
1410   public void associatedData_actionPerformed(ActionEvent e)
1411   {
1412     // Pick the tree file
1413     JalviewFileChooser chooser = new JalviewFileChooser(
1414             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1415     chooser.setFileView(new JalviewFileView());
1416     chooser.setDialogTitle(MessageManager
1417             .getString("label.load_jalview_annotations"));
1418     chooser.setToolTipText(MessageManager
1419             .getString("label.load_jalview_annotations"));
1420
1421     int value = chooser.showOpenDialog(null);
1422
1423     if (value == JalviewFileChooser.APPROVE_OPTION)
1424     {
1425       String choice = chooser.getSelectedFile().getPath();
1426       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1427       loadJalviewDataFile(choice, null, null, null);
1428     }
1429
1430   }
1431
1432   /**
1433    * Close the current view or all views in the alignment frame. If the frame
1434    * only contains one view then the alignment will be removed from memory.
1435    *
1436    * @param closeAllTabs
1437    */
1438   @Override
1439   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1440   {
1441     if (alignPanels != null && alignPanels.size() < 2)
1442     {
1443       closeAllTabs = true;
1444     }
1445
1446     try
1447     {
1448       if (alignPanels != null)
1449       {
1450         if (closeAllTabs)
1451         {
1452           if (this.isClosed())
1453           {
1454             // really close all the windows - otherwise wait till
1455             // setClosed(true) is called
1456             for (int i = 0; i < alignPanels.size(); i++)
1457             {
1458               AlignmentPanel ap = alignPanels.get(i);
1459               ap.closePanel();
1460             }
1461           }
1462         }
1463         else
1464         {
1465           closeView(alignPanel);
1466         }
1467       }
1468
1469       if (closeAllTabs)
1470       {
1471         /*
1472          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1473          * be called recursively, with the frame now in 'closed' state
1474          */
1475         this.setClosed(true);
1476       }
1477     } catch (Exception ex)
1478     {
1479       ex.printStackTrace();
1480     }
1481   }
1482
1483   /**
1484    * Close the specified panel and close up tabs appropriately.
1485    *
1486    * @param panelToClose
1487    */
1488   public void closeView(AlignmentPanel panelToClose)
1489   {
1490     int index = tabbedPane.getSelectedIndex();
1491     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1492     alignPanels.remove(panelToClose);
1493     panelToClose.closePanel();
1494     panelToClose = null;
1495
1496     tabbedPane.removeTabAt(closedindex);
1497     tabbedPane.validate();
1498
1499     if (index > closedindex || index == tabbedPane.getTabCount())
1500     {
1501       // modify currently selected tab index if necessary.
1502       index--;
1503     }
1504
1505     this.tabSelectionChanged(index);
1506   }
1507
1508   /**
1509    * DOCUMENT ME!
1510    */
1511   void updateEditMenuBar()
1512   {
1513
1514     if (viewport.getHistoryList().size() > 0)
1515     {
1516       undoMenuItem.setEnabled(true);
1517       CommandI command = viewport.getHistoryList().peek();
1518       undoMenuItem.setText(MessageManager.formatMessage(
1519               "label.undo_command",
1520               new Object[] { command.getDescription() }));
1521     }
1522     else
1523     {
1524       undoMenuItem.setEnabled(false);
1525       undoMenuItem.setText(MessageManager.getString("action.undo"));
1526     }
1527
1528     if (viewport.getRedoList().size() > 0)
1529     {
1530       redoMenuItem.setEnabled(true);
1531
1532       CommandI command = viewport.getRedoList().peek();
1533       redoMenuItem.setText(MessageManager.formatMessage(
1534               "label.redo_command",
1535               new Object[] { command.getDescription() }));
1536     }
1537     else
1538     {
1539       redoMenuItem.setEnabled(false);
1540       redoMenuItem.setText(MessageManager.getString("action.redo"));
1541     }
1542   }
1543
1544   @Override
1545   public void addHistoryItem(CommandI command)
1546   {
1547     if (command.getSize() > 0)
1548     {
1549       viewport.addToHistoryList(command);
1550       viewport.clearRedoList();
1551       updateEditMenuBar();
1552       viewport.updateHiddenColumns();
1553       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1554       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1555       // viewport.getColumnSelection()
1556       // .getHiddenColumns().size() > 0);
1557     }
1558   }
1559
1560   /**
1561    *
1562    * @return alignment objects for all views
1563    */
1564   AlignmentI[] getViewAlignments()
1565   {
1566     if (alignPanels != null)
1567     {
1568       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1569       int i = 0;
1570       for (AlignmentPanel ap : alignPanels)
1571       {
1572         als[i++] = ap.av.getAlignment();
1573       }
1574       return als;
1575     }
1576     if (viewport != null)
1577     {
1578       return new AlignmentI[] { viewport.getAlignment() };
1579     }
1580     return null;
1581   }
1582
1583   /**
1584    * DOCUMENT ME!
1585    *
1586    * @param e
1587    *          DOCUMENT ME!
1588    */
1589   @Override
1590   protected void undoMenuItem_actionPerformed(ActionEvent e)
1591   {
1592     if (viewport.getHistoryList().isEmpty())
1593     {
1594       return;
1595     }
1596     CommandI command = viewport.getHistoryList().pop();
1597     viewport.addToRedoList(command);
1598     command.undoCommand(getViewAlignments());
1599
1600     AlignmentViewport originalSource = getOriginatingSource(command);
1601     updateEditMenuBar();
1602
1603     if (originalSource != null)
1604     {
1605       if (originalSource != viewport)
1606       {
1607         Cache.log
1608                 .warn("Implementation worry: mismatch of viewport origin for undo");
1609       }
1610       originalSource.updateHiddenColumns();
1611       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1612       // null
1613       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1614       // viewport.getColumnSelection()
1615       // .getHiddenColumns().size() > 0);
1616       originalSource.firePropertyChange("alignment", null, originalSource
1617               .getAlignment().getSequences());
1618     }
1619   }
1620
1621   /**
1622    * DOCUMENT ME!
1623    *
1624    * @param e
1625    *          DOCUMENT ME!
1626    */
1627   @Override
1628   protected void redoMenuItem_actionPerformed(ActionEvent e)
1629   {
1630     if (viewport.getRedoList().size() < 1)
1631     {
1632       return;
1633     }
1634
1635     CommandI command = viewport.getRedoList().pop();
1636     viewport.addToHistoryList(command);
1637     command.doCommand(getViewAlignments());
1638
1639     AlignmentViewport originalSource = getOriginatingSource(command);
1640     updateEditMenuBar();
1641
1642     if (originalSource != null)
1643     {
1644
1645       if (originalSource != viewport)
1646       {
1647         Cache.log
1648                 .warn("Implementation worry: mismatch of viewport origin for redo");
1649       }
1650       originalSource.updateHiddenColumns();
1651       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1652       // null
1653       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1654       // viewport.getColumnSelection()
1655       // .getHiddenColumns().size() > 0);
1656       originalSource.firePropertyChange("alignment", null, originalSource
1657               .getAlignment().getSequences());
1658     }
1659   }
1660
1661   AlignmentViewport getOriginatingSource(CommandI command)
1662   {
1663     AlignmentViewport originalSource = null;
1664     // For sequence removal and addition, we need to fire
1665     // the property change event FROM the viewport where the
1666     // original alignment was altered
1667     AlignmentI al = null;
1668     if (command instanceof EditCommand)
1669     {
1670       EditCommand editCommand = (EditCommand) command;
1671       al = editCommand.getAlignment();
1672       List<Component> comps = PaintRefresher.components.get(viewport
1673               .getSequenceSetId());
1674
1675       for (Component comp : comps)
1676       {
1677         if (comp instanceof AlignmentPanel)
1678         {
1679           if (al == ((AlignmentPanel) comp).av.getAlignment())
1680           {
1681             originalSource = ((AlignmentPanel) comp).av;
1682             break;
1683           }
1684         }
1685       }
1686     }
1687
1688     if (originalSource == null)
1689     {
1690       // The original view is closed, we must validate
1691       // the current view against the closed view first
1692       if (al != null)
1693       {
1694         PaintRefresher.validateSequences(al, viewport.getAlignment());
1695       }
1696
1697       originalSource = viewport;
1698     }
1699
1700     return originalSource;
1701   }
1702
1703   /**
1704    * DOCUMENT ME!
1705    *
1706    * @param up
1707    *          DOCUMENT ME!
1708    */
1709   public void moveSelectedSequences(boolean up)
1710   {
1711     SequenceGroup sg = viewport.getSelectionGroup();
1712
1713     if (sg == null)
1714     {
1715       return;
1716     }
1717     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1718             viewport.getHiddenRepSequences(), up);
1719     alignPanel.paintAlignment(true);
1720   }
1721
1722   synchronized void slideSequences(boolean right, int size)
1723   {
1724     List<SequenceI> sg = new ArrayList<SequenceI>();
1725     if (viewport.cursorMode)
1726     {
1727       sg.add(viewport.getAlignment().getSequenceAt(
1728               alignPanel.getSeqPanel().seqCanvas.cursorY));
1729     }
1730     else if (viewport.getSelectionGroup() != null
1731             && viewport.getSelectionGroup().getSize() != viewport
1732                     .getAlignment().getHeight())
1733     {
1734       sg = viewport.getSelectionGroup().getSequences(
1735               viewport.getHiddenRepSequences());
1736     }
1737
1738     if (sg.size() < 1)
1739     {
1740       return;
1741     }
1742
1743     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1744
1745     for (SequenceI seq : viewport.getAlignment().getSequences())
1746     {
1747       if (!sg.contains(seq))
1748       {
1749         invertGroup.add(seq);
1750       }
1751     }
1752
1753     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1754
1755     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1756     for (int i = 0; i < invertGroup.size(); i++)
1757     {
1758       seqs2[i] = invertGroup.get(i);
1759     }
1760
1761     SlideSequencesCommand ssc;
1762     if (right)
1763     {
1764       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1765               size, viewport.getGapCharacter());
1766     }
1767     else
1768     {
1769       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1770               size, viewport.getGapCharacter());
1771     }
1772
1773     int groupAdjustment = 0;
1774     if (ssc.getGapsInsertedBegin() && right)
1775     {
1776       if (viewport.cursorMode)
1777       {
1778         alignPanel.getSeqPanel().moveCursor(size, 0);
1779       }
1780       else
1781       {
1782         groupAdjustment = size;
1783       }
1784     }
1785     else if (!ssc.getGapsInsertedBegin() && !right)
1786     {
1787       if (viewport.cursorMode)
1788       {
1789         alignPanel.getSeqPanel().moveCursor(-size, 0);
1790       }
1791       else
1792       {
1793         groupAdjustment = -size;
1794       }
1795     }
1796
1797     if (groupAdjustment != 0)
1798     {
1799       viewport.getSelectionGroup().setStartRes(
1800               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1801       viewport.getSelectionGroup().setEndRes(
1802               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1803     }
1804
1805     /*
1806      * just extend the last slide command if compatible; but not if in
1807      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1808      */
1809     boolean appendHistoryItem = false;
1810     Deque<CommandI> historyList = viewport.getHistoryList();
1811     boolean inSplitFrame = getSplitViewContainer() != null;
1812     if (!inSplitFrame && historyList != null && historyList.size() > 0
1813             && historyList.peek() instanceof SlideSequencesCommand)
1814     {
1815       appendHistoryItem = ssc
1816               .appendSlideCommand((SlideSequencesCommand) historyList
1817                       .peek());
1818     }
1819
1820     if (!appendHistoryItem)
1821     {
1822       addHistoryItem(ssc);
1823     }
1824
1825     repaint();
1826   }
1827
1828   /**
1829    * DOCUMENT ME!
1830    *
1831    * @param e
1832    *          DOCUMENT ME!
1833    */
1834   @Override
1835   protected void copy_actionPerformed(ActionEvent e)
1836   {
1837     System.gc();
1838     if (viewport.getSelectionGroup() == null)
1839     {
1840       return;
1841     }
1842     // TODO: preserve the ordering of displayed alignment annotation in any
1843     // internal paste (particularly sequence associated annotation)
1844     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1845     String[] omitHidden = null;
1846
1847     if (viewport.hasHiddenColumns())
1848     {
1849       omitHidden = viewport.getViewAsString(true);
1850     }
1851
1852     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1853             seqs, omitHidden, null);
1854
1855     StringSelection ss = new StringSelection(output);
1856
1857     try
1858     {
1859       jalview.gui.Desktop.internalCopy = true;
1860       // Its really worth setting the clipboard contents
1861       // to empty before setting the large StringSelection!!
1862       Toolkit.getDefaultToolkit().getSystemClipboard()
1863               .setContents(new StringSelection(""), null);
1864
1865       Toolkit.getDefaultToolkit().getSystemClipboard()
1866               .setContents(ss, Desktop.instance);
1867     } catch (OutOfMemoryError er)
1868     {
1869       new OOMWarning("copying region", er);
1870       return;
1871     }
1872
1873     ArrayList<int[]> hiddenColumns = null;
1874     if (viewport.hasHiddenColumns())
1875     {
1876       hiddenColumns = new ArrayList<int[]>();
1877       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1878               .getSelectionGroup().getEndRes();
1879       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1880       {
1881         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1882         {
1883           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1884               region[1] - hiddenOffset });
1885         }
1886       }
1887     }
1888
1889     Desktop.jalviewClipboard = new Object[] { seqs,
1890         viewport.getAlignment().getDataset(), hiddenColumns };
1891     statusBar.setText(MessageManager.formatMessage(
1892             "label.copied_sequences_to_clipboard", new Object[] { Integer
1893                     .valueOf(seqs.length).toString() }));
1894   }
1895
1896   /**
1897    * DOCUMENT ME!
1898    *
1899    * @param e
1900    *          DOCUMENT ME!
1901    */
1902   @Override
1903   protected void pasteNew_actionPerformed(ActionEvent e)
1904   {
1905     paste(true);
1906   }
1907
1908   /**
1909    * DOCUMENT ME!
1910    *
1911    * @param e
1912    *          DOCUMENT ME!
1913    */
1914   @Override
1915   protected void pasteThis_actionPerformed(ActionEvent e)
1916   {
1917     paste(false);
1918   }
1919
1920   /**
1921    * Paste contents of Jalview clipboard
1922    *
1923    * @param newAlignment
1924    *          true to paste to a new alignment, otherwise add to this.
1925    */
1926   void paste(boolean newAlignment)
1927   {
1928     boolean externalPaste = true;
1929     try
1930     {
1931       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1932       Transferable contents = c.getContents(this);
1933
1934       if (contents == null)
1935       {
1936         return;
1937       }
1938
1939       String str;
1940       FileFormatI format;
1941       try
1942       {
1943         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1944         if (str.length() < 1)
1945         {
1946           return;
1947         }
1948
1949         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1950
1951       } catch (OutOfMemoryError er)
1952       {
1953         new OOMWarning("Out of memory pasting sequences!!", er);
1954         return;
1955       }
1956
1957       SequenceI[] sequences;
1958       boolean annotationAdded = false;
1959       AlignmentI alignment = null;
1960
1961       if (Desktop.jalviewClipboard != null)
1962       {
1963         // The clipboard was filled from within Jalview, we must use the
1964         // sequences
1965         // And dataset from the copied alignment
1966         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1967         // be doubly sure that we create *new* sequence objects.
1968         sequences = new SequenceI[newseq.length];
1969         for (int i = 0; i < newseq.length; i++)
1970         {
1971           sequences[i] = new Sequence(newseq[i]);
1972         }
1973         alignment = new Alignment(sequences);
1974         externalPaste = false;
1975       }
1976       else
1977       {
1978         // parse the clipboard as an alignment.
1979         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1980                 format);
1981         sequences = alignment.getSequencesArray();
1982       }
1983
1984       int alwidth = 0;
1985       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1986       int fgroup = -1;
1987
1988       if (newAlignment)
1989       {
1990
1991         if (Desktop.jalviewClipboard != null)
1992         {
1993           // dataset is inherited
1994           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1995         }
1996         else
1997         {
1998           // new dataset is constructed
1999           alignment.setDataset(null);
2000         }
2001         alwidth = alignment.getWidth() + 1;
2002       }
2003       else
2004       {
2005         AlignmentI pastedal = alignment; // preserve pasted alignment object
2006         // Add pasted sequences and dataset into existing alignment.
2007         alignment = viewport.getAlignment();
2008         alwidth = alignment.getWidth() + 1;
2009         // decide if we need to import sequences from an existing dataset
2010         boolean importDs = Desktop.jalviewClipboard != null
2011                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2012         // importDs==true instructs us to copy over new dataset sequences from
2013         // an existing alignment
2014         Vector newDs = (importDs) ? new Vector() : null; // used to create
2015         // minimum dataset set
2016
2017         for (int i = 0; i < sequences.length; i++)
2018         {
2019           if (importDs)
2020           {
2021             newDs.addElement(null);
2022           }
2023           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2024           // paste
2025           if (importDs && ds != null)
2026           {
2027             if (!newDs.contains(ds))
2028             {
2029               newDs.setElementAt(ds, i);
2030               ds = new Sequence(ds);
2031               // update with new dataset sequence
2032               sequences[i].setDatasetSequence(ds);
2033             }
2034             else
2035             {
2036               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2037             }
2038           }
2039           else
2040           {
2041             // copy and derive new dataset sequence
2042             sequences[i] = sequences[i].deriveSequence();
2043             alignment.getDataset().addSequence(
2044                     sequences[i].getDatasetSequence());
2045             // TODO: avoid creation of duplicate dataset sequences with a
2046             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2047           }
2048           alignment.addSequence(sequences[i]); // merges dataset
2049         }
2050         if (newDs != null)
2051         {
2052           newDs.clear(); // tidy up
2053         }
2054         if (alignment.getAlignmentAnnotation() != null)
2055         {
2056           for (AlignmentAnnotation alan : alignment
2057                   .getAlignmentAnnotation())
2058           {
2059             if (alan.graphGroup > fgroup)
2060             {
2061               fgroup = alan.graphGroup;
2062             }
2063           }
2064         }
2065         if (pastedal.getAlignmentAnnotation() != null)
2066         {
2067           // Add any annotation attached to alignment.
2068           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2069           for (int i = 0; i < alann.length; i++)
2070           {
2071             annotationAdded = true;
2072             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2073             {
2074               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2075               if (newann.graphGroup > -1)
2076               {
2077                 if (newGraphGroups.size() <= newann.graphGroup
2078                         || newGraphGroups.get(newann.graphGroup) == null)
2079                 {
2080                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2081                   {
2082                     newGraphGroups.add(q, null);
2083                   }
2084                   newGraphGroups.set(newann.graphGroup, new Integer(
2085                           ++fgroup));
2086                 }
2087                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2088                         .intValue();
2089               }
2090
2091               newann.padAnnotation(alwidth);
2092               alignment.addAnnotation(newann);
2093             }
2094           }
2095         }
2096       }
2097       if (!newAlignment)
2098       {
2099         // /////
2100         // ADD HISTORY ITEM
2101         //
2102         addHistoryItem(new EditCommand(
2103                 MessageManager.getString("label.add_sequences"),
2104                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2105       }
2106       // Add any annotations attached to sequences
2107       for (int i = 0; i < sequences.length; i++)
2108       {
2109         if (sequences[i].getAnnotation() != null)
2110         {
2111           AlignmentAnnotation newann;
2112           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2113           {
2114             annotationAdded = true;
2115             newann = sequences[i].getAnnotation()[a];
2116             newann.adjustForAlignment();
2117             newann.padAnnotation(alwidth);
2118             if (newann.graphGroup > -1)
2119             {
2120               if (newann.graphGroup > -1)
2121               {
2122                 if (newGraphGroups.size() <= newann.graphGroup
2123                         || newGraphGroups.get(newann.graphGroup) == null)
2124                 {
2125                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2126                   {
2127                     newGraphGroups.add(q, null);
2128                   }
2129                   newGraphGroups.set(newann.graphGroup, new Integer(
2130                           ++fgroup));
2131                 }
2132                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2133                         .intValue();
2134               }
2135             }
2136             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2137             // was
2138             // duplicated
2139             // earlier
2140             alignment
2141                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2142           }
2143         }
2144       }
2145       if (!newAlignment)
2146       {
2147
2148         // propagate alignment changed.
2149         vpRanges.setEndSeq(alignment.getHeight());
2150         if (annotationAdded)
2151         {
2152           // Duplicate sequence annotation in all views.
2153           AlignmentI[] alview = this.getViewAlignments();
2154           for (int i = 0; i < sequences.length; i++)
2155           {
2156             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2157             if (sann == null)
2158             {
2159               continue;
2160             }
2161             for (int avnum = 0; avnum < alview.length; avnum++)
2162             {
2163               if (alview[avnum] != alignment)
2164               {
2165                 // duplicate in a view other than the one with input focus
2166                 int avwidth = alview[avnum].getWidth() + 1;
2167                 // this relies on sann being preserved after we
2168                 // modify the sequence's annotation array for each duplication
2169                 for (int a = 0; a < sann.length; a++)
2170                 {
2171                   AlignmentAnnotation newann = new AlignmentAnnotation(
2172                           sann[a]);
2173                   sequences[i].addAlignmentAnnotation(newann);
2174                   newann.padAnnotation(avwidth);
2175                   alview[avnum].addAnnotation(newann); // annotation was
2176                   // duplicated earlier
2177                   // TODO JAL-1145 graphGroups are not updated for sequence
2178                   // annotation added to several views. This may cause
2179                   // strangeness
2180                   alview[avnum].setAnnotationIndex(newann, a);
2181                 }
2182               }
2183             }
2184           }
2185           buildSortByAnnotationScoresMenu();
2186         }
2187         viewport.firePropertyChange("alignment", null,
2188                 alignment.getSequences());
2189         if (alignPanels != null)
2190         {
2191           for (AlignmentPanel ap : alignPanels)
2192           {
2193             ap.validateAnnotationDimensions(false);
2194           }
2195         }
2196         else
2197         {
2198           alignPanel.validateAnnotationDimensions(false);
2199         }
2200
2201       }
2202       else
2203       {
2204         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2205                 DEFAULT_HEIGHT);
2206         String newtitle = new String("Copied sequences");
2207
2208         if (Desktop.jalviewClipboard != null
2209                 && Desktop.jalviewClipboard[2] != null)
2210         {
2211           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2212           for (int[] region : hc)
2213           {
2214             af.viewport.hideColumns(region[0], region[1]);
2215           }
2216         }
2217
2218         // >>>This is a fix for the moment, until a better solution is
2219         // found!!<<<
2220         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2221                 .transferSettings(
2222                         alignPanel.getSeqPanel().seqCanvas
2223                                 .getFeatureRenderer());
2224
2225         // TODO: maintain provenance of an alignment, rather than just make the
2226         // title a concatenation of operations.
2227         if (!externalPaste)
2228         {
2229           if (title.startsWith("Copied sequences"))
2230           {
2231             newtitle = title;
2232           }
2233           else
2234           {
2235             newtitle = newtitle.concat("- from " + title);
2236           }
2237         }
2238         else
2239         {
2240           newtitle = new String("Pasted sequences");
2241         }
2242
2243         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2244                 DEFAULT_HEIGHT);
2245
2246       }
2247
2248     } catch (Exception ex)
2249     {
2250       ex.printStackTrace();
2251       System.out.println("Exception whilst pasting: " + ex);
2252       // could be anything being pasted in here
2253     }
2254
2255   }
2256
2257   @Override
2258   protected void expand_newalign(ActionEvent e)
2259   {
2260     try
2261     {
2262       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2263               .getAlignment(), -1);
2264       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2265               DEFAULT_HEIGHT);
2266       String newtitle = new String("Flanking alignment");
2267
2268       if (Desktop.jalviewClipboard != null
2269               && Desktop.jalviewClipboard[2] != null)
2270       {
2271         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2272         for (int region[] : hc)
2273         {
2274           af.viewport.hideColumns(region[0], region[1]);
2275         }
2276       }
2277
2278       // >>>This is a fix for the moment, until a better solution is
2279       // found!!<<<
2280       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2281               .transferSettings(
2282                       alignPanel.getSeqPanel().seqCanvas
2283                               .getFeatureRenderer());
2284
2285       // TODO: maintain provenance of an alignment, rather than just make the
2286       // title a concatenation of operations.
2287       {
2288         if (title.startsWith("Copied sequences"))
2289         {
2290           newtitle = title;
2291         }
2292         else
2293         {
2294           newtitle = newtitle.concat("- from " + title);
2295         }
2296       }
2297
2298       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2299
2300     } catch (Exception ex)
2301     {
2302       ex.printStackTrace();
2303       System.out.println("Exception whilst pasting: " + ex);
2304       // could be anything being pasted in here
2305     } catch (OutOfMemoryError oom)
2306     {
2307       new OOMWarning("Viewing flanking region of alignment", oom);
2308     }
2309   }
2310
2311   /**
2312    * DOCUMENT ME!
2313    *
2314    * @param e
2315    *          DOCUMENT ME!
2316    */
2317   @Override
2318   protected void cut_actionPerformed(ActionEvent e)
2319   {
2320     copy_actionPerformed(null);
2321     delete_actionPerformed(null);
2322   }
2323
2324   /**
2325    * DOCUMENT ME!
2326    *
2327    * @param e
2328    *          DOCUMENT ME!
2329    */
2330   @Override
2331   protected void delete_actionPerformed(ActionEvent evt)
2332   {
2333
2334     SequenceGroup sg = viewport.getSelectionGroup();
2335     if (sg == null)
2336     {
2337       return;
2338     }
2339
2340     /*
2341      * If the cut affects all sequences, warn, remove highlighted columns
2342      */
2343     if (sg.getSize() == viewport.getAlignment().getHeight())
2344     {
2345       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2346               .getAlignment().getWidth()) ? true : false;
2347       if (isEntireAlignWidth)
2348       {
2349         int confirm = JvOptionPane.showConfirmDialog(this,
2350                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2351                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2352                 JvOptionPane.OK_CANCEL_OPTION);
2353
2354         if (confirm == JvOptionPane.CANCEL_OPTION
2355                 || confirm == JvOptionPane.CLOSED_OPTION)
2356         {
2357           return;
2358         }
2359       }
2360       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2361               sg.getEndRes() + 1);
2362     }
2363     SequenceI[] cut = sg.getSequences()
2364             .toArray(new SequenceI[sg.getSize()]);
2365
2366     addHistoryItem(new EditCommand(
2367             MessageManager.getString("label.cut_sequences"), Action.CUT,
2368             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2369             viewport.getAlignment()));
2370
2371     viewport.setSelectionGroup(null);
2372     viewport.sendSelection();
2373     viewport.getAlignment().deleteGroup(sg);
2374
2375     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2376             .getSequences());
2377     if (viewport.getAlignment().getHeight() < 1)
2378     {
2379       try
2380       {
2381         this.setClosed(true);
2382       } catch (Exception ex)
2383       {
2384       }
2385     }
2386   }
2387
2388   /**
2389    * DOCUMENT ME!
2390    *
2391    * @param e
2392    *          DOCUMENT ME!
2393    */
2394   @Override
2395   protected void deleteGroups_actionPerformed(ActionEvent e)
2396   {
2397     if (avc.deleteGroups())
2398     {
2399       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2400       alignPanel.updateAnnotation();
2401       alignPanel.paintAlignment(true);
2402     }
2403   }
2404
2405   /**
2406    * DOCUMENT ME!
2407    *
2408    * @param e
2409    *          DOCUMENT ME!
2410    */
2411   @Override
2412   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2413   {
2414     SequenceGroup sg = new SequenceGroup();
2415
2416     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2417     {
2418       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2419     }
2420
2421     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2422     viewport.setSelectionGroup(sg);
2423     viewport.sendSelection();
2424     // JAL-2034 - should delegate to
2425     // alignPanel to decide if overview needs
2426     // updating.
2427     alignPanel.paintAlignment(false);
2428     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2429   }
2430
2431   /**
2432    * DOCUMENT ME!
2433    *
2434    * @param e
2435    *          DOCUMENT ME!
2436    */
2437   @Override
2438   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2439   {
2440     if (viewport.cursorMode)
2441     {
2442       alignPanel.getSeqPanel().keyboardNo1 = null;
2443       alignPanel.getSeqPanel().keyboardNo2 = null;
2444     }
2445     viewport.setSelectionGroup(null);
2446     viewport.getColumnSelection().clear();
2447     viewport.setSelectionGroup(null);
2448     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2449     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2450     // JAL-2034 - should delegate to
2451     // alignPanel to decide if overview needs
2452     // updating.
2453     alignPanel.paintAlignment(false);
2454     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2455     viewport.sendSelection();
2456   }
2457
2458   /**
2459    * DOCUMENT ME!
2460    *
2461    * @param e
2462    *          DOCUMENT ME!
2463    */
2464   @Override
2465   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2466   {
2467     SequenceGroup sg = viewport.getSelectionGroup();
2468
2469     if (sg == null)
2470     {
2471       selectAllSequenceMenuItem_actionPerformed(null);
2472
2473       return;
2474     }
2475
2476     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2477     {
2478       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2479     }
2480     // JAL-2034 - should delegate to
2481     // alignPanel to decide if overview needs
2482     // updating.
2483
2484     alignPanel.paintAlignment(true);
2485     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2486     viewport.sendSelection();
2487   }
2488
2489   @Override
2490   public void invertColSel_actionPerformed(ActionEvent e)
2491   {
2492     viewport.invertColumnSelection();
2493     alignPanel.paintAlignment(true);
2494     viewport.sendSelection();
2495   }
2496
2497   /**
2498    * DOCUMENT ME!
2499    *
2500    * @param e
2501    *          DOCUMENT ME!
2502    */
2503   @Override
2504   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2505   {
2506     trimAlignment(true);
2507   }
2508
2509   /**
2510    * DOCUMENT ME!
2511    *
2512    * @param e
2513    *          DOCUMENT ME!
2514    */
2515   @Override
2516   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2517   {
2518     trimAlignment(false);
2519   }
2520
2521   void trimAlignment(boolean trimLeft)
2522   {
2523     ColumnSelection colSel = viewport.getColumnSelection();
2524     int column;
2525
2526     if (!colSel.isEmpty())
2527     {
2528       if (trimLeft)
2529       {
2530         column = colSel.getMin();
2531       }
2532       else
2533       {
2534         column = colSel.getMax();
2535       }
2536
2537       SequenceI[] seqs;
2538       if (viewport.getSelectionGroup() != null)
2539       {
2540         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2541                 viewport.getHiddenRepSequences());
2542       }
2543       else
2544       {
2545         seqs = viewport.getAlignment().getSequencesArray();
2546       }
2547
2548       TrimRegionCommand trimRegion;
2549       if (trimLeft)
2550       {
2551         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2552                 column, viewport.getAlignment());
2553         vpRanges.setStartRes(0);
2554       }
2555       else
2556       {
2557         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2558                 column, viewport.getAlignment());
2559       }
2560
2561       statusBar.setText(MessageManager.formatMessage(
2562               "label.removed_columns",
2563               new String[] { Integer.valueOf(trimRegion.getSize())
2564                       .toString() }));
2565
2566       addHistoryItem(trimRegion);
2567
2568       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2569       {
2570         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2571                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2572         {
2573           viewport.getAlignment().deleteGroup(sg);
2574         }
2575       }
2576
2577       viewport.firePropertyChange("alignment", null, viewport
2578               .getAlignment().getSequences());
2579     }
2580   }
2581
2582   /**
2583    * DOCUMENT ME!
2584    *
2585    * @param e
2586    *          DOCUMENT ME!
2587    */
2588   @Override
2589   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2590   {
2591     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2592
2593     SequenceI[] seqs;
2594     if (viewport.getSelectionGroup() != null)
2595     {
2596       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2597               viewport.getHiddenRepSequences());
2598       start = viewport.getSelectionGroup().getStartRes();
2599       end = viewport.getSelectionGroup().getEndRes();
2600     }
2601     else
2602     {
2603       seqs = viewport.getAlignment().getSequencesArray();
2604     }
2605
2606     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2607             "Remove Gapped Columns", seqs, start, end,
2608             viewport.getAlignment());
2609
2610     addHistoryItem(removeGapCols);
2611
2612     statusBar.setText(MessageManager.formatMessage(
2613             "label.removed_empty_columns",
2614             new Object[] { Integer.valueOf(removeGapCols.getSize())
2615                     .toString() }));
2616
2617     // This is to maintain viewport position on first residue
2618     // of first sequence
2619     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2620     int startRes = seq.findPosition(vpRanges.getStartRes());
2621     // ShiftList shifts;
2622     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2623     // edit.alColumnChanges=shifts.getInverse();
2624     // if (viewport.hasHiddenColumns)
2625     // viewport.getColumnSelection().compensateForEdits(shifts);
2626     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2627     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2628             .getSequences());
2629
2630   }
2631
2632   /**
2633    * DOCUMENT ME!
2634    *
2635    * @param e
2636    *          DOCUMENT ME!
2637    */
2638   @Override
2639   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2640   {
2641     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2642
2643     SequenceI[] seqs;
2644     if (viewport.getSelectionGroup() != null)
2645     {
2646       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2647               viewport.getHiddenRepSequences());
2648       start = viewport.getSelectionGroup().getStartRes();
2649       end = viewport.getSelectionGroup().getEndRes();
2650     }
2651     else
2652     {
2653       seqs = viewport.getAlignment().getSequencesArray();
2654     }
2655
2656     // This is to maintain viewport position on first residue
2657     // of first sequence
2658     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2659     int startRes = seq.findPosition(vpRanges.getStartRes());
2660
2661     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2662             viewport.getAlignment()));
2663
2664     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2665
2666     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2667             .getSequences());
2668
2669   }
2670
2671   /**
2672    * DOCUMENT ME!
2673    *
2674    * @param e
2675    *          DOCUMENT ME!
2676    */
2677   @Override
2678   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2679   {
2680     viewport.setPadGaps(padGapsMenuitem.isSelected());
2681     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2682             .getSequences());
2683   }
2684
2685   /**
2686    * DOCUMENT ME!
2687    *
2688    * @param e
2689    *          DOCUMENT ME!
2690    */
2691   @Override
2692   public void findMenuItem_actionPerformed(ActionEvent e)
2693   {
2694     new Finder();
2695   }
2696
2697   /**
2698    * Create a new view of the current alignment.
2699    */
2700   @Override
2701   public void newView_actionPerformed(ActionEvent e)
2702   {
2703     newView(null, true);
2704   }
2705
2706   /**
2707    * Creates and shows a new view of the current alignment.
2708    *
2709    * @param viewTitle
2710    *          title of newly created view; if null, one will be generated
2711    * @param copyAnnotation
2712    *          if true then duplicate all annnotation, groups and settings
2713    * @return new alignment panel, already displayed.
2714    */
2715   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2716   {
2717     /*
2718      * Create a new AlignmentPanel (with its own, new Viewport)
2719      */
2720     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2721             true);
2722     if (!copyAnnotation)
2723     {
2724       /*
2725        * remove all groups and annotation except for the automatic stuff
2726        */
2727       newap.av.getAlignment().deleteAllGroups();
2728       newap.av.getAlignment().deleteAllAnnotations(false);
2729     }
2730
2731     newap.av.setGatherViewsHere(false);
2732
2733     if (viewport.viewName == null)
2734     {
2735       viewport.viewName = MessageManager
2736               .getString("label.view_name_original");
2737     }
2738
2739     /*
2740      * Views share the same edits undo and redo stacks
2741      */
2742     newap.av.setHistoryList(viewport.getHistoryList());
2743     newap.av.setRedoList(viewport.getRedoList());
2744
2745     /*
2746      * Views share the same mappings; need to deregister any new mappings
2747      * created by copyAlignPanel, and register the new reference to the shared
2748      * mappings
2749      */
2750     newap.av.replaceMappings(viewport.getAlignment());
2751
2752     /*
2753      * start up cDNA consensus (if applicable) now mappings are in place
2754      */
2755     if (newap.av.initComplementConsensus())
2756     {
2757       newap.refresh(true); // adjust layout of annotations
2758     }
2759
2760     newap.av.viewName = getNewViewName(viewTitle);
2761
2762     addAlignmentPanel(newap, true);
2763     newap.alignmentChanged();
2764
2765     if (alignPanels.size() == 2)
2766     {
2767       viewport.setGatherViewsHere(true);
2768     }
2769     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2770     return newap;
2771   }
2772
2773   /**
2774    * Make a new name for the view, ensuring it is unique within the current
2775    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2776    * these now use viewId. Unique view names are still desirable for usability.)
2777    *
2778    * @param viewTitle
2779    * @return
2780    */
2781   protected String getNewViewName(String viewTitle)
2782   {
2783     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2784     boolean addFirstIndex = false;
2785     if (viewTitle == null || viewTitle.trim().length() == 0)
2786     {
2787       viewTitle = MessageManager.getString("action.view");
2788       addFirstIndex = true;
2789     }
2790     else
2791     {
2792       index = 1;// we count from 1 if given a specific name
2793     }
2794     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2795
2796     List<Component> comps = PaintRefresher.components.get(viewport
2797             .getSequenceSetId());
2798
2799     List<String> existingNames = getExistingViewNames(comps);
2800
2801     while (existingNames.contains(newViewName))
2802     {
2803       newViewName = viewTitle + " " + (++index);
2804     }
2805     return newViewName;
2806   }
2807
2808   /**
2809    * Returns a list of distinct view names found in the given list of
2810    * components. View names are held on the viewport of an AlignmentPanel.
2811    *
2812    * @param comps
2813    * @return
2814    */
2815   protected List<String> getExistingViewNames(List<Component> comps)
2816   {
2817     List<String> existingNames = new ArrayList<String>();
2818     for (Component comp : comps)
2819     {
2820       if (comp instanceof AlignmentPanel)
2821       {
2822         AlignmentPanel ap = (AlignmentPanel) comp;
2823         if (!existingNames.contains(ap.av.viewName))
2824         {
2825           existingNames.add(ap.av.viewName);
2826         }
2827       }
2828     }
2829     return existingNames;
2830   }
2831
2832   /**
2833    * Explode tabbed views into separate windows.
2834    */
2835   @Override
2836   public void expandViews_actionPerformed(ActionEvent e)
2837   {
2838     Desktop.explodeViews(this);
2839   }
2840
2841   /**
2842    * Gather views in separate windows back into a tabbed presentation.
2843    */
2844   @Override
2845   public void gatherViews_actionPerformed(ActionEvent e)
2846   {
2847     Desktop.instance.gatherViews(this);
2848   }
2849
2850   /**
2851    * DOCUMENT ME!
2852    *
2853    * @param e
2854    *          DOCUMENT ME!
2855    */
2856   @Override
2857   public void font_actionPerformed(ActionEvent e)
2858   {
2859     new FontChooser(alignPanel);
2860   }
2861
2862   /**
2863    * DOCUMENT ME!
2864    *
2865    * @param e
2866    *          DOCUMENT ME!
2867    */
2868   @Override
2869   protected void seqLimit_actionPerformed(ActionEvent e)
2870   {
2871     viewport.setShowJVSuffix(seqLimits.isSelected());
2872
2873     alignPanel.getIdPanel().getIdCanvas()
2874             .setPreferredSize(alignPanel.calculateIdWidth());
2875     alignPanel.paintAlignment(true);
2876   }
2877
2878   @Override
2879   public void idRightAlign_actionPerformed(ActionEvent e)
2880   {
2881     viewport.setRightAlignIds(idRightAlign.isSelected());
2882     alignPanel.paintAlignment(true);
2883   }
2884
2885   @Override
2886   public void centreColumnLabels_actionPerformed(ActionEvent e)
2887   {
2888     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2889     alignPanel.paintAlignment(true);
2890   }
2891
2892   /*
2893    * (non-Javadoc)
2894    *
2895    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2896    */
2897   @Override
2898   protected void followHighlight_actionPerformed()
2899   {
2900     /*
2901      * Set the 'follow' flag on the Viewport (and scroll to position if now
2902      * true).
2903      */
2904     final boolean state = this.followHighlightMenuItem.getState();
2905     viewport.setFollowHighlight(state);
2906     if (state)
2907     {
2908       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2909     }
2910   }
2911
2912   /**
2913    * DOCUMENT ME!
2914    *
2915    * @param e
2916    *          DOCUMENT ME!
2917    */
2918   @Override
2919   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2920   {
2921     viewport.setColourText(colourTextMenuItem.isSelected());
2922     alignPanel.paintAlignment(true);
2923   }
2924
2925   /**
2926    * DOCUMENT ME!
2927    *
2928    * @param e
2929    *          DOCUMENT ME!
2930    */
2931   @Override
2932   public void wrapMenuItem_actionPerformed(ActionEvent e)
2933   {
2934     scaleAbove.setVisible(wrapMenuItem.isSelected());
2935     scaleLeft.setVisible(wrapMenuItem.isSelected());
2936     scaleRight.setVisible(wrapMenuItem.isSelected());
2937     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2938     alignPanel.updateLayout();
2939   }
2940
2941   @Override
2942   public void showAllSeqs_actionPerformed(ActionEvent e)
2943   {
2944     viewport.showAllHiddenSeqs();
2945   }
2946
2947   @Override
2948   public void showAllColumns_actionPerformed(ActionEvent e)
2949   {
2950     viewport.showAllHiddenColumns();
2951     repaint();
2952     viewport.sendSelection();
2953   }
2954
2955   @Override
2956   public void hideSelSequences_actionPerformed(ActionEvent e)
2957   {
2958     viewport.hideAllSelectedSeqs();
2959     // alignPanel.paintAlignment(true);
2960   }
2961
2962   /**
2963    * called by key handler and the hide all/show all menu items
2964    *
2965    * @param toggleSeqs
2966    * @param toggleCols
2967    */
2968   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2969   {
2970
2971     boolean hide = false;
2972     SequenceGroup sg = viewport.getSelectionGroup();
2973     if (!toggleSeqs && !toggleCols)
2974     {
2975       // Hide everything by the current selection - this is a hack - we do the
2976       // invert and then hide
2977       // first check that there will be visible columns after the invert.
2978       if (viewport.hasSelectedColumns()
2979               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2980                       .getEndRes()))
2981       {
2982         // now invert the sequence set, if required - empty selection implies
2983         // that no hiding is required.
2984         if (sg != null)
2985         {
2986           invertSequenceMenuItem_actionPerformed(null);
2987           sg = viewport.getSelectionGroup();
2988           toggleSeqs = true;
2989
2990         }
2991         viewport.expandColSelection(sg, true);
2992         // finally invert the column selection and get the new sequence
2993         // selection.
2994         invertColSel_actionPerformed(null);
2995         toggleCols = true;
2996       }
2997     }
2998
2999     if (toggleSeqs)
3000     {
3001       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3002       {
3003         hideSelSequences_actionPerformed(null);
3004         hide = true;
3005       }
3006       else if (!(toggleCols && viewport.hasSelectedColumns()))
3007       {
3008         showAllSeqs_actionPerformed(null);
3009       }
3010     }
3011
3012     if (toggleCols)
3013     {
3014       if (viewport.hasSelectedColumns())
3015       {
3016         hideSelColumns_actionPerformed(null);
3017         if (!toggleSeqs)
3018         {
3019           viewport.setSelectionGroup(sg);
3020         }
3021       }
3022       else if (!hide)
3023       {
3024         showAllColumns_actionPerformed(null);
3025       }
3026     }
3027   }
3028
3029   /*
3030    * (non-Javadoc)
3031    *
3032    * @see
3033    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3034    * event.ActionEvent)
3035    */
3036   @Override
3037   public void hideAllButSelection_actionPerformed(ActionEvent e)
3038   {
3039     toggleHiddenRegions(false, false);
3040     viewport.sendSelection();
3041   }
3042
3043   /*
3044    * (non-Javadoc)
3045    *
3046    * @see
3047    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3048    * .ActionEvent)
3049    */
3050   @Override
3051   public void hideAllSelection_actionPerformed(ActionEvent e)
3052   {
3053     SequenceGroup sg = viewport.getSelectionGroup();
3054     viewport.expandColSelection(sg, false);
3055     viewport.hideAllSelectedSeqs();
3056     viewport.hideSelectedColumns();
3057     alignPanel.paintAlignment(true);
3058     viewport.sendSelection();
3059   }
3060
3061   /*
3062    * (non-Javadoc)
3063    *
3064    * @see
3065    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3066    * ActionEvent)
3067    */
3068   @Override
3069   public void showAllhidden_actionPerformed(ActionEvent e)
3070   {
3071     viewport.showAllHiddenColumns();
3072     viewport.showAllHiddenSeqs();
3073     alignPanel.paintAlignment(true);
3074     viewport.sendSelection();
3075   }
3076
3077   @Override
3078   public void hideSelColumns_actionPerformed(ActionEvent e)
3079   {
3080     viewport.hideSelectedColumns();
3081     alignPanel.paintAlignment(true);
3082     viewport.sendSelection();
3083   }
3084
3085   @Override
3086   public void hiddenMarkers_actionPerformed(ActionEvent e)
3087   {
3088     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3089     repaint();
3090   }
3091
3092   /**
3093    * DOCUMENT ME!
3094    *
3095    * @param e
3096    *          DOCUMENT ME!
3097    */
3098   @Override
3099   protected void scaleAbove_actionPerformed(ActionEvent e)
3100   {
3101     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3102     alignPanel.paintAlignment(true);
3103   }
3104
3105   /**
3106    * DOCUMENT ME!
3107    *
3108    * @param e
3109    *          DOCUMENT ME!
3110    */
3111   @Override
3112   protected void scaleLeft_actionPerformed(ActionEvent e)
3113   {
3114     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3115     alignPanel.paintAlignment(true);
3116   }
3117
3118   /**
3119    * DOCUMENT ME!
3120    *
3121    * @param e
3122    *          DOCUMENT ME!
3123    */
3124   @Override
3125   protected void scaleRight_actionPerformed(ActionEvent e)
3126   {
3127     viewport.setScaleRightWrapped(scaleRight.isSelected());
3128     alignPanel.paintAlignment(true);
3129   }
3130
3131   /**
3132    * DOCUMENT ME!
3133    *
3134    * @param e
3135    *          DOCUMENT ME!
3136    */
3137   @Override
3138   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3139   {
3140     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3141     alignPanel.paintAlignment(true);
3142   }
3143
3144   /**
3145    * DOCUMENT ME!
3146    *
3147    * @param e
3148    *          DOCUMENT ME!
3149    */
3150   @Override
3151   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3152   {
3153     viewport.setShowText(viewTextMenuItem.isSelected());
3154     alignPanel.paintAlignment(true);
3155   }
3156
3157   /**
3158    * DOCUMENT ME!
3159    *
3160    * @param e
3161    *          DOCUMENT ME!
3162    */
3163   @Override
3164   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3165   {
3166     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3167     alignPanel.paintAlignment(true);
3168   }
3169
3170   public FeatureSettings featureSettings;
3171
3172   @Override
3173   public FeatureSettingsControllerI getFeatureSettingsUI()
3174   {
3175     return featureSettings;
3176   }
3177
3178   @Override
3179   public void featureSettings_actionPerformed(ActionEvent e)
3180   {
3181     if (featureSettings != null)
3182     {
3183       featureSettings.close();
3184       featureSettings = null;
3185     }
3186     if (!showSeqFeatures.isSelected())
3187     {
3188       // make sure features are actually displayed
3189       showSeqFeatures.setSelected(true);
3190       showSeqFeatures_actionPerformed(null);
3191     }
3192     featureSettings = new FeatureSettings(this);
3193   }
3194
3195   /**
3196    * Set or clear 'Show Sequence Features'
3197    *
3198    * @param evt
3199    *          DOCUMENT ME!
3200    */
3201   @Override
3202   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3203   {
3204     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3205     alignPanel.paintAlignment(true);
3206     if (alignPanel.getOverviewPanel() != null)
3207     {
3208       alignPanel.getOverviewPanel().updateOverviewImage();
3209     }
3210   }
3211
3212   /**
3213    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3214    * the annotations panel as a whole.
3215    *
3216    * The options to show/hide all annotations should be enabled when the panel
3217    * is shown, and disabled when the panel is hidden.
3218    *
3219    * @param e
3220    */
3221   @Override
3222   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3223   {
3224     final boolean setVisible = annotationPanelMenuItem.isSelected();
3225     viewport.setShowAnnotation(setVisible);
3226     this.showAllSeqAnnotations.setEnabled(setVisible);
3227     this.hideAllSeqAnnotations.setEnabled(setVisible);
3228     this.showAllAlAnnotations.setEnabled(setVisible);
3229     this.hideAllAlAnnotations.setEnabled(setVisible);
3230     alignPanel.updateLayout();
3231   }
3232
3233   @Override
3234   public void alignmentProperties()
3235   {
3236     JEditorPane editPane = new JEditorPane("text/html", "");
3237     editPane.setEditable(false);
3238     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3239             .formatAsHtml();
3240     editPane.setText(MessageManager.formatMessage("label.html_content",
3241             new Object[] { contents.toString() }));
3242     JInternalFrame frame = new JInternalFrame();
3243     frame.getContentPane().add(new JScrollPane(editPane));
3244
3245     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3246             "label.alignment_properties", new Object[] { getTitle() }),
3247             500, 400);
3248   }
3249
3250   /**
3251    * DOCUMENT ME!
3252    *
3253    * @param e
3254    *          DOCUMENT ME!
3255    */
3256   @Override
3257   public void overviewMenuItem_actionPerformed(ActionEvent e)
3258   {
3259     if (alignPanel.overviewPanel != null)
3260     {
3261       return;
3262     }
3263
3264     JInternalFrame frame = new JInternalFrame();
3265     OverviewPanel overview = new OverviewPanel(alignPanel);
3266     frame.setContentPane(overview);
3267     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3268             "label.overview_params", new Object[] { this.getTitle() }),
3269             frame.getWidth(), frame.getHeight());
3270     frame.pack();
3271     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3272     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3273     {
3274       @Override
3275       public void internalFrameClosed(
3276               javax.swing.event.InternalFrameEvent evt)
3277       {
3278         alignPanel.setOverviewPanel(null);
3279       };
3280     });
3281
3282     alignPanel.setOverviewPanel(overview);
3283   }
3284
3285   @Override
3286   public void textColour_actionPerformed()
3287   {
3288     new TextColourChooser().chooseColour(alignPanel, null);
3289   }
3290
3291   /*
3292    * public void covariationColour_actionPerformed() {
3293    * changeColour(new
3294    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3295    * ()[0])); }
3296    */
3297   @Override
3298   public void annotationColour_actionPerformed()
3299   {
3300     new AnnotationColourChooser(viewport, alignPanel);
3301   }
3302
3303   @Override
3304   public void annotationColumn_actionPerformed(ActionEvent e)
3305   {
3306     new AnnotationColumnChooser(viewport, alignPanel);
3307   }
3308
3309   /**
3310    * Action on the user checking or unchecking the option to apply the selected
3311    * colour scheme to all groups. If unchecked, groups may have their own
3312    * independent colour schemes.
3313    *
3314    * @param selected
3315    */
3316   @Override
3317   public void applyToAllGroups_actionPerformed(boolean selected)
3318   {
3319     viewport.setColourAppliesToAllGroups(selected);
3320   }
3321
3322   /**
3323    * Action on user selecting a colour from the colour menu
3324    *
3325    * @param name
3326    *          the name (not the menu item label!) of the colour scheme
3327    */
3328   @Override
3329   public void changeColour_actionPerformed(String name)
3330   {
3331     /*
3332      * 'User Defined' opens a panel to configure or load a
3333      * user-defined colour scheme
3334      */
3335     if (ResidueColourScheme.USER_DEFINED.equals(name))
3336     {
3337       new UserDefinedColours(alignPanel);
3338       return;
3339     }
3340
3341     /*
3342      * otherwise set the chosen colour scheme (or null for 'None')
3343      */
3344     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3345             viewport.getAlignment(), viewport.getHiddenRepSequences());
3346     changeColour(cs);
3347   }
3348
3349   /**
3350    * Actions on setting or changing the alignment colour scheme
3351    *
3352    * @param cs
3353    */
3354   @Override
3355   public void changeColour(ColourSchemeI cs)
3356   {
3357     // TODO: pull up to controller method
3358     ColourMenuHelper.setColourSelected(colourMenu, cs);
3359
3360     viewport.setGlobalColourScheme(cs);
3361
3362     alignPanel.paintAlignment(true);
3363   }
3364
3365   /**
3366    * Show the PID threshold slider panel
3367    */
3368   @Override
3369   protected void modifyPID_actionPerformed()
3370   {
3371     SliderPanel.setPIDSliderSource(alignPanel,
3372             viewport.getResidueShading(), alignPanel.getViewName());
3373     SliderPanel.showPIDSlider();
3374   }
3375
3376   /**
3377    * Show the Conservation slider panel
3378    */
3379   @Override
3380   protected void modifyConservation_actionPerformed()
3381   {
3382     SliderPanel.setConservationSlider(alignPanel,
3383             viewport.getResidueShading(), alignPanel.getViewName());
3384     SliderPanel.showConservationSlider();
3385   }
3386
3387   /**
3388    * Action on selecting or deselecting (Colour) By Conservation
3389    */
3390   @Override
3391   public void conservationMenuItem_actionPerformed(boolean selected)
3392   {
3393     modifyConservation.setEnabled(selected);
3394     viewport.setConservationSelected(selected);
3395     viewport.getResidueShading().setConservationApplied(selected);
3396
3397     changeColour(viewport.getGlobalColourScheme());
3398     if (selected)
3399     {
3400       modifyConservation_actionPerformed();
3401     }
3402     else
3403     {
3404       SliderPanel.hideConservationSlider();
3405     }
3406   }
3407
3408   /**
3409    * Action on selecting or deselecting (Colour) Above PID Threshold
3410    */
3411   @Override
3412   public void abovePIDThreshold_actionPerformed(boolean selected)
3413   {
3414     modifyPID.setEnabled(selected);
3415     viewport.setAbovePIDThreshold(selected);
3416     if (!selected)
3417     {
3418       viewport.getResidueShading().setThreshold(0,
3419               viewport.isIgnoreGapsConsensus());
3420     }
3421
3422     changeColour(viewport.getGlobalColourScheme());
3423     if (selected)
3424     {
3425       modifyPID_actionPerformed();
3426     }
3427     else
3428     {
3429       SliderPanel.hidePIDSlider();
3430     }
3431   }
3432
3433   /**
3434    * DOCUMENT ME!
3435    *
3436    * @param e
3437    *          DOCUMENT ME!
3438    */
3439   @Override
3440   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3441   {
3442     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3443     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3444             .getAlignment().getSequenceAt(0), null);
3445     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3446             viewport.getAlignment()));
3447     alignPanel.paintAlignment(true);
3448   }
3449
3450   /**
3451    * DOCUMENT ME!
3452    *
3453    * @param e
3454    *          DOCUMENT ME!
3455    */
3456   @Override
3457   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3458   {
3459     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3460     AlignmentSorter.sortByID(viewport.getAlignment());
3461     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3462             viewport.getAlignment()));
3463     alignPanel.paintAlignment(true);
3464   }
3465
3466   /**
3467    * DOCUMENT ME!
3468    *
3469    * @param e
3470    *          DOCUMENT ME!
3471    */
3472   @Override
3473   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3474   {
3475     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3476     AlignmentSorter.sortByLength(viewport.getAlignment());
3477     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3478             viewport.getAlignment()));
3479     alignPanel.paintAlignment(true);
3480   }
3481
3482   /**
3483    * DOCUMENT ME!
3484    *
3485    * @param e
3486    *          DOCUMENT ME!
3487    */
3488   @Override
3489   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3490   {
3491     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3492     AlignmentSorter.sortByGroup(viewport.getAlignment());
3493     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3494             viewport.getAlignment()));
3495
3496     alignPanel.paintAlignment(true);
3497   }
3498
3499   /**
3500    * DOCUMENT ME!
3501    *
3502    * @param e
3503    *          DOCUMENT ME!
3504    */
3505   @Override
3506   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3507   {
3508     new RedundancyPanel(alignPanel, this);
3509   }
3510
3511   /**
3512    * DOCUMENT ME!
3513    *
3514    * @param e
3515    *          DOCUMENT ME!
3516    */
3517   @Override
3518   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3519   {
3520     if ((viewport.getSelectionGroup() == null)
3521             || (viewport.getSelectionGroup().getSize() < 2))
3522     {
3523       JvOptionPane.showInternalMessageDialog(this, MessageManager
3524               .getString("label.you_must_select_least_two_sequences"),
3525               MessageManager.getString("label.invalid_selection"),
3526               JvOptionPane.WARNING_MESSAGE);
3527     }
3528     else
3529     {
3530       JInternalFrame frame = new JInternalFrame();
3531       frame.setContentPane(new PairwiseAlignPanel(viewport));
3532       Desktop.addInternalFrame(frame,
3533               MessageManager.getString("action.pairwise_alignment"), 600,
3534               500);
3535     }
3536   }
3537
3538   /**
3539    * DOCUMENT ME!
3540    *
3541    * @param e
3542    *          DOCUMENT ME!
3543    */
3544   @Override
3545   public void PCAMenuItem_actionPerformed(ActionEvent e)
3546   {
3547     if (((viewport.getSelectionGroup() != null)
3548             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3549             .getSelectionGroup().getSize() > 0))
3550             || (viewport.getAlignment().getHeight() < 4))
3551     {
3552       JvOptionPane
3553               .showInternalMessageDialog(
3554                       this,
3555                       MessageManager
3556                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3557                       MessageManager
3558                               .getString("label.sequence_selection_insufficient"),
3559                       JvOptionPane.WARNING_MESSAGE);
3560
3561       return;
3562     }
3563
3564     new PCAPanel(alignPanel);
3565   }
3566
3567   @Override
3568   public void autoCalculate_actionPerformed(ActionEvent e)
3569   {
3570     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3571     if (viewport.autoCalculateConsensus)
3572     {
3573       viewport.firePropertyChange("alignment", null, viewport
3574               .getAlignment().getSequences());
3575     }
3576   }
3577
3578   @Override
3579   public void sortByTreeOption_actionPerformed(ActionEvent e)
3580   {
3581     viewport.sortByTree = sortByTree.isSelected();
3582   }
3583
3584   @Override
3585   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3586   {
3587     viewport.followSelection = listenToViewSelections.isSelected();
3588   }
3589
3590   /**
3591    * DOCUMENT ME!
3592    *
3593    * @param e
3594    *          DOCUMENT ME!
3595    */
3596   @Override
3597   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3598   {
3599     newTreePanel("AV", "PID", "Average distance tree using PID");
3600   }
3601
3602   /**
3603    * DOCUMENT ME!
3604    *
3605    * @param e
3606    *          DOCUMENT ME!
3607    */
3608   @Override
3609   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3610   {
3611     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3612   }
3613
3614   /**
3615    * DOCUMENT ME!
3616    *
3617    * @param e
3618    *          DOCUMENT ME!
3619    */
3620   @Override
3621   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3622   {
3623     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3624   }
3625
3626   /**
3627    * DOCUMENT ME!
3628    *
3629    * @param e
3630    *          DOCUMENT ME!
3631    */
3632   @Override
3633   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3634   {
3635     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3636   }
3637
3638   /**
3639    * DOCUMENT ME!
3640    *
3641    * @param type
3642    *          DOCUMENT ME!
3643    * @param pwType
3644    *          DOCUMENT ME!
3645    * @param title
3646    *          DOCUMENT ME!
3647    */
3648   void newTreePanel(String type, String pwType, String title)
3649   {
3650     TreePanel tp;
3651
3652     if (viewport.getSelectionGroup() != null
3653             && viewport.getSelectionGroup().getSize() > 0)
3654     {
3655       if (viewport.getSelectionGroup().getSize() < 3)
3656       {
3657         JvOptionPane
3658                 .showMessageDialog(
3659                         Desktop.desktop,
3660                         MessageManager
3661                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3662                         MessageManager
3663                                 .getString("label.not_enough_sequences"),
3664                         JvOptionPane.WARNING_MESSAGE);
3665         return;
3666       }
3667
3668       SequenceGroup sg = viewport.getSelectionGroup();
3669
3670       /* Decide if the selection is a column region */
3671       for (SequenceI _s : sg.getSequences())
3672       {
3673         if (_s.getLength() < sg.getEndRes())
3674         {
3675           JvOptionPane
3676                   .showMessageDialog(
3677                           Desktop.desktop,
3678                           MessageManager
3679                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3680                           MessageManager
3681                                   .getString("label.sequences_selection_not_aligned"),
3682                           JvOptionPane.WARNING_MESSAGE);
3683
3684           return;
3685         }
3686       }
3687
3688       title = title + " on region";
3689       tp = new TreePanel(alignPanel, type, pwType);
3690     }
3691     else
3692     {
3693       // are the visible sequences aligned?
3694       if (!viewport.getAlignment().isAligned(false))
3695       {
3696         JvOptionPane
3697                 .showMessageDialog(
3698                         Desktop.desktop,
3699                         MessageManager
3700                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3701                         MessageManager
3702                                 .getString("label.sequences_not_aligned"),
3703                         JvOptionPane.WARNING_MESSAGE);
3704
3705         return;
3706       }
3707
3708       if (viewport.getAlignment().getHeight() < 2)
3709       {
3710         return;
3711       }
3712
3713       tp = new TreePanel(alignPanel, type, pwType);
3714     }
3715
3716     title += " from ";
3717
3718     if (viewport.viewName != null)
3719     {
3720       title += viewport.viewName + " of ";
3721     }
3722
3723     title += this.title;
3724
3725     Desktop.addInternalFrame(tp, title, 600, 500);
3726   }
3727
3728   /**
3729    * DOCUMENT ME!
3730    *
3731    * @param title
3732    *          DOCUMENT ME!
3733    * @param order
3734    *          DOCUMENT ME!
3735    */
3736   public void addSortByOrderMenuItem(String title,
3737           final AlignmentOrder order)
3738   {
3739     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3740             "action.by_title_param", new Object[] { title }));
3741     sort.add(item);
3742     item.addActionListener(new java.awt.event.ActionListener()
3743     {
3744       @Override
3745       public void actionPerformed(ActionEvent e)
3746       {
3747         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3748
3749         // TODO: JBPNote - have to map order entries to curent SequenceI
3750         // pointers
3751         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3752
3753         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3754                 .getAlignment()));
3755
3756         alignPanel.paintAlignment(true);
3757       }
3758     });
3759   }
3760
3761   /**
3762    * Add a new sort by annotation score menu item
3763    *
3764    * @param sort
3765    *          the menu to add the option to
3766    * @param scoreLabel
3767    *          the label used to retrieve scores for each sequence on the
3768    *          alignment
3769    */
3770   public void addSortByAnnotScoreMenuItem(JMenu sort,
3771           final String scoreLabel)
3772   {
3773     final JMenuItem item = new JMenuItem(scoreLabel);
3774     sort.add(item);
3775     item.addActionListener(new java.awt.event.ActionListener()
3776     {
3777       @Override
3778       public void actionPerformed(ActionEvent e)
3779       {
3780         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3781         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3782                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3783         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3784                 viewport.getAlignment()));
3785         alignPanel.paintAlignment(true);
3786       }
3787     });
3788   }
3789
3790   /**
3791    * last hash for alignment's annotation array - used to minimise cost of
3792    * rebuild.
3793    */
3794   protected int _annotationScoreVectorHash;
3795
3796   /**
3797    * search the alignment and rebuild the sort by annotation score submenu the
3798    * last alignment annotation vector hash is stored to minimize cost of
3799    * rebuilding in subsequence calls.
3800    *
3801    */
3802   @Override
3803   public void buildSortByAnnotationScoresMenu()
3804   {
3805     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3806     {
3807       return;
3808     }
3809
3810     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3811     {
3812       sortByAnnotScore.removeAll();
3813       // almost certainly a quicker way to do this - but we keep it simple
3814       Hashtable scoreSorts = new Hashtable();
3815       AlignmentAnnotation aann[];
3816       for (SequenceI sqa : viewport.getAlignment().getSequences())
3817       {
3818         aann = sqa.getAnnotation();
3819         for (int i = 0; aann != null && i < aann.length; i++)
3820         {
3821           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3822           {
3823             scoreSorts.put(aann[i].label, aann[i].label);
3824           }
3825         }
3826       }
3827       Enumeration labels = scoreSorts.keys();
3828       while (labels.hasMoreElements())
3829       {
3830         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3831                 (String) labels.nextElement());
3832       }
3833       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3834       scoreSorts.clear();
3835
3836       _annotationScoreVectorHash = viewport.getAlignment()
3837               .getAlignmentAnnotation().hashCode();
3838     }
3839   }
3840
3841   /**
3842    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3843    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3844    * call. Listeners are added to remove the menu item when the treePanel is
3845    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3846    * modified.
3847    *
3848    * @param treePanel
3849    *          Displayed tree window.
3850    * @param title
3851    *          SortBy menu item title.
3852    */
3853   @Override
3854   public void buildTreeMenu()
3855   {
3856     calculateTree.removeAll();
3857     // build the calculate menu
3858
3859     for (final String type : new String[] { "NJ", "AV" })
3860     {
3861       String treecalcnm = MessageManager.getString("label.tree_calc_"
3862               + type.toLowerCase());
3863       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3864       {
3865         JMenuItem tm = new JMenuItem();
3866         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3867         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3868                 || sm.isProtein() == !viewport.getAlignment()
3869                         .isNucleotide())
3870         {
3871           String smn = MessageManager.getStringOrReturn(
3872                   "label.score_model_", sm.getName());
3873           final String title = MessageManager.formatMessage(
3874                   "label.treecalc_title", treecalcnm, smn);
3875           tm.setText(title);//
3876           tm.addActionListener(new java.awt.event.ActionListener()
3877           {
3878             @Override
3879             public void actionPerformed(ActionEvent e)
3880             {
3881               newTreePanel(type, pwtype, title);
3882             }
3883           });
3884           calculateTree.add(tm);
3885         }
3886
3887       }
3888     }
3889     sortByTreeMenu.removeAll();
3890
3891     List<Component> comps = PaintRefresher.components.get(viewport
3892             .getSequenceSetId());
3893     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3894     for (Component comp : comps)
3895     {
3896       if (comp instanceof TreePanel)
3897       {
3898         treePanels.add((TreePanel) comp);
3899       }
3900     }
3901
3902     if (treePanels.size() < 1)
3903     {
3904       sortByTreeMenu.setVisible(false);
3905       return;
3906     }
3907
3908     sortByTreeMenu.setVisible(true);
3909
3910     for (final TreePanel tp : treePanels)
3911     {
3912       final JMenuItem item = new JMenuItem(tp.getTitle());
3913       item.addActionListener(new java.awt.event.ActionListener()
3914       {
3915         @Override
3916         public void actionPerformed(ActionEvent e)
3917         {
3918           tp.sortByTree_actionPerformed();
3919           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3920
3921         }
3922       });
3923
3924       sortByTreeMenu.add(item);
3925     }
3926   }
3927
3928   public boolean sortBy(AlignmentOrder alorder, String undoname)
3929   {
3930     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3931     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3932     if (undoname != null)
3933     {
3934       addHistoryItem(new OrderCommand(undoname, oldOrder,
3935               viewport.getAlignment()));
3936     }
3937     alignPanel.paintAlignment(true);
3938     return true;
3939   }
3940
3941   /**
3942    * Work out whether the whole set of sequences or just the selected set will
3943    * be submitted for multiple alignment.
3944    *
3945    */
3946   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3947   {
3948     // Now, check we have enough sequences
3949     AlignmentView msa = null;
3950
3951     if ((viewport.getSelectionGroup() != null)
3952             && (viewport.getSelectionGroup().getSize() > 1))
3953     {
3954       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3955       // some common interface!
3956       /*
3957        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3958        * SequenceI[sz = seqs.getSize(false)];
3959        *
3960        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3961        * seqs.getSequenceAt(i); }
3962        */
3963       msa = viewport.getAlignmentView(true);
3964     }
3965     else if (viewport.getSelectionGroup() != null
3966             && viewport.getSelectionGroup().getSize() == 1)
3967     {
3968       int option = JvOptionPane.showConfirmDialog(this,
3969               MessageManager.getString("warn.oneseq_msainput_selection"),
3970               MessageManager.getString("label.invalid_selection"),
3971               JvOptionPane.OK_CANCEL_OPTION);
3972       if (option == JvOptionPane.OK_OPTION)
3973       {
3974         msa = viewport.getAlignmentView(false);
3975       }
3976     }
3977     else
3978     {
3979       msa = viewport.getAlignmentView(false);
3980     }
3981     return msa;
3982   }
3983
3984   /**
3985    * Decides what is submitted to a secondary structure prediction service: the
3986    * first sequence in the alignment, or in the current selection, or, if the
3987    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3988    * region or the whole alignment. (where the first sequence in the set is the
3989    * one that the prediction will be for).
3990    */
3991   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3992   {
3993     AlignmentView seqs = null;
3994
3995     if ((viewport.getSelectionGroup() != null)
3996             && (viewport.getSelectionGroup().getSize() > 0))
3997     {
3998       seqs = viewport.getAlignmentView(true);
3999     }
4000     else
4001     {
4002       seqs = viewport.getAlignmentView(false);
4003     }
4004     // limit sequences - JBPNote in future - could spawn multiple prediction
4005     // jobs
4006     // TODO: viewport.getAlignment().isAligned is a global state - the local
4007     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4008     if (!viewport.getAlignment().isAligned(false))
4009     {
4010       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4011       // TODO: if seqs.getSequences().length>1 then should really have warned
4012       // user!
4013
4014     }
4015     return seqs;
4016   }
4017
4018   /**
4019    * DOCUMENT ME!
4020    *
4021    * @param e
4022    *          DOCUMENT ME!
4023    */
4024   @Override
4025   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4026   {
4027     // Pick the tree file
4028     JalviewFileChooser chooser = new JalviewFileChooser(
4029             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4030     chooser.setFileView(new JalviewFileView());
4031     chooser.setDialogTitle(MessageManager
4032             .getString("label.select_newick_like_tree_file"));
4033     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4034
4035     int value = chooser.showOpenDialog(null);
4036
4037     if (value == JalviewFileChooser.APPROVE_OPTION)
4038     {
4039       String choice = chooser.getSelectedFile().getPath();
4040       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4041       jalview.io.NewickFile fin = null;
4042       try
4043       {
4044         fin = new NewickFile(choice, DataSourceType.FILE);
4045         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4046       } catch (Exception ex)
4047       {
4048         JvOptionPane
4049                 .showMessageDialog(
4050                         Desktop.desktop,
4051                         ex.getMessage(),
4052                         MessageManager
4053                                 .getString("label.problem_reading_tree_file"),
4054                         JvOptionPane.WARNING_MESSAGE);
4055         ex.printStackTrace();
4056       }
4057       if (fin != null && fin.hasWarningMessage())
4058       {
4059         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4060                 .getWarningMessage(), MessageManager
4061                 .getString("label.possible_problem_with_tree_file"),
4062                 JvOptionPane.WARNING_MESSAGE);
4063       }
4064     }
4065   }
4066
4067   public TreePanel ShowNewickTree(NewickFile nf, String title)
4068   {
4069     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4070   }
4071
4072   public TreePanel ShowNewickTree(NewickFile nf, String title,
4073           AlignmentView input)
4074   {
4075     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4076   }
4077
4078   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4079           int h, int x, int y)
4080   {
4081     return ShowNewickTree(nf, title, null, w, h, x, y);
4082   }
4083
4084   /**
4085    * Add a treeviewer for the tree extracted from a newick file object to the
4086    * current alignment view
4087    *
4088    * @param nf
4089    *          the tree
4090    * @param title
4091    *          tree viewer title
4092    * @param input
4093    *          Associated alignment input data (or null)
4094    * @param w
4095    *          width
4096    * @param h
4097    *          height
4098    * @param x
4099    *          position
4100    * @param y
4101    *          position
4102    * @return TreePanel handle
4103    */
4104   public TreePanel ShowNewickTree(NewickFile nf, String title,
4105           AlignmentView input, int w, int h, int x, int y)
4106   {
4107     TreePanel tp = null;
4108
4109     try
4110     {
4111       nf.parse();
4112
4113       if (nf.getTree() != null)
4114       {
4115         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4116
4117         tp.setSize(w, h);
4118
4119         if (x > 0 && y > 0)
4120         {
4121           tp.setLocation(x, y);
4122         }
4123
4124         Desktop.addInternalFrame(tp, title, w, h);
4125       }
4126     } catch (Exception ex)
4127     {
4128       ex.printStackTrace();
4129     }
4130
4131     return tp;
4132   }
4133
4134   private boolean buildingMenu = false;
4135
4136   /**
4137    * Generates menu items and listener event actions for web service clients
4138    *
4139    */
4140   public void BuildWebServiceMenu()
4141   {
4142     while (buildingMenu)
4143     {
4144       try
4145       {
4146         System.err.println("Waiting for building menu to finish.");
4147         Thread.sleep(10);
4148       } catch (Exception e)
4149       {
4150       }
4151     }
4152     final AlignFrame me = this;
4153     buildingMenu = true;
4154     new Thread(new Runnable()
4155     {
4156       @Override
4157       public void run()
4158       {
4159         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4160         try
4161         {
4162           // System.err.println("Building ws menu again "
4163           // + Thread.currentThread());
4164           // TODO: add support for context dependent disabling of services based
4165           // on
4166           // alignment and current selection
4167           // TODO: add additional serviceHandle parameter to specify abstract
4168           // handler
4169           // class independently of AbstractName
4170           // TODO: add in rediscovery GUI function to restart discoverer
4171           // TODO: group services by location as well as function and/or
4172           // introduce
4173           // object broker mechanism.
4174           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4175           final IProgressIndicator af = me;
4176
4177           /*
4178            * do not i18n these strings - they are hard-coded in class
4179            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4180            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4181            */
4182           final JMenu msawsmenu = new JMenu("Alignment");
4183           final JMenu secstrmenu = new JMenu(
4184                   "Secondary Structure Prediction");
4185           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4186           final JMenu analymenu = new JMenu("Analysis");
4187           final JMenu dismenu = new JMenu("Protein Disorder");
4188           // JAL-940 - only show secondary structure prediction services from
4189           // the legacy server
4190           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4191               // &&
4192           Discoverer.services != null && (Discoverer.services.size() > 0))
4193           {
4194             // TODO: refactor to allow list of AbstractName/Handler bindings to
4195             // be
4196             // stored or retrieved from elsewhere
4197             // No MSAWS used any more:
4198             // Vector msaws = null; // (Vector)
4199             // Discoverer.services.get("MsaWS");
4200             Vector secstrpr = (Vector) Discoverer.services
4201                     .get("SecStrPred");
4202             if (secstrpr != null)
4203             {
4204               // Add any secondary structure prediction services
4205               for (int i = 0, j = secstrpr.size(); i < j; i++)
4206               {
4207                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4208                         .get(i);
4209                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4210                         .getServiceClient(sh);
4211                 int p = secstrmenu.getItemCount();
4212                 impl.attachWSMenuEntry(secstrmenu, me);
4213                 int q = secstrmenu.getItemCount();
4214                 for (int litm = p; litm < q; litm++)
4215                 {
4216                   legacyItems.add(secstrmenu.getItem(litm));
4217                 }
4218               }
4219             }
4220           }
4221
4222           // Add all submenus in the order they should appear on the web
4223           // services menu
4224           wsmenu.add(msawsmenu);
4225           wsmenu.add(secstrmenu);
4226           wsmenu.add(dismenu);
4227           wsmenu.add(analymenu);
4228           // No search services yet
4229           // wsmenu.add(seqsrchmenu);
4230
4231           javax.swing.SwingUtilities.invokeLater(new Runnable()
4232           {
4233             @Override
4234             public void run()
4235             {
4236               try
4237               {
4238                 webService.removeAll();
4239                 // first, add discovered services onto the webservices menu
4240                 if (wsmenu.size() > 0)
4241                 {
4242                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4243                   {
4244                     webService.add(wsmenu.get(i));
4245                   }
4246                 }
4247                 else
4248                 {
4249                   webService.add(me.webServiceNoServices);
4250                 }
4251                 // TODO: move into separate menu builder class.
4252                 boolean new_sspred = false;
4253                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4254                 {
4255                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4256                   if (jws2servs != null)
4257                   {
4258                     if (jws2servs.hasServices())
4259                     {
4260                       jws2servs.attachWSMenuEntry(webService, me);
4261                       for (Jws2Instance sv : jws2servs.getServices())
4262                       {
4263                         if (sv.description.toLowerCase().contains("jpred"))
4264                         {
4265                           for (JMenuItem jmi : legacyItems)
4266                           {
4267                             jmi.setVisible(false);
4268                           }
4269                         }
4270                       }
4271
4272                     }
4273                     if (jws2servs.isRunning())
4274                     {
4275                       JMenuItem tm = new JMenuItem(
4276                               "Still discovering JABA Services");
4277                       tm.setEnabled(false);
4278                       webService.add(tm);
4279                     }
4280                   }
4281                 }
4282                 build_urlServiceMenu(me.webService);
4283                 build_fetchdbmenu(webService);
4284                 for (JMenu item : wsmenu)
4285                 {
4286                   if (item.getItemCount() == 0)
4287                   {
4288                     item.setEnabled(false);
4289                   }
4290                   else
4291                   {
4292                     item.setEnabled(true);
4293                   }
4294                 }
4295               } catch (Exception e)
4296               {
4297                 Cache.log
4298                         .debug("Exception during web service menu building process.",
4299                                 e);
4300               }
4301             }
4302           });
4303         } catch (Exception e)
4304         {
4305         }
4306         buildingMenu = false;
4307       }
4308     }).start();
4309
4310   }
4311
4312   /**
4313    * construct any groupURL type service menu entries.
4314    *
4315    * @param webService
4316    */
4317   private void build_urlServiceMenu(JMenu webService)
4318   {
4319     // TODO: remove this code when 2.7 is released
4320     // DEBUG - alignmentView
4321     /*
4322      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4323      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4324      *
4325      * @Override public void actionPerformed(ActionEvent e) {
4326      * jalview.datamodel.AlignmentView
4327      * .testSelectionViews(af.viewport.getAlignment(),
4328      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4329      *
4330      * }); webService.add(testAlView);
4331      */
4332     // TODO: refactor to RestClient discoverer and merge menu entries for
4333     // rest-style services with other types of analysis/calculation service
4334     // SHmmr test client - still being implemented.
4335     // DEBUG - alignmentView
4336
4337     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4338             .getRestClients())
4339     {
4340       client.attachWSMenuEntry(
4341               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4342               this);
4343     }
4344   }
4345
4346   /**
4347    * Searches the alignment sequences for xRefs and builds the Show
4348    * Cross-References menu (formerly called Show Products), with database
4349    * sources for which cross-references are found (protein sources for a
4350    * nucleotide alignment and vice versa)
4351    *
4352    * @return true if Show Cross-references menu should be enabled
4353    */
4354   public boolean canShowProducts()
4355   {
4356     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4357     AlignmentI dataset = viewport.getAlignment().getDataset();
4358
4359     showProducts.removeAll();
4360     final boolean dna = viewport.getAlignment().isNucleotide();
4361
4362     if (seqs == null || seqs.length == 0)
4363     {
4364       // nothing to see here.
4365       return false;
4366     }
4367
4368     boolean showp = false;
4369     try
4370     {
4371       List<String> ptypes = new CrossRef(seqs, dataset)
4372               .findXrefSourcesForSequences(dna);
4373
4374       for (final String source : ptypes)
4375       {
4376         showp = true;
4377         final AlignFrame af = this;
4378         JMenuItem xtype = new JMenuItem(source);
4379         xtype.addActionListener(new ActionListener()
4380         {
4381           @Override
4382           public void actionPerformed(ActionEvent e)
4383           {
4384             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4385           }
4386         });
4387         showProducts.add(xtype);
4388       }
4389       showProducts.setVisible(showp);
4390       showProducts.setEnabled(showp);
4391     } catch (Exception e)
4392     {
4393       Cache.log
4394               .warn("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,
4413           final boolean _odna, final String source)
4414   {
4415     new Thread(CrossRefAction.showProductsFor(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(ActionEvent e)
4425   {
4426     AlignmentI al = null;
4427     try
4428     {
4429       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4430
4431       al = dna.translateCdna();
4432     } catch (Exception ex)
4433     {
4434       jalview.bin.Cache.log.error(
4435               "Exception during translation. Please report this !", ex);
4436       final String msg = MessageManager
4437               .getString("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
4448               .getString("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.formatMessage(
4459               "label.translation_of_params",
4460               new Object[] { this.getTitle() });
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
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(String file, DataSourceType sourceType)
4495   {
4496     return avc.parseFeaturesFile(file, sourceType,
4497             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4498
4499   }
4500
4501   @Override
4502   public void refreshFeatureUI(boolean enableIfNecessary)
4503   {
4504     // note - currently this is only still here rather than in the controller
4505     // because of the featureSettings hard reference that is yet to be
4506     // abstracted
4507     if (enableIfNecessary)
4508     {
4509       viewport.setShowSequenceFeatures(true);
4510       showSeqFeatures.setSelected(true);
4511     }
4512
4513   }
4514
4515   @Override
4516   public void dragEnter(DropTargetDragEvent evt)
4517   {
4518   }
4519
4520   @Override
4521   public void dragExit(DropTargetEvent evt)
4522   {
4523   }
4524
4525   @Override
4526   public void dragOver(DropTargetDragEvent evt)
4527   {
4528   }
4529
4530   @Override
4531   public void dropActionChanged(DropTargetDragEvent evt)
4532   {
4533   }
4534
4535   @Override
4536   public void drop(DropTargetDropEvent evt)
4537   {
4538     // JAL-1552 - acceptDrop required before getTransferable call for
4539     // Java's Transferable for native dnd
4540     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4541     Transferable t = evt.getTransferable();
4542     List<String> files = new ArrayList<String>();
4543     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4544
4545     try
4546     {
4547       Desktop.transferFromDropTarget(files, protocols, evt, t);
4548     } catch (Exception e)
4549     {
4550       e.printStackTrace();
4551     }
4552     if (files != null)
4553     {
4554       try
4555       {
4556         // check to see if any of these files have names matching sequences in
4557         // the alignment
4558         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4559                 .getAlignment().getSequencesArray());
4560         /**
4561          * Object[] { String,SequenceI}
4562          */
4563         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4564         ArrayList<String> filesnotmatched = new ArrayList<String>();
4565         for (int i = 0; i < files.size(); i++)
4566         {
4567           String file = files.get(i).toString();
4568           String pdbfn = "";
4569           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4570           if (protocol == DataSourceType.FILE)
4571           {
4572             File fl = new File(file);
4573             pdbfn = fl.getName();
4574           }
4575           else if (protocol == DataSourceType.URL)
4576           {
4577             URL url = new URL(file);
4578             pdbfn = url.getFile();
4579           }
4580           if (pdbfn.length() > 0)
4581           {
4582             // attempt to find a match in the alignment
4583             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4584             int l = 0, c = pdbfn.indexOf(".");
4585             while (mtch == null && c != -1)
4586             {
4587               do
4588               {
4589                 l = c;
4590               } while ((c = pdbfn.indexOf(".", l)) > l);
4591               if (l > -1)
4592               {
4593                 pdbfn = pdbfn.substring(0, l);
4594               }
4595               mtch = idm.findAllIdMatches(pdbfn);
4596             }
4597             if (mtch != null)
4598             {
4599               FileFormatI type = null;
4600               try
4601               {
4602                 type = new IdentifyFile().identify(file, protocol);
4603               } catch (Exception ex)
4604               {
4605                 type = null;
4606               }
4607               if (type != null && type.isStructureFile())
4608               {
4609                 filesmatched.add(new Object[] { file, protocol, mtch });
4610                 continue;
4611               }
4612             }
4613             // File wasn't named like one of the sequences or wasn't a PDB file.
4614             filesnotmatched.add(file);
4615           }
4616         }
4617         int assocfiles = 0;
4618         if (filesmatched.size() > 0)
4619         {
4620           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4621                   || JvOptionPane
4622                           .showConfirmDialog(
4623                                   this,
4624                                   MessageManager
4625                                           .formatMessage(
4626                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4627                                                   new Object[] { Integer
4628                                                           .valueOf(
4629                                                                   filesmatched
4630                                                                           .size())
4631                                                           .toString() }),
4632                                   MessageManager
4633                                           .getString("label.automatically_associate_structure_files_by_name"),
4634                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4635
4636           {
4637             for (Object[] fm : filesmatched)
4638             {
4639               // try and associate
4640               // TODO: may want to set a standard ID naming formalism for
4641               // associating PDB files which have no IDs.
4642               for (SequenceI toassoc : (SequenceI[]) fm[2])
4643               {
4644                 PDBEntry pe = new AssociatePdbFileWithSeq()
4645                         .associatePdbWithSeq((String) fm[0],
4646                                 (DataSourceType) fm[1], toassoc, false,
4647                                 Desktop.instance);
4648                 if (pe != null)
4649                 {
4650                   System.err.println("Associated file : "
4651                           + ((String) fm[0]) + " with "
4652                           + toassoc.getDisplayId(true));
4653                   assocfiles++;
4654                 }
4655               }
4656               alignPanel.paintAlignment(true);
4657             }
4658           }
4659         }
4660         if (filesnotmatched.size() > 0)
4661         {
4662           if (assocfiles > 0
4663                   && (Cache.getDefault(
4664                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4665                           .showConfirmDialog(
4666                                   this,
4667                                   "<html>"
4668                                           + MessageManager
4669                                                   .formatMessage(
4670                                                           "label.ignore_unmatched_dropped_files_info",
4671                                                           new Object[] { Integer
4672                                                                   .valueOf(
4673                                                                           filesnotmatched
4674                                                                                   .size())
4675                                                                   .toString() })
4676                                           + "</html>",
4677                                   MessageManager
4678                                           .getString("label.ignore_unmatched_dropped_files"),
4679                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4680           {
4681             return;
4682           }
4683           for (String fn : filesnotmatched)
4684           {
4685             loadJalviewDataFile(fn, null, null, null);
4686           }
4687
4688         }
4689       } catch (Exception ex)
4690       {
4691         ex.printStackTrace();
4692       }
4693     }
4694   }
4695
4696   /**
4697    * Attempt to load a "dropped" file or URL string: First by testing whether
4698    * it's an Annotation file, then a JNet file, and finally a features file. If
4699    * all are false then the user may have dropped an alignment file onto this
4700    * AlignFrame.
4701    *
4702    * @param file
4703    *          either a filename or a URL string.
4704    */
4705   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4706           FileFormatI format, SequenceI assocSeq)
4707   {
4708     try
4709     {
4710       if (sourceType == null)
4711       {
4712         sourceType = FormatAdapter.checkProtocol(file);
4713       }
4714       // if the file isn't identified, or not positively identified as some
4715       // other filetype (PFAM is default unidentified alignment file type) then
4716       // try to parse as annotation.
4717       boolean isAnnotation = (format == null || FileFormat.Pfam
4718               .equals(format)) ? new AnnotationFile()
4719               .annotateAlignmentView(viewport, file, sourceType) : false;
4720
4721       if (!isAnnotation)
4722       {
4723         // first see if its a T-COFFEE score file
4724         TCoffeeScoreFile tcf = null;
4725         try
4726         {
4727           tcf = new TCoffeeScoreFile(file, sourceType);
4728           if (tcf.isValid())
4729           {
4730             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4731             {
4732               buildColourMenu();
4733               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4734               isAnnotation = true;
4735               statusBar
4736                       .setText(MessageManager
4737                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4738             }
4739             else
4740             {
4741               // some problem - if no warning its probable that the ID matching
4742               // process didn't work
4743               JvOptionPane
4744                       .showMessageDialog(
4745                               Desktop.desktop,
4746                               tcf.getWarningMessage() == null ? MessageManager
4747                                       .getString("label.check_file_matches_sequence_ids_alignment")
4748                                       : tcf.getWarningMessage(),
4749                               MessageManager
4750                                       .getString("label.problem_reading_tcoffee_score_file"),
4751                               JvOptionPane.WARNING_MESSAGE);
4752             }
4753           }
4754           else
4755           {
4756             tcf = null;
4757           }
4758         } catch (Exception x)
4759         {
4760           Cache.log
4761                   .debug("Exception when processing data source as T-COFFEE score file",
4762                           x);
4763           tcf = null;
4764         }
4765         if (tcf == null)
4766         {
4767           // try to see if its a JNet 'concise' style annotation file *before*
4768           // we
4769           // try to parse it as a features file
4770           if (format == null)
4771           {
4772             format = new IdentifyFile().identify(file, sourceType);
4773           }
4774           if (FileFormat.Jnet.equals(format))
4775           {
4776             JPredFile predictions = new JPredFile(file, sourceType);
4777             new JnetAnnotationMaker();
4778             JnetAnnotationMaker.add_annotation(predictions,
4779                     viewport.getAlignment(), 0, false);
4780             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4781             viewport.getAlignment().setSeqrep(repseq);
4782             ColumnSelection cs = new ColumnSelection();
4783             cs.hideInsertionsFor(repseq);
4784             viewport.setColumnSelection(cs);
4785             isAnnotation = true;
4786           }
4787           // else if (IdentifyFile.FeaturesFile.equals(format))
4788           else if (FileFormat.Features.equals(format))
4789           {
4790             if (parseFeaturesFile(file, sourceType))
4791             {
4792               alignPanel.paintAlignment(true);
4793             }
4794           }
4795           else
4796           {
4797             new FileLoader().LoadFile(viewport, file, sourceType, format);
4798           }
4799         }
4800       }
4801       if (isAnnotation)
4802       {
4803
4804         alignPanel.adjustAnnotationHeight();
4805         viewport.updateSequenceIdColours();
4806         buildSortByAnnotationScoresMenu();
4807         alignPanel.paintAlignment(true);
4808       }
4809     } catch (Exception ex)
4810     {
4811       ex.printStackTrace();
4812     } catch (OutOfMemoryError oom)
4813     {
4814       try
4815       {
4816         System.gc();
4817       } catch (Exception x)
4818       {
4819       }
4820       new OOMWarning(
4821               "loading data "
4822                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4823                               : "using " + sourceType + " from " + file)
4824                               : ".")
4825                       + (format != null ? "(parsing as '" + format
4826                               + "' file)" : ""), oom, Desktop.desktop);
4827     }
4828   }
4829
4830   /**
4831    * Method invoked by the ChangeListener on the tabbed pane, in other words
4832    * when a different tabbed pane is selected by the user or programmatically.
4833    */
4834   @Override
4835   public void tabSelectionChanged(int index)
4836   {
4837     if (index > -1)
4838     {
4839       alignPanel = alignPanels.get(index);
4840       viewport = alignPanel.av;
4841       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4842       setMenusFromViewport(viewport);
4843     }
4844
4845     /*
4846      * 'focus' any colour slider that is open to the selected viewport
4847      */
4848     if (viewport.getConservationSelected())
4849     {
4850       SliderPanel.setConservationSlider(alignPanel,
4851               viewport.getResidueShading(), alignPanel.getViewName());
4852     }
4853     else
4854     {
4855       SliderPanel.hideConservationSlider();
4856     }
4857     if (viewport.getAbovePIDThreshold())
4858     {
4859       SliderPanel.setPIDSliderSource(alignPanel,
4860               viewport.getResidueShading(), alignPanel.getViewName());
4861     }
4862     else
4863     {
4864       SliderPanel.hidePIDSlider();
4865     }
4866
4867     /*
4868      * If there is a frame linked to this one in a SplitPane, switch it to the
4869      * same view tab index. No infinite recursion of calls should happen, since
4870      * tabSelectionChanged() should not get invoked on setting the selected
4871      * index to an unchanged value. Guard against setting an invalid index
4872      * before the new view peer tab has been created.
4873      */
4874     final AlignViewportI peer = viewport.getCodingComplement();
4875     if (peer != null)
4876     {
4877       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4878       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4879       {
4880         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4881       }
4882     }
4883   }
4884
4885   /**
4886    * On right mouse click on view tab, prompt for and set new view name.
4887    */
4888   @Override
4889   public void tabbedPane_mousePressed(MouseEvent e)
4890   {
4891     if (e.isPopupTrigger())
4892     {
4893       String msg = MessageManager.getString("label.enter_view_name");
4894       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4895               JvOptionPane.QUESTION_MESSAGE);
4896
4897       if (reply != null)
4898       {
4899         viewport.viewName = reply;
4900         // TODO warn if reply is in getExistingViewNames()?
4901         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4902       }
4903     }
4904   }
4905
4906   public AlignViewport getCurrentView()
4907   {
4908     return viewport;
4909   }
4910
4911   /**
4912    * Open the dialog for regex description parsing.
4913    */
4914   @Override
4915   protected void extractScores_actionPerformed(ActionEvent e)
4916   {
4917     ParseProperties pp = new jalview.analysis.ParseProperties(
4918             viewport.getAlignment());
4919     // TODO: verify regex and introduce GUI dialog for version 2.5
4920     // if (pp.getScoresFromDescription("col", "score column ",
4921     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4922     // true)>0)
4923     if (pp.getScoresFromDescription("description column",
4924             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4925     {
4926       buildSortByAnnotationScoresMenu();
4927     }
4928   }
4929
4930   /*
4931    * (non-Javadoc)
4932    *
4933    * @see
4934    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4935    * )
4936    */
4937   @Override
4938   protected void showDbRefs_actionPerformed(ActionEvent e)
4939   {
4940     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4941   }
4942
4943   /*
4944    * (non-Javadoc)
4945    *
4946    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4947    * ActionEvent)
4948    */
4949   @Override
4950   protected void showNpFeats_actionPerformed(ActionEvent e)
4951   {
4952     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4953   }
4954
4955   /**
4956    * find the viewport amongst the tabs in this alignment frame and close that
4957    * tab
4958    *
4959    * @param av
4960    */
4961   public boolean closeView(AlignViewportI av)
4962   {
4963     if (viewport == av)
4964     {
4965       this.closeMenuItem_actionPerformed(false);
4966       return true;
4967     }
4968     Component[] comp = tabbedPane.getComponents();
4969     for (int i = 0; comp != null && i < comp.length; i++)
4970     {
4971       if (comp[i] instanceof AlignmentPanel)
4972       {
4973         if (((AlignmentPanel) comp[i]).av == av)
4974         {
4975           // close the view.
4976           closeView((AlignmentPanel) comp[i]);
4977           return true;
4978         }
4979       }
4980     }
4981     return false;
4982   }
4983
4984   protected void build_fetchdbmenu(JMenu webService)
4985   {
4986     // Temporary hack - DBRef Fetcher always top level ws entry.
4987     // TODO We probably want to store a sequence database checklist in
4988     // preferences and have checkboxes.. rather than individual sources selected
4989     // here
4990     final JMenu rfetch = new JMenu(
4991             MessageManager.getString("action.fetch_db_references"));
4992     rfetch.setToolTipText(MessageManager
4993             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4994     webService.add(rfetch);
4995
4996     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4997             MessageManager.getString("option.trim_retrieved_seqs"));
4998     trimrs.setToolTipText(MessageManager
4999             .getString("label.trim_retrieved_sequences"));
5000     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5001     trimrs.addActionListener(new ActionListener()
5002     {
5003       @Override
5004       public void actionPerformed(ActionEvent e)
5005       {
5006         trimrs.setSelected(trimrs.isSelected());
5007         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5008                 Boolean.valueOf(trimrs.isSelected()).toString());
5009       };
5010     });
5011     rfetch.add(trimrs);
5012     JMenuItem fetchr = new JMenuItem(
5013             MessageManager.getString("label.standard_databases"));
5014     fetchr.setToolTipText(MessageManager
5015             .getString("label.fetch_embl_uniprot"));
5016     fetchr.addActionListener(new ActionListener()
5017     {
5018
5019       @Override
5020       public void actionPerformed(ActionEvent e)
5021       {
5022         new Thread(new Runnable()
5023         {
5024           @Override
5025           public void run()
5026           {
5027             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5028                     .getAlignment().isNucleotide();
5029             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5030                     .getSequenceSelection(), alignPanel.alignFrame, null,
5031                     alignPanel.alignFrame.featureSettings, isNucleotide);
5032             dbRefFetcher.addListener(new FetchFinishedListenerI()
5033             {
5034               @Override
5035               public void finished()
5036               {
5037                 AlignFrame.this.setMenusForViewport();
5038               }
5039             });
5040             dbRefFetcher.fetchDBRefs(false);
5041           }
5042         }).start();
5043
5044       }
5045
5046     });
5047     rfetch.add(fetchr);
5048     final AlignFrame me = this;
5049     new Thread(new Runnable()
5050     {
5051       @Override
5052       public void run()
5053       {
5054         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5055                 .getSequenceFetcherSingleton(me);
5056         javax.swing.SwingUtilities.invokeLater(new Runnable()
5057         {
5058           @Override
5059           public void run()
5060           {
5061             String[] dbclasses = sf.getOrderedSupportedSources();
5062             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5063             // jalview.util.QuickSort.sort(otherdb, otherdb);
5064             List<DbSourceProxy> otherdb;
5065             JMenu dfetch = new JMenu();
5066             JMenu ifetch = new JMenu();
5067             JMenuItem fetchr = null;
5068             int comp = 0, icomp = 0, mcomp = 15;
5069             String mname = null;
5070             int dbi = 0;
5071             for (String dbclass : dbclasses)
5072             {
5073               otherdb = sf.getSourceProxy(dbclass);
5074               // add a single entry for this class, or submenu allowing 'fetch
5075               // all' or pick one
5076               if (otherdb == null || otherdb.size() < 1)
5077               {
5078                 continue;
5079               }
5080               // List<DbSourceProxy> dbs=otherdb;
5081               // otherdb=new ArrayList<DbSourceProxy>();
5082               // for (DbSourceProxy db:dbs)
5083               // {
5084               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5085               // }
5086               if (mname == null)
5087               {
5088                 mname = "From " + dbclass;
5089               }
5090               if (otherdb.size() == 1)
5091               {
5092                 final DbSourceProxy[] dassource = otherdb
5093                         .toArray(new DbSourceProxy[0]);
5094                 DbSourceProxy src = otherdb.get(0);
5095                 fetchr = new JMenuItem(src.getDbSource());
5096                 fetchr.addActionListener(new ActionListener()
5097                 {
5098
5099                   @Override
5100                   public void actionPerformed(ActionEvent e)
5101                   {
5102                     new Thread(new Runnable()
5103                     {
5104
5105                       @Override
5106                       public void run()
5107                       {
5108                         boolean isNucleotide = alignPanel.alignFrame
5109                                 .getViewport().getAlignment()
5110                                 .isNucleotide();
5111                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5112                                 alignPanel.av.getSequenceSelection(),
5113                                 alignPanel.alignFrame, dassource,
5114                                 alignPanel.alignFrame.featureSettings,
5115                                 isNucleotide);
5116                         dbRefFetcher
5117                                 .addListener(new FetchFinishedListenerI()
5118                                 {
5119                                   @Override
5120                                   public void finished()
5121                                   {
5122                                     AlignFrame.this.setMenusForViewport();
5123                                   }
5124                                 });
5125                         dbRefFetcher.fetchDBRefs(false);
5126                       }
5127                     }).start();
5128                   }
5129
5130                 });
5131                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5132                         MessageManager.formatMessage(
5133                                 "label.fetch_retrieve_from",
5134                                 new Object[] { src.getDbName() })));
5135                 dfetch.add(fetchr);
5136                 comp++;
5137               }
5138               else
5139               {
5140                 final DbSourceProxy[] dassource = otherdb
5141                         .toArray(new DbSourceProxy[0]);
5142                 // fetch all entry
5143                 DbSourceProxy src = otherdb.get(0);
5144                 fetchr = new JMenuItem(MessageManager.formatMessage(
5145                         "label.fetch_all_param",
5146                         new Object[] { src.getDbSource() }));
5147                 fetchr.addActionListener(new ActionListener()
5148                 {
5149                   @Override
5150                   public void actionPerformed(ActionEvent e)
5151                   {
5152                     new Thread(new Runnable()
5153                     {
5154
5155                       @Override
5156                       public void run()
5157                       {
5158                         boolean isNucleotide = alignPanel.alignFrame
5159                                 .getViewport().getAlignment()
5160                                 .isNucleotide();
5161                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5162                                 alignPanel.av.getSequenceSelection(),
5163                                 alignPanel.alignFrame, dassource,
5164                                 alignPanel.alignFrame.featureSettings,
5165                                 isNucleotide);
5166                         dbRefFetcher
5167                                 .addListener(new FetchFinishedListenerI()
5168                                 {
5169                                   @Override
5170                                   public void finished()
5171                                   {
5172                                     AlignFrame.this.setMenusForViewport();
5173                                   }
5174                                 });
5175                         dbRefFetcher.fetchDBRefs(false);
5176                       }
5177                     }).start();
5178                   }
5179                 });
5180
5181                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5182                         MessageManager.formatMessage(
5183                                 "label.fetch_retrieve_from_all_sources",
5184                                 new Object[] {
5185                                     Integer.valueOf(otherdb.size())
5186                                             .toString(), src.getDbSource(),
5187                                     src.getDbName() })));
5188                 dfetch.add(fetchr);
5189                 comp++;
5190                 // and then build the rest of the individual menus
5191                 ifetch = new JMenu(MessageManager.formatMessage(
5192                         "label.source_from_db_source",
5193                         new Object[] { src.getDbSource() }));
5194                 icomp = 0;
5195                 String imname = null;
5196                 int i = 0;
5197                 for (DbSourceProxy sproxy : otherdb)
5198                 {
5199                   String dbname = sproxy.getDbName();
5200                   String sname = dbname.length() > 5 ? dbname.substring(0,
5201                           5) + "..." : dbname;
5202                   String msname = dbname.length() > 10 ? dbname.substring(
5203                           0, 10) + "..." : dbname;
5204                   if (imname == null)
5205                   {
5206                     imname = MessageManager.formatMessage(
5207                             "label.from_msname", new Object[] { sname });
5208                   }
5209                   fetchr = new JMenuItem(msname);
5210                   final DbSourceProxy[] dassrc = { sproxy };
5211                   fetchr.addActionListener(new ActionListener()
5212                   {
5213
5214                     @Override
5215                     public void actionPerformed(ActionEvent e)
5216                     {
5217                       new Thread(new Runnable()
5218                       {
5219
5220                         @Override
5221                         public void run()
5222                         {
5223                           boolean isNucleotide = alignPanel.alignFrame
5224                                   .getViewport().getAlignment()
5225                                   .isNucleotide();
5226                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5227                                   alignPanel.av.getSequenceSelection(),
5228                                   alignPanel.alignFrame, dassrc,
5229                                   alignPanel.alignFrame.featureSettings,
5230                                   isNucleotide);
5231                           dbRefFetcher
5232                                   .addListener(new FetchFinishedListenerI()
5233                                   {
5234                                     @Override
5235                                     public void finished()
5236                                     {
5237                                       AlignFrame.this.setMenusForViewport();
5238                                     }
5239                                   });
5240                           dbRefFetcher.fetchDBRefs(false);
5241                         }
5242                       }).start();
5243                     }
5244
5245                   });
5246                   fetchr.setToolTipText("<html>"
5247                           + MessageManager.formatMessage(
5248                                   "label.fetch_retrieve_from", new Object[]
5249                                   { dbname }));
5250                   ifetch.add(fetchr);
5251                   ++i;
5252                   if (++icomp >= mcomp || i == (otherdb.size()))
5253                   {
5254                     ifetch.setText(MessageManager.formatMessage(
5255                             "label.source_to_target", imname, sname));
5256                     dfetch.add(ifetch);
5257                     ifetch = new JMenu();
5258                     imname = null;
5259                     icomp = 0;
5260                     comp++;
5261                   }
5262                 }
5263               }
5264               ++dbi;
5265               if (comp >= mcomp || dbi >= (dbclasses.length))
5266               {
5267                 dfetch.setText(MessageManager.formatMessage(
5268                         "label.source_to_target", mname, dbclass));
5269                 rfetch.add(dfetch);
5270                 dfetch = new JMenu();
5271                 mname = null;
5272                 comp = 0;
5273               }
5274             }
5275           }
5276         });
5277       }
5278     }).start();
5279
5280   }
5281
5282   /**
5283    * Left justify the whole alignment.
5284    */
5285   @Override
5286   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5287   {
5288     AlignmentI al = viewport.getAlignment();
5289     al.justify(false);
5290     viewport.firePropertyChange("alignment", null, al);
5291   }
5292
5293   /**
5294    * Right justify the whole alignment.
5295    */
5296   @Override
5297   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5298   {
5299     AlignmentI al = viewport.getAlignment();
5300     al.justify(true);
5301     viewport.firePropertyChange("alignment", null, al);
5302   }
5303
5304   @Override
5305   public void setShowSeqFeatures(boolean b)
5306   {
5307     showSeqFeatures.setSelected(b);
5308     viewport.setShowSequenceFeatures(b);
5309   }
5310
5311   /*
5312    * (non-Javadoc)
5313    *
5314    * @see
5315    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5316    * awt.event.ActionEvent)
5317    */
5318   @Override
5319   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5320   {
5321     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5322     alignPanel.paintAlignment(true);
5323   }
5324
5325   /*
5326    * (non-Javadoc)
5327    *
5328    * @see
5329    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5330    * .ActionEvent)
5331    */
5332   @Override
5333   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5334   {
5335     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5336     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5337
5338   }
5339
5340   /*
5341    * (non-Javadoc)
5342    *
5343    * @see
5344    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5345    * .event.ActionEvent)
5346    */
5347   @Override
5348   protected void showGroupConservation_actionPerformed(ActionEvent e)
5349   {
5350     viewport.setShowGroupConservation(showGroupConservation.getState());
5351     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5352   }
5353
5354   /*
5355    * (non-Javadoc)
5356    *
5357    * @see
5358    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5359    * .event.ActionEvent)
5360    */
5361   @Override
5362   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5363   {
5364     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5365     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5366   }
5367
5368   /*
5369    * (non-Javadoc)
5370    *
5371    * @see
5372    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5373    * .event.ActionEvent)
5374    */
5375   @Override
5376   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5377   {
5378     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5379     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5380   }
5381
5382   @Override
5383   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5384   {
5385     showSequenceLogo.setState(true);
5386     viewport.setShowSequenceLogo(true);
5387     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5388     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5389   }
5390
5391   @Override
5392   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5393   {
5394     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5395   }
5396
5397   /*
5398    * (non-Javadoc)
5399    *
5400    * @see
5401    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5402    * .event.ActionEvent)
5403    */
5404   @Override
5405   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5406   {
5407     if (avc.makeGroupsFromSelection())
5408     {
5409       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5410       alignPanel.updateAnnotation();
5411       alignPanel.paintAlignment(true);
5412     }
5413   }
5414
5415   public void clearAlignmentSeqRep()
5416   {
5417     // TODO refactor alignmentseqrep to controller
5418     if (viewport.getAlignment().hasSeqrep())
5419     {
5420       viewport.getAlignment().setSeqrep(null);
5421       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5422       alignPanel.updateAnnotation();
5423       alignPanel.paintAlignment(true);
5424     }
5425   }
5426
5427   @Override
5428   protected void createGroup_actionPerformed(ActionEvent e)
5429   {
5430     if (avc.createGroup())
5431     {
5432       alignPanel.alignmentChanged();
5433     }
5434   }
5435
5436   @Override
5437   protected void unGroup_actionPerformed(ActionEvent e)
5438   {
5439     if (avc.unGroup())
5440     {
5441       alignPanel.alignmentChanged();
5442     }
5443   }
5444
5445   /**
5446    * make the given alignmentPanel the currently selected tab
5447    *
5448    * @param alignmentPanel
5449    */
5450   public void setDisplayedView(AlignmentPanel alignmentPanel)
5451   {
5452     if (!viewport.getSequenceSetId().equals(
5453             alignmentPanel.av.getSequenceSetId()))
5454     {
5455       throw new Error(
5456               MessageManager
5457                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5458     }
5459     if (tabbedPane != null
5460             && tabbedPane.getTabCount() > 0
5461             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5462                     .getSelectedIndex())
5463     {
5464       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5465     }
5466   }
5467
5468   /**
5469    * Action on selection of menu options to Show or Hide annotations.
5470    *
5471    * @param visible
5472    * @param forSequences
5473    *          update sequence-related annotations
5474    * @param forAlignment
5475    *          update non-sequence-related annotations
5476    */
5477   @Override
5478   protected void setAnnotationsVisibility(boolean visible,
5479           boolean forSequences, boolean forAlignment)
5480   {
5481     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5482             .getAlignmentAnnotation();
5483     if (anns == null)
5484     {
5485       return;
5486     }
5487     for (AlignmentAnnotation aa : anns)
5488     {
5489       /*
5490        * don't display non-positional annotations on an alignment
5491        */
5492       if (aa.annotations == null)
5493       {
5494         continue;
5495       }
5496       boolean apply = (aa.sequenceRef == null && forAlignment)
5497               || (aa.sequenceRef != null && forSequences);
5498       if (apply)
5499       {
5500         aa.visible = visible;
5501       }
5502     }
5503     alignPanel.validateAnnotationDimensions(true);
5504     alignPanel.alignmentChanged();
5505   }
5506
5507   /**
5508    * Store selected annotation sort order for the view and repaint.
5509    */
5510   @Override
5511   protected void sortAnnotations_actionPerformed()
5512   {
5513     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5514     this.alignPanel.av
5515             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5516     alignPanel.paintAlignment(true);
5517   }
5518
5519   /**
5520    *
5521    * @return alignment panels in this alignment frame
5522    */
5523   public List<? extends AlignmentViewPanel> getAlignPanels()
5524   {
5525     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5526   }
5527
5528   /**
5529    * Open a new alignment window, with the cDNA associated with this (protein)
5530    * alignment, aligned as is the protein.
5531    */
5532   protected void viewAsCdna_actionPerformed()
5533   {
5534     // TODO no longer a menu action - refactor as required
5535     final AlignmentI alignment = getViewport().getAlignment();
5536     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5537     if (mappings == null)
5538     {
5539       return;
5540     }
5541     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5542     for (SequenceI aaSeq : alignment.getSequences())
5543     {
5544       for (AlignedCodonFrame acf : mappings)
5545       {
5546         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5547         if (dnaSeq != null)
5548         {
5549           /*
5550            * There is a cDNA mapping for this protein sequence - add to new
5551            * alignment. It will share the same dataset sequence as other mapped
5552            * cDNA (no new mappings need to be created).
5553            */
5554           final Sequence newSeq = new Sequence(dnaSeq);
5555           newSeq.setDatasetSequence(dnaSeq);
5556           cdnaSeqs.add(newSeq);
5557         }
5558       }
5559     }
5560     if (cdnaSeqs.size() == 0)
5561     {
5562       // show a warning dialog no mapped cDNA
5563       return;
5564     }
5565     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5566             .size()]));
5567     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5568             AlignFrame.DEFAULT_HEIGHT);
5569     cdna.alignAs(alignment);
5570     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5571             + this.title;
5572     Desktop.addInternalFrame(alignFrame, newtitle,
5573             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5574   }
5575
5576   /**
5577    * Set visibility of dna/protein complement view (available when shown in a
5578    * split frame).
5579    *
5580    * @param show
5581    */
5582   @Override
5583   protected void showComplement_actionPerformed(boolean show)
5584   {
5585     SplitContainerI sf = getSplitViewContainer();
5586     if (sf != null)
5587     {
5588       sf.setComplementVisible(this, show);
5589     }
5590   }
5591
5592   /**
5593    * Generate the reverse (optionally complemented) of the selected sequences,
5594    * and add them to the alignment
5595    */
5596   @Override
5597   protected void showReverse_actionPerformed(boolean complement)
5598   {
5599     AlignmentI al = null;
5600     try
5601     {
5602       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5603       al = dna.reverseCdna(complement);
5604       viewport.addAlignment(al, "");
5605       addHistoryItem(new EditCommand(
5606               MessageManager.getString("label.add_sequences"),
5607               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5608               viewport.getAlignment()));
5609     } catch (Exception ex)
5610     {
5611       System.err.println(ex.getMessage());
5612       return;
5613     }
5614   }
5615
5616   /**
5617    * Try to run a script in the Groovy console, having first ensured that this
5618    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5619    * be targeted at this alignment.
5620    */
5621   @Override
5622   protected void runGroovy_actionPerformed()
5623   {
5624     Jalview.setCurrentAlignFrame(this);
5625     groovy.ui.Console console = Desktop.getGroovyConsole();
5626     if (console != null)
5627     {
5628       try
5629       {
5630         console.runScript();
5631       } catch (Exception ex)
5632       {
5633         System.err.println((ex.toString()));
5634         JvOptionPane
5635                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5636                         .getString("label.couldnt_run_groovy_script"),
5637                         MessageManager
5638                                 .getString("label.groovy_support_failed"),
5639                         JvOptionPane.ERROR_MESSAGE);
5640       }
5641     }
5642     else
5643     {
5644       System.err.println("Can't run Groovy script as console not found");
5645     }
5646   }
5647
5648   /**
5649    * Hides columns containing (or not containing) a specified feature, provided
5650    * that would not leave all columns hidden
5651    *
5652    * @param featureType
5653    * @param columnsContaining
5654    * @return
5655    */
5656   public boolean hideFeatureColumns(String featureType,
5657           boolean columnsContaining)
5658   {
5659     boolean notForHiding = avc.markColumnsContainingFeatures(
5660             columnsContaining, false, false, featureType);
5661     if (notForHiding)
5662     {
5663       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5664               false, featureType))
5665       {
5666         getViewport().hideSelectedColumns();
5667         return true;
5668       }
5669     }
5670     return false;
5671   }
5672
5673   @Override
5674   protected void selectHighlightedColumns_actionPerformed(
5675           ActionEvent actionEvent)
5676   {
5677     // include key modifier check in case user selects from menu
5678     avc.markHighlightedColumns(
5679             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5680             true,
5681             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5682   }
5683
5684   /**
5685    * Rebuilds the Colour menu, including any user-defined colours which have
5686    * been loaded either on startup or during the session
5687    */
5688   public void buildColourMenu()
5689   {
5690     colourMenu.removeAll();
5691
5692     colourMenu.add(applyToAllGroups);
5693     colourMenu.add(textColour);
5694     colourMenu.addSeparator();
5695
5696     ColourMenuHelper.addMenuItems(colourMenu, this,
5697             viewport.getAlignment(), false);
5698
5699     colourMenu.addSeparator();
5700     colourMenu.add(conservationMenuItem);
5701     colourMenu.add(modifyConservation);
5702     colourMenu.add(abovePIDThreshold);
5703     colourMenu.add(modifyPID);
5704     colourMenu.add(annotationColour);
5705
5706     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5707     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5708   }
5709 }
5710
5711 class PrintThread extends Thread
5712 {
5713   AlignmentPanel ap;
5714
5715   public PrintThread(AlignmentPanel ap)
5716   {
5717     this.ap = ap;
5718   }
5719
5720   static PageFormat pf;
5721
5722   @Override
5723   public void run()
5724   {
5725     PrinterJob printJob = PrinterJob.getPrinterJob();
5726
5727     if (pf != null)
5728     {
5729       printJob.setPrintable(ap, pf);
5730     }
5731     else
5732     {
5733       printJob.setPrintable(ap);
5734     }
5735
5736     if (printJob.printDialog())
5737     {
5738       try
5739       {
5740         printJob.print();
5741       } catch (Exception PrintException)
5742       {
5743         PrintException.printStackTrace();
5744       }
5745     }
5746   }
5747 }