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             alignPanel.scrollUp(true);
 685           }
 686           else
 687           {
 688             alignPanel.setScrollValues(vpRanges.getStartRes(),
 689                     2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
 690           }
 691           break;
 692         case KeyEvent.VK_PAGE_DOWN:
 693           if (viewport.getWrapAlignment())
 694           {
 695             alignPanel.scrollUp(false);
 696           }
 697           else
 698           {
 699             alignPanel.setScrollValues(vpRanges.getStartRes(),
 700                     vpRanges.getEndSeq());
 701           }
 702           break;
 703         }
 704       }
 705
 706       @Override
 707       public void keyReleased(KeyEvent evt)
 708       {
 709         switch (evt.getKeyCode())
 710         {
 711         case KeyEvent.VK_LEFT:
 712           if (evt.isAltDown() || !viewport.cursorMode)
 713           {
 714             viewport.firePropertyChange("alignment", null, viewport
 715                     .getAlignment().getSequences());
 716           }
 717           break;
 718
 719         case KeyEvent.VK_RIGHT:
 720           if (evt.isAltDown() || !viewport.cursorMode)
 721           {
 722             viewport.firePropertyChange("alignment", null, viewport
 723                     .getAlignment().getSequences());
 724           }
 725           break;
 726         }
 727       }
 728     });
 729   }
 730
 731   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 732   {
 733     ap.alignFrame = this;
 734     avc = new jalview.controller.AlignViewController(this, viewport,
 735             alignPanel);
 736
 737     alignPanels.add(ap);
 738
 739     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 740
 741     int aSize = alignPanels.size();
 742
 743     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 744
 745     if (aSize == 1 && ap.av.viewName == null)
 746     {
 747       this.getContentPane().add(ap, BorderLayout.CENTER);
 748     }
 749     else
 750     {
 751       if (aSize == 2)
 752       {
 753         setInitialTabVisible();
 754       }
 755
 756       expandViews.setEnabled(true);
 757       gatherViews.setEnabled(true);
 758       tabbedPane.addTab(ap.av.viewName, ap);
 759
 760       ap.setVisible(false);
 761     }
 762
 763     if (newPanel)
 764     {
 765       if (ap.av.isPadGaps())
 766       {
 767         ap.av.getAlignment().padGaps();
 768       }
 769       ap.av.updateConservation(ap);
 770       ap.av.updateConsensus(ap);
 771       ap.av.updateStrucConsensus(ap);
 772     }
 773   }
 774
 775   public void setInitialTabVisible()
 776   {
 777     expandViews.setEnabled(true);
 778     gatherViews.setEnabled(true);
 779     tabbedPane.setVisible(true);
 780     AlignmentPanel first = alignPanels.get(0);
 781     tabbedPane.addTab(first.av.viewName, first);
 782     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 783   }
 784
 785   public AlignViewport getViewport()
 786   {
 787     return viewport;
 788   }
 789
 790   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 791   private void addServiceListeners()
 792   {
 793     final java.beans.PropertyChangeListener thisListener;
 794     Desktop.instance.addJalviewPropertyChangeListener("services",
 795             thisListener = new java.beans.PropertyChangeListener()
 796             {
 797               @Override
 798               public void propertyChange(PropertyChangeEvent evt)
 799               {
 800                 // // System.out.println("Discoverer property change.");
 801                 // if (evt.getPropertyName().equals("services"))
 802                 {
 803                   SwingUtilities.invokeLater(new Runnable()
 804                   {
 805
 806                     @Override
 807                     public void run()
 808                     {
 809                       System.err
 810                               .println("Rebuild WS Menu for service change");
 811                       BuildWebServiceMenu();
 812                     }
 813
 814                   });
 815                 }
 816               }
 817             });
 818     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 819     {
 820       @Override
 821       public void internalFrameClosed(
 822               javax.swing.event.InternalFrameEvent evt)
 823       {
 824         // System.out.println("deregistering discoverer listener");
 825         Desktop.instance.removeJalviewPropertyChangeListener("services",
 826                 thisListener);
 827         closeMenuItem_actionPerformed(true);
 828       };
 829     });
 830     // Finally, build the menu once to get current service state
 831     new Thread(new Runnable()
 832     {
 833       @Override
 834       public void run()
 835       {
 836         BuildWebServiceMenu();
 837       }
 838     }).start();
 839   }
 840
 841   /**
 842    * Configure menu items that vary according to whether the alignment is
 843    * nucleotide or protein
 844    */
 845   public void setGUINucleotide()
 846   {
 847     AlignmentI al = getViewport().getAlignment();
 848     boolean nucleotide = al.isNucleotide();
 849
 850     showTranslation.setVisible(nucleotide);
 851     showReverse.setVisible(nucleotide);
 852     showReverseComplement.setVisible(nucleotide);
 853     conservationMenuItem.setEnabled(!nucleotide);
 854     modifyConservation.setEnabled(!nucleotide
 855             && conservationMenuItem.isSelected());
 856     showGroupConservation.setEnabled(!nucleotide);
 857
 858     showComplementMenuItem.setText(nucleotide ? MessageManager
 859             .getString("label.protein") : MessageManager
 860             .getString("label.nucleotide"));
 861   }
 862
 863   /**
 864    * set up menus for the current viewport. This may be called after any
 865    * operation that affects the data in the current view (selection changed,
 866    * etc) to update the menus to reflect the new state.
 867    */
 868   @Override
 869   public void setMenusForViewport()
 870   {
 871     setMenusFromViewport(viewport);
 872   }
 873
 874   /**
 875    * Need to call this method when tabs are selected for multiple views, or when
 876    * loading from Jalview2XML.java
 877    *
 878    * @param av
 879    *          AlignViewport
 880    */
 881   void setMenusFromViewport(AlignViewport av)
 882   {
 883     padGapsMenuitem.setSelected(av.isPadGaps());
 884     colourTextMenuItem.setSelected(av.isShowColourText());
 885     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 886     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 887     conservationMenuItem.setSelected(av.getConservationSelected());
 888     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 889     seqLimits.setSelected(av.getShowJVSuffix());
 890     idRightAlign.setSelected(av.isRightAlignIds());
 891     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 892     renderGapsMenuItem.setSelected(av.isRenderGaps());
 893     wrapMenuItem.setSelected(av.getWrapAlignment());
 894     scaleAbove.setVisible(av.getWrapAlignment());
 895     scaleLeft.setVisible(av.getWrapAlignment());
 896     scaleRight.setVisible(av.getWrapAlignment());
 897     annotationPanelMenuItem.setState(av.isShowAnnotation());
 898     /*
 899      * Show/hide annotations only enabled if annotation panel is shown
 900      */
 901     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 902     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 904     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 905     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 906     viewTextMenuItem.setSelected(av.getShowText());
 907     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 908     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 909     showGroupConservation.setSelected(av.isShowGroupConservation());
 910     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 911     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 912     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 913
 914     ColourMenuHelper.setColourSelected(colourMenu,
 915             av.getGlobalColourScheme());
 916
 917     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 918     hiddenMarkers.setState(av.getShowHiddenMarkers());
 919     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 920     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 921     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 922     autoCalculate.setSelected(av.autoCalculateConsensus);
 923     sortByTree.setSelected(av.sortByTree);
 924     listenToViewSelections.setSelected(av.followSelection);
 925
 926     showProducts.setEnabled(canShowProducts());
 927     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 928
 929     updateEditMenuBar();
 930   }
 931
 932   /**
 933    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 934    *
 935    * @param b
 936    */
 937   public void setGroovyEnabled(boolean b)
 938   {
 939     runGroovy.setEnabled(b);
 940   }
 941
 942   private IProgressIndicator progressBar;
 943
 944   /*
 945    * (non-Javadoc)
 946    *
 947    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 948    */
 949   @Override
 950   public void setProgressBar(String message, long id)
 951   {
 952     progressBar.setProgressBar(message, id);
 953   }
 954
 955   @Override
 956   public void registerHandler(final long id,
 957           final IProgressIndicatorHandler handler)
 958   {
 959     progressBar.registerHandler(id, handler);
 960   }
 961
 962   /**
 963    *
 964    * @return true if any progress bars are still active
 965    */
 966   @Override
 967   public boolean operationInProgress()
 968   {
 969     return progressBar.operationInProgress();
 970   }
 971
 972   @Override
 973   public void setStatus(String text)
 974   {
 975     statusBar.setText(text);
 976   }
 977
 978   /*
 979    * Added so Castor Mapping file can obtain Jalview Version
 980    */
 981   public String getVersion()
 982   {
 983     return jalview.bin.Cache.getProperty("VERSION");
 984   }
 985
 986   public FeatureRenderer getFeatureRenderer()
 987   {
 988     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 989   }
 990
 991   @Override
 992   public void fetchSequence_actionPerformed(ActionEvent e)
 993   {
 994     new jalview.gui.SequenceFetcher(this);
 995   }
 996
 997   @Override
 998   public void addFromFile_actionPerformed(ActionEvent e)
 999   {
1000     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1001   }
1002
1003   @Override
1004   public void reload_actionPerformed(ActionEvent e)
1005   {
1006     if (fileName != null)
1007     {
1008       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1009       // originating file's format
1010       // TODO: work out how to recover feature settings for correct view(s) when
1011       // file is reloaded.
1012       if (FileFormat.Jalview.equals(currentFileFormat))
1013       {
1014         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1015         for (int i = 0; i < frames.length; i++)
1016         {
1017           if (frames[i] instanceof AlignFrame && frames[i] != this
1018                   && ((AlignFrame) frames[i]).fileName != null
1019                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1020           {
1021             try
1022             {
1023               frames[i].setSelected(true);
1024               Desktop.instance.closeAssociatedWindows();
1025             } catch (java.beans.PropertyVetoException ex)
1026             {
1027             }
1028           }
1029
1030         }
1031         Desktop.instance.closeAssociatedWindows();
1032
1033         FileLoader loader = new FileLoader();
1034         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1035                 : DataSourceType.FILE;
1036         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1037       }
1038       else
1039       {
1040         Rectangle bounds = this.getBounds();
1041
1042         FileLoader loader = new FileLoader();
1043         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1044                 : DataSourceType.FILE;
1045         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1046                 protocol, currentFileFormat);
1047
1048         newframe.setBounds(bounds);
1049         if (featureSettings != null && featureSettings.isShowing())
1050         {
1051           final Rectangle fspos = featureSettings.frame.getBounds();
1052           // TODO: need a 'show feature settings' function that takes bounds -
1053           // need to refactor Desktop.addFrame
1054           newframe.featureSettings_actionPerformed(null);
1055           final FeatureSettings nfs = newframe.featureSettings;
1056           SwingUtilities.invokeLater(new Runnable()
1057           {
1058             @Override
1059             public void run()
1060             {
1061               nfs.frame.setBounds(fspos);
1062             }
1063           });
1064           this.featureSettings.close();
1065           this.featureSettings = null;
1066         }
1067         this.closeMenuItem_actionPerformed(true);
1068       }
1069     }
1070   }
1071
1072   @Override
1073   public void addFromText_actionPerformed(ActionEvent e)
1074   {
1075     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1076             .getAlignPanel());
1077   }
1078
1079   @Override
1080   public void addFromURL_actionPerformed(ActionEvent e)
1081   {
1082     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1083   }
1084
1085   @Override
1086   public void save_actionPerformed(ActionEvent e)
1087   {
1088     if (fileName == null || (currentFileFormat == null)
1089             || fileName.startsWith("http"))
1090     {
1091       saveAs_actionPerformed(null);
1092     }
1093     else
1094     {
1095       saveAlignment(fileName, currentFileFormat);
1096     }
1097   }
1098
1099   /**
1100    * DOCUMENT ME!
1101    *
1102    * @param e
1103    *          DOCUMENT ME!
1104    */
1105   @Override
1106   public void saveAs_actionPerformed(ActionEvent e)
1107   {
1108     String format = currentFileFormat == null ? null : currentFileFormat
1109             .getName();
1110     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1111             Cache.getProperty("LAST_DIRECTORY"), format);
1112
1113     chooser.setFileView(new JalviewFileView());
1114     chooser.setDialogTitle(MessageManager
1115             .getString("label.save_alignment_to_file"));
1116     chooser.setToolTipText(MessageManager.getString("action.save"));
1117
1118     int value = chooser.showSaveDialog(this);
1119
1120     if (value == JalviewFileChooser.APPROVE_OPTION)
1121     {
1122       currentFileFormat = chooser.getSelectedFormat();
1123       while (currentFileFormat == null)
1124       {
1125         JvOptionPane
1126                 .showInternalMessageDialog(
1127                         Desktop.desktop,
1128                         MessageManager
1129                                 .getString("label.select_file_format_before_saving"),
1130                         MessageManager
1131                                 .getString("label.file_format_not_specified"),
1132                         JvOptionPane.WARNING_MESSAGE);
1133         currentFileFormat = chooser.getSelectedFormat();
1134         value = chooser.showSaveDialog(this);
1135         if (value != JalviewFileChooser.APPROVE_OPTION)
1136         {
1137           return;
1138         }
1139       }
1140
1141       fileName = chooser.getSelectedFile().getPath();
1142
1143       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1144
1145       Cache.setProperty("LAST_DIRECTORY", fileName);
1146       saveAlignment(fileName, currentFileFormat);
1147     }
1148   }
1149
1150   public boolean saveAlignment(String file, FileFormatI format)
1151   {
1152     boolean success = true;
1153
1154     if (FileFormat.Jalview.equals(format))
1155     {
1156       String shortName = title;
1157
1158       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1159       {
1160         shortName = shortName.substring(shortName
1161                 .lastIndexOf(java.io.File.separatorChar) + 1);
1162       }
1163
1164       success = new Jalview2XML().saveAlignment(this, file, shortName);
1165
1166       statusBar.setText(MessageManager.formatMessage(
1167               "label.successfully_saved_to_file_in_format", new Object[] {
1168                   fileName, format }));
1169
1170     }
1171     else
1172     {
1173       AlignmentExportData exportData = getAlignmentForExport(format,
1174               viewport, null);
1175       if (exportData.getSettings().isCancelled())
1176       {
1177         return false;
1178       }
1179       FormatAdapter f = new FormatAdapter(alignPanel,
1180               exportData.getSettings());
1181       String output = f.formatSequences(
1182               format,
1183               exportData.getAlignment(), // class cast exceptions will
1184               // occur in the distant future
1185               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1186               f.getCacheSuffixDefault(format),
1187               viewport.getColumnSelection());
1188
1189       if (output == null)
1190       {
1191         success = false;
1192       }
1193       else
1194       {
1195         try
1196         {
1197           PrintWriter out = new PrintWriter(new FileWriter(file));
1198
1199           out.print(output);
1200           out.close();
1201           this.setTitle(file);
1202           statusBar.setText(MessageManager.formatMessage(
1203                   "label.successfully_saved_to_file_in_format",
1204                   new Object[] { fileName, format.getName() }));
1205         } catch (Exception ex)
1206         {
1207           success = false;
1208           ex.printStackTrace();
1209         }
1210       }
1211     }
1212
1213     if (!success)
1214     {
1215       JvOptionPane.showInternalMessageDialog(this, MessageManager
1216               .formatMessage("label.couldnt_save_file",
1217                       new Object[] { fileName }), MessageManager
1218               .getString("label.error_saving_file"),
1219               JvOptionPane.WARNING_MESSAGE);
1220     }
1221
1222     return success;
1223   }
1224
1225   private void warningMessage(String warning, String title)
1226   {
1227     if (new jalview.util.Platform().isHeadless())
1228     {
1229       System.err.println("Warning: " + title + "\nWarning: " + warning);
1230
1231     }
1232     else
1233     {
1234       JvOptionPane.showInternalMessageDialog(this, warning, title,
1235               JvOptionPane.WARNING_MESSAGE);
1236     }
1237     return;
1238   }
1239
1240   /**
1241    * DOCUMENT ME!
1242    *
1243    * @param e
1244    *          DOCUMENT ME!
1245    */
1246   @Override
1247   protected void outputText_actionPerformed(ActionEvent e)
1248   {
1249     FileFormatI fileFormat = FileFormats.getInstance().forName(
1250             e.getActionCommand());
1251     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1252             viewport, null);
1253     if (exportData.getSettings().isCancelled())
1254     {
1255       return;
1256     }
1257     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1258     cap.setForInput(null);
1259     try
1260     {
1261       FileFormatI format = fileFormat;
1262       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1263               .formatSequences(format, exportData.getAlignment(),
1264                       exportData.getOmitHidden(),
1265                       exportData.getStartEndPostions(),
1266                       viewport.getColumnSelection()));
1267       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1268               "label.alignment_output_command",
1269               new Object[] { e.getActionCommand() }), 600, 500);
1270     } catch (OutOfMemoryError oom)
1271     {
1272       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1273       cap.dispose();
1274     }
1275
1276   }
1277
1278   public static AlignmentExportData getAlignmentForExport(
1279           FileFormatI format, AlignViewportI viewport,
1280           AlignExportSettingI exportSettings)
1281   {
1282     AlignmentI alignmentToExport = null;
1283     AlignExportSettingI settings = exportSettings;
1284     String[] omitHidden = null;
1285
1286     HiddenSequences hiddenSeqs = viewport.getAlignment()
1287             .getHiddenSequences();
1288
1289     alignmentToExport = viewport.getAlignment();
1290
1291     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1292     if (settings == null)
1293     {
1294       settings = new AlignExportSettings(hasHiddenSeqs,
1295               viewport.hasHiddenColumns(), format);
1296     }
1297     // settings.isExportAnnotations();
1298
1299     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1300     {
1301       omitHidden = viewport.getViewAsString(false,
1302               settings.isExportHiddenSequences());
1303     }
1304
1305     int[] alignmentStartEnd = new int[2];
1306     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1307     {
1308       alignmentToExport = hiddenSeqs.getFullAlignment();
1309     }
1310     else
1311     {
1312       alignmentToExport = viewport.getAlignment();
1313     }
1314     alignmentStartEnd = alignmentToExport
1315             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1316                     .getHiddenColumns());
1317     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1318             omitHidden, alignmentStartEnd, settings);
1319     return ed;
1320   }
1321
1322   /**
1323    * DOCUMENT ME!
1324    *
1325    * @param e
1326    *          DOCUMENT ME!
1327    */
1328   @Override
1329   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1330   {
1331     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1332     htmlSVG.exportHTML(null);
1333   }
1334
1335   @Override
1336   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1337   {
1338     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1339     bjs.exportHTML(null);
1340   }
1341
1342   public void createImageMap(File file, String image)
1343   {
1344     alignPanel.makePNGImageMap(file, image);
1345   }
1346
1347   /**
1348    * DOCUMENT ME!
1349    *
1350    * @param e
1351    *          DOCUMENT ME!
1352    */
1353   @Override
1354   public void createPNG(File f)
1355   {
1356     alignPanel.makePNG(f);
1357   }
1358
1359   /**
1360    * DOCUMENT ME!
1361    *
1362    * @param e
1363    *          DOCUMENT ME!
1364    */
1365   @Override
1366   public void createEPS(File f)
1367   {
1368     alignPanel.makeEPS(f);
1369   }
1370
1371   @Override
1372   public void createSVG(File f)
1373   {
1374     alignPanel.makeSVG(f);
1375   }
1376
1377   @Override
1378   public void pageSetup_actionPerformed(ActionEvent e)
1379   {
1380     PrinterJob printJob = PrinterJob.getPrinterJob();
1381     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1382   }
1383
1384   /**
1385    * DOCUMENT ME!
1386    *
1387    * @param e
1388    *          DOCUMENT ME!
1389    */
1390   @Override
1391   public void printMenuItem_actionPerformed(ActionEvent e)
1392   {
1393     // Putting in a thread avoids Swing painting problems
1394     PrintThread thread = new PrintThread(alignPanel);
1395     thread.start();
1396   }
1397
1398   @Override
1399   public void exportFeatures_actionPerformed(ActionEvent e)
1400   {
1401     new AnnotationExporter().exportFeatures(alignPanel);
1402   }
1403
1404   @Override
1405   public void exportAnnotations_actionPerformed(ActionEvent e)
1406   {
1407     new AnnotationExporter().exportAnnotations(alignPanel);
1408   }
1409
1410   @Override
1411   public void associatedData_actionPerformed(ActionEvent e)
1412   {
1413     // Pick the tree file
1414     JalviewFileChooser chooser = new JalviewFileChooser(
1415             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1416     chooser.setFileView(new JalviewFileView());
1417     chooser.setDialogTitle(MessageManager
1418             .getString("label.load_jalview_annotations"));
1419     chooser.setToolTipText(MessageManager
1420             .getString("label.load_jalview_annotations"));
1421
1422     int value = chooser.showOpenDialog(null);
1423
1424     if (value == JalviewFileChooser.APPROVE_OPTION)
1425     {
1426       String choice = chooser.getSelectedFile().getPath();
1427       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1428       loadJalviewDataFile(choice, null, null, null);
1429     }
1430
1431   }
1432
1433   /**
1434    * Close the current view or all views in the alignment frame. If the frame
1435    * only contains one view then the alignment will be removed from memory.
1436    *
1437    * @param closeAllTabs
1438    */
1439   @Override
1440   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1441   {
1442     if (alignPanels != null && alignPanels.size() < 2)
1443     {
1444       closeAllTabs = true;
1445     }
1446
1447     try
1448     {
1449       if (alignPanels != null)
1450       {
1451         if (closeAllTabs)
1452         {
1453           if (this.isClosed())
1454           {
1455             // really close all the windows - otherwise wait till
1456             // setClosed(true) is called
1457             for (int i = 0; i < alignPanels.size(); i++)
1458             {
1459               AlignmentPanel ap = alignPanels.get(i);
1460               ap.closePanel();
1461             }
1462           }
1463         }
1464         else
1465         {
1466           closeView(alignPanel);
1467         }
1468       }
1469
1470       if (closeAllTabs)
1471       {
1472         /*
1473          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1474          * be called recursively, with the frame now in 'closed' state
1475          */
1476         this.setClosed(true);
1477       }
1478     } catch (Exception ex)
1479     {
1480       ex.printStackTrace();
1481     }
1482   }
1483
1484   /**
1485    * Close the specified panel and close up tabs appropriately.
1486    *
1487    * @param panelToClose
1488    */
1489   public void closeView(AlignmentPanel panelToClose)
1490   {
1491     int index = tabbedPane.getSelectedIndex();
1492     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1493     alignPanels.remove(panelToClose);
1494     panelToClose.closePanel();
1495     panelToClose = null;
1496
1497     tabbedPane.removeTabAt(closedindex);
1498     tabbedPane.validate();
1499
1500     if (index > closedindex || index == tabbedPane.getTabCount())
1501     {
1502       // modify currently selected tab index if necessary.
1503       index--;
1504     }
1505
1506     this.tabSelectionChanged(index);
1507   }
1508
1509   /**
1510    * DOCUMENT ME!
1511    */
1512   void updateEditMenuBar()
1513   {
1514
1515     if (viewport.getHistoryList().size() > 0)
1516     {
1517       undoMenuItem.setEnabled(true);
1518       CommandI command = viewport.getHistoryList().peek();
1519       undoMenuItem.setText(MessageManager.formatMessage(
1520               "label.undo_command",
1521               new Object[] { command.getDescription() }));
1522     }
1523     else
1524     {
1525       undoMenuItem.setEnabled(false);
1526       undoMenuItem.setText(MessageManager.getString("action.undo"));
1527     }
1528
1529     if (viewport.getRedoList().size() > 0)
1530     {
1531       redoMenuItem.setEnabled(true);
1532
1533       CommandI command = viewport.getRedoList().peek();
1534       redoMenuItem.setText(MessageManager.formatMessage(
1535               "label.redo_command",
1536               new Object[] { command.getDescription() }));
1537     }
1538     else
1539     {
1540       redoMenuItem.setEnabled(false);
1541       redoMenuItem.setText(MessageManager.getString("action.redo"));
1542     }
1543   }
1544
1545   @Override
1546   public void addHistoryItem(CommandI command)
1547   {
1548     if (command.getSize() > 0)
1549     {
1550       viewport.addToHistoryList(command);
1551       viewport.clearRedoList();
1552       updateEditMenuBar();
1553       viewport.updateHiddenColumns();
1554       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1555       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1556       // viewport.getColumnSelection()
1557       // .getHiddenColumns().size() > 0);
1558     }
1559   }
1560
1561   /**
1562    *
1563    * @return alignment objects for all views
1564    */
1565   AlignmentI[] getViewAlignments()
1566   {
1567     if (alignPanels != null)
1568     {
1569       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1570       int i = 0;
1571       for (AlignmentPanel ap : alignPanels)
1572       {
1573         als[i++] = ap.av.getAlignment();
1574       }
1575       return als;
1576     }
1577     if (viewport != null)
1578     {
1579       return new AlignmentI[] { viewport.getAlignment() };
1580     }
1581     return null;
1582   }
1583
1584   /**
1585    * DOCUMENT ME!
1586    *
1587    * @param e
1588    *          DOCUMENT ME!
1589    */
1590   @Override
1591   protected void undoMenuItem_actionPerformed(ActionEvent e)
1592   {
1593     if (viewport.getHistoryList().isEmpty())
1594     {
1595       return;
1596     }
1597     CommandI command = viewport.getHistoryList().pop();
1598     viewport.addToRedoList(command);
1599     command.undoCommand(getViewAlignments());
1600
1601     AlignmentViewport originalSource = getOriginatingSource(command);
1602     updateEditMenuBar();
1603
1604     if (originalSource != null)
1605     {
1606       if (originalSource != viewport)
1607       {
1608         Cache.log
1609                 .warn("Implementation worry: mismatch of viewport origin for undo");
1610       }
1611       originalSource.updateHiddenColumns();
1612       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1613       // null
1614       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1615       // viewport.getColumnSelection()
1616       // .getHiddenColumns().size() > 0);
1617       originalSource.firePropertyChange("alignment", null, originalSource
1618               .getAlignment().getSequences());
1619     }
1620   }
1621
1622   /**
1623    * DOCUMENT ME!
1624    *
1625    * @param e
1626    *          DOCUMENT ME!
1627    */
1628   @Override
1629   protected void redoMenuItem_actionPerformed(ActionEvent e)
1630   {
1631     if (viewport.getRedoList().size() < 1)
1632     {
1633       return;
1634     }
1635
1636     CommandI command = viewport.getRedoList().pop();
1637     viewport.addToHistoryList(command);
1638     command.doCommand(getViewAlignments());
1639
1640     AlignmentViewport originalSource = getOriginatingSource(command);
1641     updateEditMenuBar();
1642
1643     if (originalSource != null)
1644     {
1645
1646       if (originalSource != viewport)
1647       {
1648         Cache.log
1649                 .warn("Implementation worry: mismatch of viewport origin for redo");
1650       }
1651       originalSource.updateHiddenColumns();
1652       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1653       // null
1654       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1655       // viewport.getColumnSelection()
1656       // .getHiddenColumns().size() > 0);
1657       originalSource.firePropertyChange("alignment", null, originalSource
1658               .getAlignment().getSequences());
1659     }
1660   }
1661
1662   AlignmentViewport getOriginatingSource(CommandI command)
1663   {
1664     AlignmentViewport originalSource = null;
1665     // For sequence removal and addition, we need to fire
1666     // the property change event FROM the viewport where the
1667     // original alignment was altered
1668     AlignmentI al = null;
1669     if (command instanceof EditCommand)
1670     {
1671       EditCommand editCommand = (EditCommand) command;
1672       al = editCommand.getAlignment();
1673       List<Component> comps = PaintRefresher.components.get(viewport
1674               .getSequenceSetId());
1675
1676       for (Component comp : comps)
1677       {
1678         if (comp instanceof AlignmentPanel)
1679         {
1680           if (al == ((AlignmentPanel) comp).av.getAlignment())
1681           {
1682             originalSource = ((AlignmentPanel) comp).av;
1683             break;
1684           }
1685         }
1686       }
1687     }
1688
1689     if (originalSource == null)
1690     {
1691       // The original view is closed, we must validate
1692       // the current view against the closed view first
1693       if (al != null)
1694       {
1695         PaintRefresher.validateSequences(al, viewport.getAlignment());
1696       }
1697
1698       originalSource = viewport;
1699     }
1700
1701     return originalSource;
1702   }
1703
1704   /**
1705    * DOCUMENT ME!
1706    *
1707    * @param up
1708    *          DOCUMENT ME!
1709    */
1710   public void moveSelectedSequences(boolean up)
1711   {
1712     SequenceGroup sg = viewport.getSelectionGroup();
1713
1714     if (sg == null)
1715     {
1716       return;
1717     }
1718     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1719             viewport.getHiddenRepSequences(), up);
1720     alignPanel.paintAlignment(true);
1721   }
1722
1723   synchronized void slideSequences(boolean right, int size)
1724   {
1725     List<SequenceI> sg = new ArrayList<SequenceI>();
1726     if (viewport.cursorMode)
1727     {
1728       sg.add(viewport.getAlignment().getSequenceAt(
1729               alignPanel.getSeqPanel().seqCanvas.cursorY));
1730     }
1731     else if (viewport.getSelectionGroup() != null
1732             && viewport.getSelectionGroup().getSize() != viewport
1733                     .getAlignment().getHeight())
1734     {
1735       sg = viewport.getSelectionGroup().getSequences(
1736               viewport.getHiddenRepSequences());
1737     }
1738
1739     if (sg.size() < 1)
1740     {
1741       return;
1742     }
1743
1744     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1745
1746     for (SequenceI seq : viewport.getAlignment().getSequences())
1747     {
1748       if (!sg.contains(seq))
1749       {
1750         invertGroup.add(seq);
1751       }
1752     }
1753
1754     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1755
1756     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1757     for (int i = 0; i < invertGroup.size(); i++)
1758     {
1759       seqs2[i] = invertGroup.get(i);
1760     }
1761
1762     SlideSequencesCommand ssc;
1763     if (right)
1764     {
1765       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1766               size, viewport.getGapCharacter());
1767     }
1768     else
1769     {
1770       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1771               size, viewport.getGapCharacter());
1772     }
1773
1774     int groupAdjustment = 0;
1775     if (ssc.getGapsInsertedBegin() && right)
1776     {
1777       if (viewport.cursorMode)
1778       {
1779         alignPanel.getSeqPanel().moveCursor(size, 0);
1780       }
1781       else
1782       {
1783         groupAdjustment = size;
1784       }
1785     }
1786     else if (!ssc.getGapsInsertedBegin() && !right)
1787     {
1788       if (viewport.cursorMode)
1789       {
1790         alignPanel.getSeqPanel().moveCursor(-size, 0);
1791       }
1792       else
1793       {
1794         groupAdjustment = -size;
1795       }
1796     }
1797
1798     if (groupAdjustment != 0)
1799     {
1800       viewport.getSelectionGroup().setStartRes(
1801               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1802       viewport.getSelectionGroup().setEndRes(
1803               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1804     }
1805
1806     /*
1807      * just extend the last slide command if compatible; but not if in
1808      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1809      */
1810     boolean appendHistoryItem = false;
1811     Deque<CommandI> historyList = viewport.getHistoryList();
1812     boolean inSplitFrame = getSplitViewContainer() != null;
1813     if (!inSplitFrame && historyList != null && historyList.size() > 0
1814             && historyList.peek() instanceof SlideSequencesCommand)
1815     {
1816       appendHistoryItem = ssc
1817               .appendSlideCommand((SlideSequencesCommand) historyList
1818                       .peek());
1819     }
1820
1821     if (!appendHistoryItem)
1822     {
1823       addHistoryItem(ssc);
1824     }
1825
1826     repaint();
1827   }
1828
1829   /**
1830    * DOCUMENT ME!
1831    *
1832    * @param e
1833    *          DOCUMENT ME!
1834    */
1835   @Override
1836   protected void copy_actionPerformed(ActionEvent e)
1837   {
1838     System.gc();
1839     if (viewport.getSelectionGroup() == null)
1840     {
1841       return;
1842     }
1843     // TODO: preserve the ordering of displayed alignment annotation in any
1844     // internal paste (particularly sequence associated annotation)
1845     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1846     String[] omitHidden = null;
1847
1848     if (viewport.hasHiddenColumns())
1849     {
1850       omitHidden = viewport.getViewAsString(true);
1851     }
1852
1853     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1854             seqs, omitHidden, null);
1855
1856     StringSelection ss = new StringSelection(output);
1857
1858     try
1859     {
1860       jalview.gui.Desktop.internalCopy = true;
1861       // Its really worth setting the clipboard contents
1862       // to empty before setting the large StringSelection!!
1863       Toolkit.getDefaultToolkit().getSystemClipboard()
1864               .setContents(new StringSelection(""), null);
1865
1866       Toolkit.getDefaultToolkit().getSystemClipboard()
1867               .setContents(ss, Desktop.instance);
1868     } catch (OutOfMemoryError er)
1869     {
1870       new OOMWarning("copying region", er);
1871       return;
1872     }
1873
1874     ArrayList<int[]> hiddenColumns = null;
1875     if (viewport.hasHiddenColumns())
1876     {
1877       hiddenColumns = new ArrayList<int[]>();
1878       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1879               .getSelectionGroup().getEndRes();
1880       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1881       {
1882         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1883         {
1884           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1885               region[1] - hiddenOffset });
1886         }
1887       }
1888     }
1889
1890     Desktop.jalviewClipboard = new Object[] { seqs,
1891         viewport.getAlignment().getDataset(), hiddenColumns };
1892     statusBar.setText(MessageManager.formatMessage(
1893             "label.copied_sequences_to_clipboard", new Object[] { Integer
1894                     .valueOf(seqs.length).toString() }));
1895   }
1896
1897   /**
1898    * DOCUMENT ME!
1899    *
1900    * @param e
1901    *          DOCUMENT ME!
1902    */
1903   @Override
1904   protected void pasteNew_actionPerformed(ActionEvent e)
1905   {
1906     paste(true);
1907   }
1908
1909   /**
1910    * DOCUMENT ME!
1911    *
1912    * @param e
1913    *          DOCUMENT ME!
1914    */
1915   @Override
1916   protected void pasteThis_actionPerformed(ActionEvent e)
1917   {
1918     paste(false);
1919   }
1920
1921   /**
1922    * Paste contents of Jalview clipboard
1923    *
1924    * @param newAlignment
1925    *          true to paste to a new alignment, otherwise add to this.
1926    */
1927   void paste(boolean newAlignment)
1928   {
1929     boolean externalPaste = true;
1930     try
1931     {
1932       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1933       Transferable contents = c.getContents(this);
1934
1935       if (contents == null)
1936       {
1937         return;
1938       }
1939
1940       String str;
1941       FileFormatI format;
1942       try
1943       {
1944         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1945         if (str.length() < 1)
1946         {
1947           return;
1948         }
1949
1950         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1951
1952       } catch (OutOfMemoryError er)
1953       {
1954         new OOMWarning("Out of memory pasting sequences!!", er);
1955         return;
1956       }
1957
1958       SequenceI[] sequences;
1959       boolean annotationAdded = false;
1960       AlignmentI alignment = null;
1961
1962       if (Desktop.jalviewClipboard != null)
1963       {
1964         // The clipboard was filled from within Jalview, we must use the
1965         // sequences
1966         // And dataset from the copied alignment
1967         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1968         // be doubly sure that we create *new* sequence objects.
1969         sequences = new SequenceI[newseq.length];
1970         for (int i = 0; i < newseq.length; i++)
1971         {
1972           sequences[i] = new Sequence(newseq[i]);
1973         }
1974         alignment = new Alignment(sequences);
1975         externalPaste = false;
1976       }
1977       else
1978       {
1979         // parse the clipboard as an alignment.
1980         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1981                 format);
1982         sequences = alignment.getSequencesArray();
1983       }
1984
1985       int alwidth = 0;
1986       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1987       int fgroup = -1;
1988
1989       if (newAlignment)
1990       {
1991
1992         if (Desktop.jalviewClipboard != null)
1993         {
1994           // dataset is inherited
1995           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1996         }
1997         else
1998         {
1999           // new dataset is constructed
2000           alignment.setDataset(null);
2001         }
2002         alwidth = alignment.getWidth() + 1;
2003       }
2004       else
2005       {
2006         AlignmentI pastedal = alignment; // preserve pasted alignment object
2007         // Add pasted sequences and dataset into existing alignment.
2008         alignment = viewport.getAlignment();
2009         alwidth = alignment.getWidth() + 1;
2010         // decide if we need to import sequences from an existing dataset
2011         boolean importDs = Desktop.jalviewClipboard != null
2012                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2013         // importDs==true instructs us to copy over new dataset sequences from
2014         // an existing alignment
2015         Vector newDs = (importDs) ? new Vector() : null; // used to create
2016         // minimum dataset set
2017
2018         for (int i = 0; i < sequences.length; i++)
2019         {
2020           if (importDs)
2021           {
2022             newDs.addElement(null);
2023           }
2024           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2025           // paste
2026           if (importDs && ds != null)
2027           {
2028             if (!newDs.contains(ds))
2029             {
2030               newDs.setElementAt(ds, i);
2031               ds = new Sequence(ds);
2032               // update with new dataset sequence
2033               sequences[i].setDatasetSequence(ds);
2034             }
2035             else
2036             {
2037               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2038             }
2039           }
2040           else
2041           {
2042             // copy and derive new dataset sequence
2043             sequences[i] = sequences[i].deriveSequence();
2044             alignment.getDataset().addSequence(
2045                     sequences[i].getDatasetSequence());
2046             // TODO: avoid creation of duplicate dataset sequences with a
2047             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2048           }
2049           alignment.addSequence(sequences[i]); // merges dataset
2050         }
2051         if (newDs != null)
2052         {
2053           newDs.clear(); // tidy up
2054         }
2055         if (alignment.getAlignmentAnnotation() != null)
2056         {
2057           for (AlignmentAnnotation alan : alignment
2058                   .getAlignmentAnnotation())
2059           {
2060             if (alan.graphGroup > fgroup)
2061             {
2062               fgroup = alan.graphGroup;
2063             }
2064           }
2065         }
2066         if (pastedal.getAlignmentAnnotation() != null)
2067         {
2068           // Add any annotation attached to alignment.
2069           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2070           for (int i = 0; i < alann.length; i++)
2071           {
2072             annotationAdded = true;
2073             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2074             {
2075               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2076               if (newann.graphGroup > -1)
2077               {
2078                 if (newGraphGroups.size() <= newann.graphGroup
2079                         || newGraphGroups.get(newann.graphGroup) == null)
2080                 {
2081                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2082                   {
2083                     newGraphGroups.add(q, null);
2084                   }
2085                   newGraphGroups.set(newann.graphGroup, new Integer(
2086                           ++fgroup));
2087                 }
2088                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2089                         .intValue();
2090               }
2091
2092               newann.padAnnotation(alwidth);
2093               alignment.addAnnotation(newann);
2094             }
2095           }
2096         }
2097       }
2098       if (!newAlignment)
2099       {
2100         // /////
2101         // ADD HISTORY ITEM
2102         //
2103         addHistoryItem(new EditCommand(
2104                 MessageManager.getString("label.add_sequences"),
2105                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2106       }
2107       // Add any annotations attached to sequences
2108       for (int i = 0; i < sequences.length; i++)
2109       {
2110         if (sequences[i].getAnnotation() != null)
2111         {
2112           AlignmentAnnotation newann;
2113           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2114           {
2115             annotationAdded = true;
2116             newann = sequences[i].getAnnotation()[a];
2117             newann.adjustForAlignment();
2118             newann.padAnnotation(alwidth);
2119             if (newann.graphGroup > -1)
2120             {
2121               if (newann.graphGroup > -1)
2122               {
2123                 if (newGraphGroups.size() <= newann.graphGroup
2124                         || newGraphGroups.get(newann.graphGroup) == null)
2125                 {
2126                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2127                   {
2128                     newGraphGroups.add(q, null);
2129                   }
2130                   newGraphGroups.set(newann.graphGroup, new Integer(
2131                           ++fgroup));
2132                 }
2133                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2134                         .intValue();
2135               }
2136             }
2137             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2138             // was
2139             // duplicated
2140             // earlier
2141             alignment
2142                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2143           }
2144         }
2145       }
2146       if (!newAlignment)
2147       {
2148
2149         // propagate alignment changed.
2150         vpRanges.setEndSeq(alignment.getHeight());
2151         if (annotationAdded)
2152         {
2153           // Duplicate sequence annotation in all views.
2154           AlignmentI[] alview = this.getViewAlignments();
2155           for (int i = 0; i < sequences.length; i++)
2156           {
2157             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2158             if (sann == null)
2159             {
2160               continue;
2161             }
2162             for (int avnum = 0; avnum < alview.length; avnum++)
2163             {
2164               if (alview[avnum] != alignment)
2165               {
2166                 // duplicate in a view other than the one with input focus
2167                 int avwidth = alview[avnum].getWidth() + 1;
2168                 // this relies on sann being preserved after we
2169                 // modify the sequence's annotation array for each duplication
2170                 for (int a = 0; a < sann.length; a++)
2171                 {
2172                   AlignmentAnnotation newann = new AlignmentAnnotation(
2173                           sann[a]);
2174                   sequences[i].addAlignmentAnnotation(newann);
2175                   newann.padAnnotation(avwidth);
2176                   alview[avnum].addAnnotation(newann); // annotation was
2177                   // duplicated earlier
2178                   // TODO JAL-1145 graphGroups are not updated for sequence
2179                   // annotation added to several views. This may cause
2180                   // strangeness
2181                   alview[avnum].setAnnotationIndex(newann, a);
2182                 }
2183               }
2184             }
2185           }
2186           buildSortByAnnotationScoresMenu();
2187         }
2188         viewport.firePropertyChange("alignment", null,
2189                 alignment.getSequences());
2190         if (alignPanels != null)
2191         {
2192           for (AlignmentPanel ap : alignPanels)
2193           {
2194             ap.validateAnnotationDimensions(false);
2195           }
2196         }
2197         else
2198         {
2199           alignPanel.validateAnnotationDimensions(false);
2200         }
2201
2202       }
2203       else
2204       {
2205         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2206                 DEFAULT_HEIGHT);
2207         String newtitle = new String("Copied sequences");
2208
2209         if (Desktop.jalviewClipboard != null
2210                 && Desktop.jalviewClipboard[2] != null)
2211         {
2212           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2213           for (int[] region : hc)
2214           {
2215             af.viewport.hideColumns(region[0], region[1]);
2216           }
2217         }
2218
2219         // >>>This is a fix for the moment, until a better solution is
2220         // found!!<<<
2221         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2222                 .transferSettings(
2223                         alignPanel.getSeqPanel().seqCanvas
2224                                 .getFeatureRenderer());
2225
2226         // TODO: maintain provenance of an alignment, rather than just make the
2227         // title a concatenation of operations.
2228         if (!externalPaste)
2229         {
2230           if (title.startsWith("Copied sequences"))
2231           {
2232             newtitle = title;
2233           }
2234           else
2235           {
2236             newtitle = newtitle.concat("- from " + title);
2237           }
2238         }
2239         else
2240         {
2241           newtitle = new String("Pasted sequences");
2242         }
2243
2244         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2245                 DEFAULT_HEIGHT);
2246
2247       }
2248
2249     } catch (Exception ex)
2250     {
2251       ex.printStackTrace();
2252       System.out.println("Exception whilst pasting: " + ex);
2253       // could be anything being pasted in here
2254     }
2255
2256   }
2257
2258   @Override
2259   protected void expand_newalign(ActionEvent e)
2260   {
2261     try
2262     {
2263       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2264               .getAlignment(), -1);
2265       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2266               DEFAULT_HEIGHT);
2267       String newtitle = new String("Flanking alignment");
2268
2269       if (Desktop.jalviewClipboard != null
2270               && Desktop.jalviewClipboard[2] != null)
2271       {
2272         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2273         for (int region[] : hc)
2274         {
2275           af.viewport.hideColumns(region[0], region[1]);
2276         }
2277       }
2278
2279       // >>>This is a fix for the moment, until a better solution is
2280       // found!!<<<
2281       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2282               .transferSettings(
2283                       alignPanel.getSeqPanel().seqCanvas
2284                               .getFeatureRenderer());
2285
2286       // TODO: maintain provenance of an alignment, rather than just make the
2287       // title a concatenation of operations.
2288       {
2289         if (title.startsWith("Copied sequences"))
2290         {
2291           newtitle = title;
2292         }
2293         else
2294         {
2295           newtitle = newtitle.concat("- from " + title);
2296         }
2297       }
2298
2299       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2300
2301     } catch (Exception ex)
2302     {
2303       ex.printStackTrace();
2304       System.out.println("Exception whilst pasting: " + ex);
2305       // could be anything being pasted in here
2306     } catch (OutOfMemoryError oom)
2307     {
2308       new OOMWarning("Viewing flanking region of alignment", oom);
2309     }
2310   }
2311
2312   /**
2313    * DOCUMENT ME!
2314    *
2315    * @param e
2316    *          DOCUMENT ME!
2317    */
2318   @Override
2319   protected void cut_actionPerformed(ActionEvent e)
2320   {
2321     copy_actionPerformed(null);
2322     delete_actionPerformed(null);
2323   }
2324
2325   /**
2326    * DOCUMENT ME!
2327    *
2328    * @param e
2329    *          DOCUMENT ME!
2330    */
2331   @Override
2332   protected void delete_actionPerformed(ActionEvent evt)
2333   {
2334
2335     SequenceGroup sg = viewport.getSelectionGroup();
2336     if (sg == null)
2337     {
2338       return;
2339     }
2340
2341     /*
2342      * If the cut affects all sequences, warn, remove highlighted columns
2343      */
2344     if (sg.getSize() == viewport.getAlignment().getHeight())
2345     {
2346       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2347               .getAlignment().getWidth()) ? true : false;
2348       if (isEntireAlignWidth)
2349       {
2350         int confirm = JvOptionPane.showConfirmDialog(this,
2351                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2352                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2353                 JvOptionPane.OK_CANCEL_OPTION);
2354
2355         if (confirm == JvOptionPane.CANCEL_OPTION
2356                 || confirm == JvOptionPane.CLOSED_OPTION)
2357         {
2358           return;
2359         }
2360       }
2361       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2362               sg.getEndRes() + 1);
2363     }
2364     SequenceI[] cut = sg.getSequences()
2365             .toArray(new SequenceI[sg.getSize()]);
2366
2367     addHistoryItem(new EditCommand(
2368             MessageManager.getString("label.cut_sequences"), Action.CUT,
2369             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2370             viewport.getAlignment()));
2371
2372     viewport.setSelectionGroup(null);
2373     viewport.sendSelection();
2374     viewport.getAlignment().deleteGroup(sg);
2375
2376     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2377             .getSequences());
2378     if (viewport.getAlignment().getHeight() < 1)
2379     {
2380       try
2381       {
2382         this.setClosed(true);
2383       } catch (Exception ex)
2384       {
2385       }
2386     }
2387   }
2388
2389   /**
2390    * DOCUMENT ME!
2391    *
2392    * @param e
2393    *          DOCUMENT ME!
2394    */
2395   @Override
2396   protected void deleteGroups_actionPerformed(ActionEvent e)
2397   {
2398     if (avc.deleteGroups())
2399     {
2400       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2401       alignPanel.updateAnnotation();
2402       alignPanel.paintAlignment(true);
2403     }
2404   }
2405
2406   /**
2407    * DOCUMENT ME!
2408    *
2409    * @param e
2410    *          DOCUMENT ME!
2411    */
2412   @Override
2413   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2414   {
2415     SequenceGroup sg = new SequenceGroup();
2416
2417     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2418     {
2419       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2420     }
2421
2422     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2423     viewport.setSelectionGroup(sg);
2424     viewport.sendSelection();
2425     // JAL-2034 - should delegate to
2426     // alignPanel to decide if overview needs
2427     // updating.
2428     alignPanel.paintAlignment(false);
2429     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2430   }
2431
2432   /**
2433    * DOCUMENT ME!
2434    *
2435    * @param e
2436    *          DOCUMENT ME!
2437    */
2438   @Override
2439   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2440   {
2441     if (viewport.cursorMode)
2442     {
2443       alignPanel.getSeqPanel().keyboardNo1 = null;
2444       alignPanel.getSeqPanel().keyboardNo2 = null;
2445     }
2446     viewport.setSelectionGroup(null);
2447     viewport.getColumnSelection().clear();
2448     viewport.setSelectionGroup(null);
2449     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2450     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2451     // JAL-2034 - should delegate to
2452     // alignPanel to decide if overview needs
2453     // updating.
2454     alignPanel.paintAlignment(false);
2455     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2456     viewport.sendSelection();
2457   }
2458
2459   /**
2460    * DOCUMENT ME!
2461    *
2462    * @param e
2463    *          DOCUMENT ME!
2464    */
2465   @Override
2466   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2467   {
2468     SequenceGroup sg = viewport.getSelectionGroup();
2469
2470     if (sg == null)
2471     {
2472       selectAllSequenceMenuItem_actionPerformed(null);
2473
2474       return;
2475     }
2476
2477     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2478     {
2479       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2480     }
2481     // JAL-2034 - should delegate to
2482     // alignPanel to decide if overview needs
2483     // updating.
2484
2485     alignPanel.paintAlignment(true);
2486     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2487     viewport.sendSelection();
2488   }
2489
2490   @Override
2491   public void invertColSel_actionPerformed(ActionEvent e)
2492   {
2493     viewport.invertColumnSelection();
2494     alignPanel.paintAlignment(true);
2495     viewport.sendSelection();
2496   }
2497
2498   /**
2499    * DOCUMENT ME!
2500    *
2501    * @param e
2502    *          DOCUMENT ME!
2503    */
2504   @Override
2505   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506   {
2507     trimAlignment(true);
2508   }
2509
2510   /**
2511    * DOCUMENT ME!
2512    *
2513    * @param e
2514    *          DOCUMENT ME!
2515    */
2516   @Override
2517   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2518   {
2519     trimAlignment(false);
2520   }
2521
2522   void trimAlignment(boolean trimLeft)
2523   {
2524     ColumnSelection colSel = viewport.getColumnSelection();
2525     int column;
2526
2527     if (!colSel.isEmpty())
2528     {
2529       if (trimLeft)
2530       {
2531         column = colSel.getMin();
2532       }
2533       else
2534       {
2535         column = colSel.getMax();
2536       }
2537
2538       SequenceI[] seqs;
2539       if (viewport.getSelectionGroup() != null)
2540       {
2541         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2542                 viewport.getHiddenRepSequences());
2543       }
2544       else
2545       {
2546         seqs = viewport.getAlignment().getSequencesArray();
2547       }
2548
2549       TrimRegionCommand trimRegion;
2550       if (trimLeft)
2551       {
2552         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2553                 column, viewport.getAlignment());
2554         vpRanges.setStartRes(0);
2555       }
2556       else
2557       {
2558         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2559                 column, viewport.getAlignment());
2560       }
2561
2562       statusBar.setText(MessageManager.formatMessage(
2563               "label.removed_columns",
2564               new String[] { Integer.valueOf(trimRegion.getSize())
2565                       .toString() }));
2566
2567       addHistoryItem(trimRegion);
2568
2569       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2570       {
2571         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2572                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2573         {
2574           viewport.getAlignment().deleteGroup(sg);
2575         }
2576       }
2577
2578       viewport.firePropertyChange("alignment", null, viewport
2579               .getAlignment().getSequences());
2580     }
2581   }
2582
2583   /**
2584    * DOCUMENT ME!
2585    *
2586    * @param e
2587    *          DOCUMENT ME!
2588    */
2589   @Override
2590   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2591   {
2592     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2593
2594     SequenceI[] seqs;
2595     if (viewport.getSelectionGroup() != null)
2596     {
2597       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2598               viewport.getHiddenRepSequences());
2599       start = viewport.getSelectionGroup().getStartRes();
2600       end = viewport.getSelectionGroup().getEndRes();
2601     }
2602     else
2603     {
2604       seqs = viewport.getAlignment().getSequencesArray();
2605     }
2606
2607     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2608             "Remove Gapped Columns", seqs, start, end,
2609             viewport.getAlignment());
2610
2611     addHistoryItem(removeGapCols);
2612
2613     statusBar.setText(MessageManager.formatMessage(
2614             "label.removed_empty_columns",
2615             new Object[] { Integer.valueOf(removeGapCols.getSize())
2616                     .toString() }));
2617
2618     // This is to maintain viewport position on first residue
2619     // of first sequence
2620     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2621     int startRes = seq.findPosition(vpRanges.getStartRes());
2622     // ShiftList shifts;
2623     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2624     // edit.alColumnChanges=shifts.getInverse();
2625     // if (viewport.hasHiddenColumns)
2626     // viewport.getColumnSelection().compensateForEdits(shifts);
2627     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2628     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2629             .getSequences());
2630
2631   }
2632
2633   /**
2634    * DOCUMENT ME!
2635    *
2636    * @param e
2637    *          DOCUMENT ME!
2638    */
2639   @Override
2640   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2641   {
2642     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2643
2644     SequenceI[] seqs;
2645     if (viewport.getSelectionGroup() != null)
2646     {
2647       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2648               viewport.getHiddenRepSequences());
2649       start = viewport.getSelectionGroup().getStartRes();
2650       end = viewport.getSelectionGroup().getEndRes();
2651     }
2652     else
2653     {
2654       seqs = viewport.getAlignment().getSequencesArray();
2655     }
2656
2657     // This is to maintain viewport position on first residue
2658     // of first sequence
2659     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2660     int startRes = seq.findPosition(vpRanges.getStartRes());
2661
2662     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2663             viewport.getAlignment()));
2664
2665     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2666
2667     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2668             .getSequences());
2669
2670   }
2671
2672   /**
2673    * DOCUMENT ME!
2674    *
2675    * @param e
2676    *          DOCUMENT ME!
2677    */
2678   @Override
2679   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2680   {
2681     viewport.setPadGaps(padGapsMenuitem.isSelected());
2682     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2683             .getSequences());
2684   }
2685
2686   /**
2687    * DOCUMENT ME!
2688    *
2689    * @param e
2690    *          DOCUMENT ME!
2691    */
2692   @Override
2693   public void findMenuItem_actionPerformed(ActionEvent e)
2694   {
2695     new Finder();
2696   }
2697
2698   /**
2699    * Create a new view of the current alignment.
2700    */
2701   @Override
2702   public void newView_actionPerformed(ActionEvent e)
2703   {
2704     newView(null, true);
2705   }
2706
2707   /**
2708    * Creates and shows a new view of the current alignment.
2709    *
2710    * @param viewTitle
2711    *          title of newly created view; if null, one will be generated
2712    * @param copyAnnotation
2713    *          if true then duplicate all annnotation, groups and settings
2714    * @return new alignment panel, already displayed.
2715    */
2716   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2717   {
2718     /*
2719      * Create a new AlignmentPanel (with its own, new Viewport)
2720      */
2721     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2722             true);
2723     if (!copyAnnotation)
2724     {
2725       /*
2726        * remove all groups and annotation except for the automatic stuff
2727        */
2728       newap.av.getAlignment().deleteAllGroups();
2729       newap.av.getAlignment().deleteAllAnnotations(false);
2730     }
2731
2732     newap.av.setGatherViewsHere(false);
2733
2734     if (viewport.viewName == null)
2735     {
2736       viewport.viewName = MessageManager
2737               .getString("label.view_name_original");
2738     }
2739
2740     /*
2741      * Views share the same edits undo and redo stacks
2742      */
2743     newap.av.setHistoryList(viewport.getHistoryList());
2744     newap.av.setRedoList(viewport.getRedoList());
2745
2746     /*
2747      * Views share the same mappings; need to deregister any new mappings
2748      * created by copyAlignPanel, and register the new reference to the shared
2749      * mappings
2750      */
2751     newap.av.replaceMappings(viewport.getAlignment());
2752
2753     newap.av.viewName = getNewViewName(viewTitle);
2754
2755     addAlignmentPanel(newap, true);
2756     newap.alignmentChanged();
2757
2758     if (alignPanels.size() == 2)
2759     {
2760       viewport.setGatherViewsHere(true);
2761     }
2762     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2763     return newap;
2764   }
2765
2766   /**
2767    * Make a new name for the view, ensuring it is unique within the current
2768    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2769    * these now use viewId. Unique view names are still desirable for usability.)
2770    *
2771    * @param viewTitle
2772    * @return
2773    */
2774   protected String getNewViewName(String viewTitle)
2775   {
2776     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2777     boolean addFirstIndex = false;
2778     if (viewTitle == null || viewTitle.trim().length() == 0)
2779     {
2780       viewTitle = MessageManager.getString("action.view");
2781       addFirstIndex = true;
2782     }
2783     else
2784     {
2785       index = 1;// we count from 1 if given a specific name
2786     }
2787     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2788
2789     List<Component> comps = PaintRefresher.components.get(viewport
2790             .getSequenceSetId());
2791
2792     List<String> existingNames = getExistingViewNames(comps);
2793
2794     while (existingNames.contains(newViewName))
2795     {
2796       newViewName = viewTitle + " " + (++index);
2797     }
2798     return newViewName;
2799   }
2800
2801   /**
2802    * Returns a list of distinct view names found in the given list of
2803    * components. View names are held on the viewport of an AlignmentPanel.
2804    *
2805    * @param comps
2806    * @return
2807    */
2808   protected List<String> getExistingViewNames(List<Component> comps)
2809   {
2810     List<String> existingNames = new ArrayList<String>();
2811     for (Component comp : comps)
2812     {
2813       if (comp instanceof AlignmentPanel)
2814       {
2815         AlignmentPanel ap = (AlignmentPanel) comp;
2816         if (!existingNames.contains(ap.av.viewName))
2817         {
2818           existingNames.add(ap.av.viewName);
2819         }
2820       }
2821     }
2822     return existingNames;
2823   }
2824
2825   /**
2826    * Explode tabbed views into separate windows.
2827    */
2828   @Override
2829   public void expandViews_actionPerformed(ActionEvent e)
2830   {
2831     Desktop.explodeViews(this);
2832   }
2833
2834   /**
2835    * Gather views in separate windows back into a tabbed presentation.
2836    */
2837   @Override
2838   public void gatherViews_actionPerformed(ActionEvent e)
2839   {
2840     Desktop.instance.gatherViews(this);
2841   }
2842
2843   /**
2844    * DOCUMENT ME!
2845    *
2846    * @param e
2847    *          DOCUMENT ME!
2848    */
2849   @Override
2850   public void font_actionPerformed(ActionEvent e)
2851   {
2852     new FontChooser(alignPanel);
2853   }
2854
2855   /**
2856    * DOCUMENT ME!
2857    *
2858    * @param e
2859    *          DOCUMENT ME!
2860    */
2861   @Override
2862   protected void seqLimit_actionPerformed(ActionEvent e)
2863   {
2864     viewport.setShowJVSuffix(seqLimits.isSelected());
2865
2866     alignPanel.getIdPanel().getIdCanvas()
2867             .setPreferredSize(alignPanel.calculateIdWidth());
2868     alignPanel.paintAlignment(true);
2869   }
2870
2871   @Override
2872   public void idRightAlign_actionPerformed(ActionEvent e)
2873   {
2874     viewport.setRightAlignIds(idRightAlign.isSelected());
2875     alignPanel.paintAlignment(true);
2876   }
2877
2878   @Override
2879   public void centreColumnLabels_actionPerformed(ActionEvent e)
2880   {
2881     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2882     alignPanel.paintAlignment(true);
2883   }
2884
2885   /*
2886    * (non-Javadoc)
2887    *
2888    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2889    */
2890   @Override
2891   protected void followHighlight_actionPerformed()
2892   {
2893     /*
2894      * Set the 'follow' flag on the Viewport (and scroll to position if now
2895      * true).
2896      */
2897     final boolean state = this.followHighlightMenuItem.getState();
2898     viewport.setFollowHighlight(state);
2899     if (state)
2900     {
2901       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2902     }
2903   }
2904
2905   /**
2906    * DOCUMENT ME!
2907    *
2908    * @param e
2909    *          DOCUMENT ME!
2910    */
2911   @Override
2912   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2913   {
2914     viewport.setColourText(colourTextMenuItem.isSelected());
2915     alignPanel.paintAlignment(true);
2916   }
2917
2918   /**
2919    * DOCUMENT ME!
2920    *
2921    * @param e
2922    *          DOCUMENT ME!
2923    */
2924   @Override
2925   public void wrapMenuItem_actionPerformed(ActionEvent e)
2926   {
2927     scaleAbove.setVisible(wrapMenuItem.isSelected());
2928     scaleLeft.setVisible(wrapMenuItem.isSelected());
2929     scaleRight.setVisible(wrapMenuItem.isSelected());
2930     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2931     alignPanel.updateLayout();
2932   }
2933
2934   @Override
2935   public void showAllSeqs_actionPerformed(ActionEvent e)
2936   {
2937     viewport.showAllHiddenSeqs();
2938   }
2939
2940   @Override
2941   public void showAllColumns_actionPerformed(ActionEvent e)
2942   {
2943     viewport.showAllHiddenColumns();
2944     repaint();
2945     viewport.sendSelection();
2946   }
2947
2948   @Override
2949   public void hideSelSequences_actionPerformed(ActionEvent e)
2950   {
2951     viewport.hideAllSelectedSeqs();
2952     // alignPanel.paintAlignment(true);
2953   }
2954
2955   /**
2956    * called by key handler and the hide all/show all menu items
2957    *
2958    * @param toggleSeqs
2959    * @param toggleCols
2960    */
2961   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2962   {
2963
2964     boolean hide = false;
2965     SequenceGroup sg = viewport.getSelectionGroup();
2966     if (!toggleSeqs && !toggleCols)
2967     {
2968       // Hide everything by the current selection - this is a hack - we do the
2969       // invert and then hide
2970       // first check that there will be visible columns after the invert.
2971       if (viewport.hasSelectedColumns()
2972               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2973                       .getEndRes()))
2974       {
2975         // now invert the sequence set, if required - empty selection implies
2976         // that no hiding is required.
2977         if (sg != null)
2978         {
2979           invertSequenceMenuItem_actionPerformed(null);
2980           sg = viewport.getSelectionGroup();
2981           toggleSeqs = true;
2982
2983         }
2984         viewport.expandColSelection(sg, true);
2985         // finally invert the column selection and get the new sequence
2986         // selection.
2987         invertColSel_actionPerformed(null);
2988         toggleCols = true;
2989       }
2990     }
2991
2992     if (toggleSeqs)
2993     {
2994       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2995       {
2996         hideSelSequences_actionPerformed(null);
2997         hide = true;
2998       }
2999       else if (!(toggleCols && viewport.hasSelectedColumns()))
3000       {
3001         showAllSeqs_actionPerformed(null);
3002       }
3003     }
3004
3005     if (toggleCols)
3006     {
3007       if (viewport.hasSelectedColumns())
3008       {
3009         hideSelColumns_actionPerformed(null);
3010         if (!toggleSeqs)
3011         {
3012           viewport.setSelectionGroup(sg);
3013         }
3014       }
3015       else if (!hide)
3016       {
3017         showAllColumns_actionPerformed(null);
3018       }
3019     }
3020   }
3021
3022   /*
3023    * (non-Javadoc)
3024    *
3025    * @see
3026    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3027    * event.ActionEvent)
3028    */
3029   @Override
3030   public void hideAllButSelection_actionPerformed(ActionEvent e)
3031   {
3032     toggleHiddenRegions(false, false);
3033     viewport.sendSelection();
3034   }
3035
3036   /*
3037    * (non-Javadoc)
3038    *
3039    * @see
3040    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3041    * .ActionEvent)
3042    */
3043   @Override
3044   public void hideAllSelection_actionPerformed(ActionEvent e)
3045   {
3046     SequenceGroup sg = viewport.getSelectionGroup();
3047     viewport.expandColSelection(sg, false);
3048     viewport.hideAllSelectedSeqs();
3049     viewport.hideSelectedColumns();
3050     alignPanel.paintAlignment(true);
3051     viewport.sendSelection();
3052   }
3053
3054   /*
3055    * (non-Javadoc)
3056    *
3057    * @see
3058    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3059    * ActionEvent)
3060    */
3061   @Override
3062   public void showAllhidden_actionPerformed(ActionEvent e)
3063   {
3064     viewport.showAllHiddenColumns();
3065     viewport.showAllHiddenSeqs();
3066     alignPanel.paintAlignment(true);
3067     viewport.sendSelection();
3068   }
3069
3070   @Override
3071   public void hideSelColumns_actionPerformed(ActionEvent e)
3072   {
3073     viewport.hideSelectedColumns();
3074     alignPanel.paintAlignment(true);
3075     viewport.sendSelection();
3076   }
3077
3078   @Override
3079   public void hiddenMarkers_actionPerformed(ActionEvent e)
3080   {
3081     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3082     repaint();
3083   }
3084
3085   /**
3086    * DOCUMENT ME!
3087    *
3088    * @param e
3089    *          DOCUMENT ME!
3090    */
3091   @Override
3092   protected void scaleAbove_actionPerformed(ActionEvent e)
3093   {
3094     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3095     alignPanel.paintAlignment(true);
3096   }
3097
3098   /**
3099    * DOCUMENT ME!
3100    *
3101    * @param e
3102    *          DOCUMENT ME!
3103    */
3104   @Override
3105   protected void scaleLeft_actionPerformed(ActionEvent e)
3106   {
3107     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3108     alignPanel.paintAlignment(true);
3109   }
3110
3111   /**
3112    * DOCUMENT ME!
3113    *
3114    * @param e
3115    *          DOCUMENT ME!
3116    */
3117   @Override
3118   protected void scaleRight_actionPerformed(ActionEvent e)
3119   {
3120     viewport.setScaleRightWrapped(scaleRight.isSelected());
3121     alignPanel.paintAlignment(true);
3122   }
3123
3124   /**
3125    * DOCUMENT ME!
3126    *
3127    * @param e
3128    *          DOCUMENT ME!
3129    */
3130   @Override
3131   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3132   {
3133     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3134     alignPanel.paintAlignment(true);
3135   }
3136
3137   /**
3138    * DOCUMENT ME!
3139    *
3140    * @param e
3141    *          DOCUMENT ME!
3142    */
3143   @Override
3144   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3145   {
3146     viewport.setShowText(viewTextMenuItem.isSelected());
3147     alignPanel.paintAlignment(true);
3148   }
3149
3150   /**
3151    * DOCUMENT ME!
3152    *
3153    * @param e
3154    *          DOCUMENT ME!
3155    */
3156   @Override
3157   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3158   {
3159     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3160     alignPanel.paintAlignment(true);
3161   }
3162
3163   public FeatureSettings featureSettings;
3164
3165   @Override
3166   public FeatureSettingsControllerI getFeatureSettingsUI()
3167   {
3168     return featureSettings;
3169   }
3170
3171   @Override
3172   public void featureSettings_actionPerformed(ActionEvent e)
3173   {
3174     if (featureSettings != null)
3175     {
3176       featureSettings.close();
3177       featureSettings = null;
3178     }
3179     if (!showSeqFeatures.isSelected())
3180     {
3181       // make sure features are actually displayed
3182       showSeqFeatures.setSelected(true);
3183       showSeqFeatures_actionPerformed(null);
3184     }
3185     featureSettings = new FeatureSettings(this);
3186   }
3187
3188   /**
3189    * Set or clear 'Show Sequence Features'
3190    *
3191    * @param evt
3192    *          DOCUMENT ME!
3193    */
3194   @Override
3195   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3196   {
3197     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3198     alignPanel.paintAlignment(true);
3199     if (alignPanel.getOverviewPanel() != null)
3200     {
3201       alignPanel.getOverviewPanel().updateOverviewImage();
3202     }
3203   }
3204
3205   /**
3206    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3207    * the annotations panel as a whole.
3208    *
3209    * The options to show/hide all annotations should be enabled when the panel
3210    * is shown, and disabled when the panel is hidden.
3211    *
3212    * @param e
3213    */
3214   @Override
3215   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3216   {
3217     final boolean setVisible = annotationPanelMenuItem.isSelected();
3218     viewport.setShowAnnotation(setVisible);
3219     this.showAllSeqAnnotations.setEnabled(setVisible);
3220     this.hideAllSeqAnnotations.setEnabled(setVisible);
3221     this.showAllAlAnnotations.setEnabled(setVisible);
3222     this.hideAllAlAnnotations.setEnabled(setVisible);
3223     alignPanel.updateLayout();
3224   }
3225
3226   @Override
3227   public void alignmentProperties()
3228   {
3229     JEditorPane editPane = new JEditorPane("text/html", "");
3230     editPane.setEditable(false);
3231     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3232             .formatAsHtml();
3233     editPane.setText(MessageManager.formatMessage("label.html_content",
3234             new Object[] { contents.toString() }));
3235     JInternalFrame frame = new JInternalFrame();
3236     frame.getContentPane().add(new JScrollPane(editPane));
3237
3238     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3239             "label.alignment_properties", new Object[] { getTitle() }),
3240             500, 400);
3241   }
3242
3243   /**
3244    * DOCUMENT ME!
3245    *
3246    * @param e
3247    *          DOCUMENT ME!
3248    */
3249   @Override
3250   public void overviewMenuItem_actionPerformed(ActionEvent e)
3251   {
3252     if (alignPanel.overviewPanel != null)
3253     {
3254       return;
3255     }
3256
3257     JInternalFrame frame = new JInternalFrame();
3258     OverviewPanel overview = new OverviewPanel(alignPanel);
3259     frame.setContentPane(overview);
3260     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3261             "label.overview_params", new Object[] { this.getTitle() }),
3262             frame.getWidth(), frame.getHeight());
3263     frame.pack();
3264     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3265     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3266     {
3267       @Override
3268       public void internalFrameClosed(
3269               javax.swing.event.InternalFrameEvent evt)
3270       {
3271         alignPanel.setOverviewPanel(null);
3272       };
3273     });
3274
3275     alignPanel.setOverviewPanel(overview);
3276   }
3277
3278   @Override
3279   public void textColour_actionPerformed()
3280   {
3281     new TextColourChooser().chooseColour(alignPanel, null);
3282   }
3283
3284   /*
3285    * public void covariationColour_actionPerformed() {
3286    * changeColour(new
3287    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3288    * ()[0])); }
3289    */
3290   @Override
3291   public void annotationColour_actionPerformed()
3292   {
3293     new AnnotationColourChooser(viewport, alignPanel);
3294   }
3295
3296   @Override
3297   public void annotationColumn_actionPerformed(ActionEvent e)
3298   {
3299     new AnnotationColumnChooser(viewport, alignPanel);
3300   }
3301
3302   /**
3303    * Action on the user checking or unchecking the option to apply the selected
3304    * colour scheme to all groups. If unchecked, groups may have their own
3305    * independent colour schemes.
3306    *
3307    * @param selected
3308    */
3309   @Override
3310   public void applyToAllGroups_actionPerformed(boolean selected)
3311   {
3312     viewport.setColourAppliesToAllGroups(selected);
3313   }
3314
3315   /**
3316    * Action on user selecting a colour from the colour menu
3317    *
3318    * @param name
3319    *          the name (not the menu item label!) of the colour scheme
3320    */
3321   @Override
3322   public void changeColour_actionPerformed(String name)
3323   {
3324     /*
3325      * 'User Defined' opens a panel to configure or load a
3326      * user-defined colour scheme
3327      */
3328     if (ResidueColourScheme.USER_DEFINED.equals(name))
3329     {
3330       new UserDefinedColours(alignPanel, null);
3331       return;
3332     }
3333
3334     /*
3335      * otherwise set the chosen colour scheme (or null for 'None')
3336      */
3337     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3338             viewport.getAlignment(), viewport.getHiddenRepSequences());
3339     changeColour(cs);
3340   }
3341
3342   /**
3343    * Actions on setting or changing the alignment colour scheme
3344    *
3345    * @param cs
3346    */
3347   @Override
3348   public void changeColour(ColourSchemeI cs)
3349   {
3350     // TODO: pull up to controller method
3351     if (cs != null)
3352     {
3353       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3354     }
3355
3356     viewport.setGlobalColourScheme(cs);
3357
3358     alignPanel.paintAlignment(true);
3359   }
3360
3361   /**
3362    * Show the PID threshold slider panel
3363    */
3364   @Override
3365   protected void modifyPID_actionPerformed()
3366   {
3367     SliderPanel.setPIDSliderSource(alignPanel,
3368             viewport.getResidueShading(), alignPanel.getViewName());
3369     SliderPanel.showPIDSlider();
3370   }
3371
3372   /**
3373    * Show the Conservation slider panel
3374    */
3375   @Override
3376   protected void modifyConservation_actionPerformed()
3377   {
3378     SliderPanel.setConservationSlider(alignPanel,
3379             viewport.getResidueShading(), alignPanel.getViewName());
3380     SliderPanel.showConservationSlider();
3381   }
3382
3383   /**
3384    * Action on selecting or deselecting (Colour) By Conservation
3385    */
3386   @Override
3387   public void conservationMenuItem_actionPerformed(boolean selected)
3388   {
3389     modifyConservation.setEnabled(selected);
3390     viewport.setConservationSelected(selected);
3391     viewport.getResidueShading().setConservationApplied(selected);
3392
3393     changeColour(viewport.getGlobalColourScheme());
3394     if (selected)
3395     {
3396       modifyConservation_actionPerformed();
3397     }
3398     else
3399     {
3400       SliderPanel.hideConservationSlider();
3401     }
3402   }
3403
3404   /**
3405    * Action on selecting or deselecting (Colour) Above PID Threshold
3406    */
3407   @Override
3408   public void abovePIDThreshold_actionPerformed(boolean selected)
3409   {
3410     modifyPID.setEnabled(selected);
3411     viewport.setAbovePIDThreshold(selected);
3412     if (!selected)
3413     {
3414       viewport.getResidueShading().setThreshold(0,
3415               viewport.isIgnoreGapsConsensus());
3416     }
3417
3418     changeColour(viewport.getGlobalColourScheme());
3419     if (selected)
3420     {
3421       modifyPID_actionPerformed();
3422     }
3423     else
3424     {
3425       SliderPanel.hidePIDSlider();
3426     }
3427   }
3428
3429   /**
3430    * DOCUMENT ME!
3431    *
3432    * @param e
3433    *          DOCUMENT ME!
3434    */
3435   @Override
3436   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3437   {
3438     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3439     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3440             .getAlignment().getSequenceAt(0), null);
3441     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3442             viewport.getAlignment()));
3443     alignPanel.paintAlignment(true);
3444   }
3445
3446   /**
3447    * DOCUMENT ME!
3448    *
3449    * @param e
3450    *          DOCUMENT ME!
3451    */
3452   @Override
3453   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3454   {
3455     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3456     AlignmentSorter.sortByID(viewport.getAlignment());
3457     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3458             viewport.getAlignment()));
3459     alignPanel.paintAlignment(true);
3460   }
3461
3462   /**
3463    * DOCUMENT ME!
3464    *
3465    * @param e
3466    *          DOCUMENT ME!
3467    */
3468   @Override
3469   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3470   {
3471     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472     AlignmentSorter.sortByLength(viewport.getAlignment());
3473     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3474             viewport.getAlignment()));
3475     alignPanel.paintAlignment(true);
3476   }
3477
3478   /**
3479    * DOCUMENT ME!
3480    *
3481    * @param e
3482    *          DOCUMENT ME!
3483    */
3484   @Override
3485   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3486   {
3487     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488     AlignmentSorter.sortByGroup(viewport.getAlignment());
3489     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3490             viewport.getAlignment()));
3491
3492     alignPanel.paintAlignment(true);
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param e
3499    *          DOCUMENT ME!
3500    */
3501   @Override
3502   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3503   {
3504     new RedundancyPanel(alignPanel, this);
3505   }
3506
3507   /**
3508    * DOCUMENT ME!
3509    *
3510    * @param e
3511    *          DOCUMENT ME!
3512    */
3513   @Override
3514   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3515   {
3516     if ((viewport.getSelectionGroup() == null)
3517             || (viewport.getSelectionGroup().getSize() < 2))
3518     {
3519       JvOptionPane.showInternalMessageDialog(this, MessageManager
3520               .getString("label.you_must_select_least_two_sequences"),
3521               MessageManager.getString("label.invalid_selection"),
3522               JvOptionPane.WARNING_MESSAGE);
3523     }
3524     else
3525     {
3526       JInternalFrame frame = new JInternalFrame();
3527       frame.setContentPane(new PairwiseAlignPanel(viewport));
3528       Desktop.addInternalFrame(frame,
3529               MessageManager.getString("action.pairwise_alignment"), 600,
3530               500);
3531     }
3532   }
3533
3534   /**
3535    * DOCUMENT ME!
3536    *
3537    * @param e
3538    *          DOCUMENT ME!
3539    */
3540   @Override
3541   public void PCAMenuItem_actionPerformed(ActionEvent e)
3542   {
3543     if (((viewport.getSelectionGroup() != null)
3544             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3545             .getSelectionGroup().getSize() > 0))
3546             || (viewport.getAlignment().getHeight() < 4))
3547     {
3548       JvOptionPane
3549               .showInternalMessageDialog(
3550                       this,
3551                       MessageManager
3552                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3553                       MessageManager
3554                               .getString("label.sequence_selection_insufficient"),
3555                       JvOptionPane.WARNING_MESSAGE);
3556
3557       return;
3558     }
3559
3560     new PCAPanel(alignPanel);
3561   }
3562
3563   @Override
3564   public void autoCalculate_actionPerformed(ActionEvent e)
3565   {
3566     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3567     if (viewport.autoCalculateConsensus)
3568     {
3569       viewport.firePropertyChange("alignment", null, viewport
3570               .getAlignment().getSequences());
3571     }
3572   }
3573
3574   @Override
3575   public void sortByTreeOption_actionPerformed(ActionEvent e)
3576   {
3577     viewport.sortByTree = sortByTree.isSelected();
3578   }
3579
3580   @Override
3581   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3582   {
3583     viewport.followSelection = listenToViewSelections.isSelected();
3584   }
3585
3586   /**
3587    * DOCUMENT ME!
3588    *
3589    * @param e
3590    *          DOCUMENT ME!
3591    */
3592   @Override
3593   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3594   {
3595     newTreePanel("AV", "PID", "Average distance tree using PID");
3596   }
3597
3598   /**
3599    * DOCUMENT ME!
3600    *
3601    * @param e
3602    *          DOCUMENT ME!
3603    */
3604   @Override
3605   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3606   {
3607     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3608   }
3609
3610   /**
3611    * DOCUMENT ME!
3612    *
3613    * @param e
3614    *          DOCUMENT ME!
3615    */
3616   @Override
3617   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3618   {
3619     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3620   }
3621
3622   /**
3623    * DOCUMENT ME!
3624    *
3625    * @param e
3626    *          DOCUMENT ME!
3627    */
3628   @Override
3629   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3630   {
3631     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3632   }
3633
3634   /**
3635    * DOCUMENT ME!
3636    *
3637    * @param type
3638    *          DOCUMENT ME!
3639    * @param pwType
3640    *          DOCUMENT ME!
3641    * @param title
3642    *          DOCUMENT ME!
3643    */
3644   void newTreePanel(String type, String pwType, String title)
3645   {
3646     TreePanel tp;
3647
3648     if (viewport.getSelectionGroup() != null
3649             && viewport.getSelectionGroup().getSize() > 0)
3650     {
3651       if (viewport.getSelectionGroup().getSize() < 3)
3652       {
3653         JvOptionPane
3654                 .showMessageDialog(
3655                         Desktop.desktop,
3656                         MessageManager
3657                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3658                         MessageManager
3659                                 .getString("label.not_enough_sequences"),
3660                         JvOptionPane.WARNING_MESSAGE);
3661         return;
3662       }
3663
3664       SequenceGroup sg = viewport.getSelectionGroup();
3665
3666       /* Decide if the selection is a column region */
3667       for (SequenceI _s : sg.getSequences())
3668       {
3669         if (_s.getLength() < sg.getEndRes())
3670         {
3671           JvOptionPane
3672                   .showMessageDialog(
3673                           Desktop.desktop,
3674                           MessageManager
3675                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3676                           MessageManager
3677                                   .getString("label.sequences_selection_not_aligned"),
3678                           JvOptionPane.WARNING_MESSAGE);
3679
3680           return;
3681         }
3682       }
3683
3684       title = title + " on region";
3685       tp = new TreePanel(alignPanel, type, pwType);
3686     }
3687     else
3688     {
3689       // are the visible sequences aligned?
3690       if (!viewport.getAlignment().isAligned(false))
3691       {
3692         JvOptionPane
3693                 .showMessageDialog(
3694                         Desktop.desktop,
3695                         MessageManager
3696                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3697                         MessageManager
3698                                 .getString("label.sequences_not_aligned"),
3699                         JvOptionPane.WARNING_MESSAGE);
3700
3701         return;
3702       }
3703
3704       if (viewport.getAlignment().getHeight() < 2)
3705       {
3706         return;
3707       }
3708
3709       tp = new TreePanel(alignPanel, type, pwType);
3710     }
3711
3712     title += " from ";
3713
3714     if (viewport.viewName != null)
3715     {
3716       title += viewport.viewName + " of ";
3717     }
3718
3719     title += this.title;
3720
3721     Desktop.addInternalFrame(tp, title, 600, 500);
3722   }
3723
3724   /**
3725    * DOCUMENT ME!
3726    *
3727    * @param title
3728    *          DOCUMENT ME!
3729    * @param order
3730    *          DOCUMENT ME!
3731    */
3732   public void addSortByOrderMenuItem(String title,
3733           final AlignmentOrder order)
3734   {
3735     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3736             "action.by_title_param", new Object[] { title }));
3737     sort.add(item);
3738     item.addActionListener(new java.awt.event.ActionListener()
3739     {
3740       @Override
3741       public void actionPerformed(ActionEvent e)
3742       {
3743         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3744
3745         // TODO: JBPNote - have to map order entries to curent SequenceI
3746         // pointers
3747         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3748
3749         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3750                 .getAlignment()));
3751
3752         alignPanel.paintAlignment(true);
3753       }
3754     });
3755   }
3756
3757   /**
3758    * Add a new sort by annotation score menu item
3759    *
3760    * @param sort
3761    *          the menu to add the option to
3762    * @param scoreLabel
3763    *          the label used to retrieve scores for each sequence on the
3764    *          alignment
3765    */
3766   public void addSortByAnnotScoreMenuItem(JMenu sort,
3767           final String scoreLabel)
3768   {
3769     final JMenuItem item = new JMenuItem(scoreLabel);
3770     sort.add(item);
3771     item.addActionListener(new java.awt.event.ActionListener()
3772     {
3773       @Override
3774       public void actionPerformed(ActionEvent e)
3775       {
3776         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3777         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3778                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3779         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3780                 viewport.getAlignment()));
3781         alignPanel.paintAlignment(true);
3782       }
3783     });
3784   }
3785
3786   /**
3787    * last hash for alignment's annotation array - used to minimise cost of
3788    * rebuild.
3789    */
3790   protected int _annotationScoreVectorHash;
3791
3792   /**
3793    * search the alignment and rebuild the sort by annotation score submenu the
3794    * last alignment annotation vector hash is stored to minimize cost of
3795    * rebuilding in subsequence calls.
3796    *
3797    */
3798   @Override
3799   public void buildSortByAnnotationScoresMenu()
3800   {
3801     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3802     {
3803       return;
3804     }
3805
3806     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3807     {
3808       sortByAnnotScore.removeAll();
3809       // almost certainly a quicker way to do this - but we keep it simple
3810       Hashtable scoreSorts = new Hashtable();
3811       AlignmentAnnotation aann[];
3812       for (SequenceI sqa : viewport.getAlignment().getSequences())
3813       {
3814         aann = sqa.getAnnotation();
3815         for (int i = 0; aann != null && i < aann.length; i++)
3816         {
3817           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3818           {
3819             scoreSorts.put(aann[i].label, aann[i].label);
3820           }
3821         }
3822       }
3823       Enumeration labels = scoreSorts.keys();
3824       while (labels.hasMoreElements())
3825       {
3826         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3827                 (String) labels.nextElement());
3828       }
3829       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3830       scoreSorts.clear();
3831
3832       _annotationScoreVectorHash = viewport.getAlignment()
3833               .getAlignmentAnnotation().hashCode();
3834     }
3835   }
3836
3837   /**
3838    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3839    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3840    * call. Listeners are added to remove the menu item when the treePanel is
3841    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3842    * modified.
3843    *
3844    * @param treePanel
3845    *          Displayed tree window.
3846    * @param title
3847    *          SortBy menu item title.
3848    */
3849   @Override
3850   public void buildTreeMenu()
3851   {
3852     calculateTree.removeAll();
3853     // build the calculate menu
3854
3855     for (final String type : new String[] { "NJ", "AV" })
3856     {
3857       String treecalcnm = MessageManager.getString("label.tree_calc_"
3858               + type.toLowerCase());
3859       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3860       {
3861         JMenuItem tm = new JMenuItem();
3862         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3863         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3864                 || sm.isProtein() == !viewport.getAlignment()
3865                         .isNucleotide())
3866         {
3867           String smn = MessageManager.getStringOrReturn(
3868                   "label.score_model_", sm.getName());
3869           final String title = MessageManager.formatMessage(
3870                   "label.treecalc_title", treecalcnm, smn);
3871           tm.setText(title);//
3872           tm.addActionListener(new java.awt.event.ActionListener()
3873           {
3874             @Override
3875             public void actionPerformed(ActionEvent e)
3876             {
3877               newTreePanel(type, pwtype, title);
3878             }
3879           });
3880           calculateTree.add(tm);
3881         }
3882
3883       }
3884     }
3885     sortByTreeMenu.removeAll();
3886
3887     List<Component> comps = PaintRefresher.components.get(viewport
3888             .getSequenceSetId());
3889     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3890     for (Component comp : comps)
3891     {
3892       if (comp instanceof TreePanel)
3893       {
3894         treePanels.add((TreePanel) comp);
3895       }
3896     }
3897
3898     if (treePanels.size() < 1)
3899     {
3900       sortByTreeMenu.setVisible(false);
3901       return;
3902     }
3903
3904     sortByTreeMenu.setVisible(true);
3905
3906     for (final TreePanel tp : treePanels)
3907     {
3908       final JMenuItem item = new JMenuItem(tp.getTitle());
3909       item.addActionListener(new java.awt.event.ActionListener()
3910       {
3911         @Override
3912         public void actionPerformed(ActionEvent e)
3913         {
3914           tp.sortByTree_actionPerformed();
3915           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3916
3917         }
3918       });
3919
3920       sortByTreeMenu.add(item);
3921     }
3922   }
3923
3924   public boolean sortBy(AlignmentOrder alorder, String undoname)
3925   {
3926     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3927     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3928     if (undoname != null)
3929     {
3930       addHistoryItem(new OrderCommand(undoname, oldOrder,
3931               viewport.getAlignment()));
3932     }
3933     alignPanel.paintAlignment(true);
3934     return true;
3935   }
3936
3937   /**
3938    * Work out whether the whole set of sequences or just the selected set will
3939    * be submitted for multiple alignment.
3940    *
3941    */
3942   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3943   {
3944     // Now, check we have enough sequences
3945     AlignmentView msa = null;
3946
3947     if ((viewport.getSelectionGroup() != null)
3948             && (viewport.getSelectionGroup().getSize() > 1))
3949     {
3950       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3951       // some common interface!
3952       /*
3953        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3954        * SequenceI[sz = seqs.getSize(false)];
3955        *
3956        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3957        * seqs.getSequenceAt(i); }
3958        */
3959       msa = viewport.getAlignmentView(true);
3960     }
3961     else if (viewport.getSelectionGroup() != null
3962             && viewport.getSelectionGroup().getSize() == 1)
3963     {
3964       int option = JvOptionPane.showConfirmDialog(this,
3965               MessageManager.getString("warn.oneseq_msainput_selection"),
3966               MessageManager.getString("label.invalid_selection"),
3967               JvOptionPane.OK_CANCEL_OPTION);
3968       if (option == JvOptionPane.OK_OPTION)
3969       {
3970         msa = viewport.getAlignmentView(false);
3971       }
3972     }
3973     else
3974     {
3975       msa = viewport.getAlignmentView(false);
3976     }
3977     return msa;
3978   }
3979
3980   /**
3981    * Decides what is submitted to a secondary structure prediction service: the
3982    * first sequence in the alignment, or in the current selection, or, if the
3983    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3984    * region or the whole alignment. (where the first sequence in the set is the
3985    * one that the prediction will be for).
3986    */
3987   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3988   {
3989     AlignmentView seqs = null;
3990
3991     if ((viewport.getSelectionGroup() != null)
3992             && (viewport.getSelectionGroup().getSize() > 0))
3993     {
3994       seqs = viewport.getAlignmentView(true);
3995     }
3996     else
3997     {
3998       seqs = viewport.getAlignmentView(false);
3999     }
4000     // limit sequences - JBPNote in future - could spawn multiple prediction
4001     // jobs
4002     // TODO: viewport.getAlignment().isAligned is a global state - the local
4003     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4004     if (!viewport.getAlignment().isAligned(false))
4005     {
4006       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4007       // TODO: if seqs.getSequences().length>1 then should really have warned
4008       // user!
4009
4010     }
4011     return seqs;
4012   }
4013
4014   /**
4015    * DOCUMENT ME!
4016    *
4017    * @param e
4018    *          DOCUMENT ME!
4019    */
4020   @Override
4021   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4022   {
4023     // Pick the tree file
4024     JalviewFileChooser chooser = new JalviewFileChooser(
4025             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4026     chooser.setFileView(new JalviewFileView());
4027     chooser.setDialogTitle(MessageManager
4028             .getString("label.select_newick_like_tree_file"));
4029     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4030
4031     int value = chooser.showOpenDialog(null);
4032
4033     if (value == JalviewFileChooser.APPROVE_OPTION)
4034     {
4035       String choice = chooser.getSelectedFile().getPath();
4036       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4037       jalview.io.NewickFile fin = null;
4038       try
4039       {
4040         fin = new NewickFile(choice, DataSourceType.FILE);
4041         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4042       } catch (Exception ex)
4043       {
4044         JvOptionPane
4045                 .showMessageDialog(
4046                         Desktop.desktop,
4047                         ex.getMessage(),
4048                         MessageManager
4049                                 .getString("label.problem_reading_tree_file"),
4050                         JvOptionPane.WARNING_MESSAGE);
4051         ex.printStackTrace();
4052       }
4053       if (fin != null && fin.hasWarningMessage())
4054       {
4055         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4056                 .getWarningMessage(), MessageManager
4057                 .getString("label.possible_problem_with_tree_file"),
4058                 JvOptionPane.WARNING_MESSAGE);
4059       }
4060     }
4061   }
4062
4063   public TreePanel ShowNewickTree(NewickFile nf, String title)
4064   {
4065     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4066   }
4067
4068   public TreePanel ShowNewickTree(NewickFile nf, String title,
4069           AlignmentView input)
4070   {
4071     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4072   }
4073
4074   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4075           int h, int x, int y)
4076   {
4077     return ShowNewickTree(nf, title, null, w, h, x, y);
4078   }
4079
4080   /**
4081    * Add a treeviewer for the tree extracted from a newick file object to the
4082    * current alignment view
4083    *
4084    * @param nf
4085    *          the tree
4086    * @param title
4087    *          tree viewer title
4088    * @param input
4089    *          Associated alignment input data (or null)
4090    * @param w
4091    *          width
4092    * @param h
4093    *          height
4094    * @param x
4095    *          position
4096    * @param y
4097    *          position
4098    * @return TreePanel handle
4099    */
4100   public TreePanel ShowNewickTree(NewickFile nf, String title,
4101           AlignmentView input, int w, int h, int x, int y)
4102   {
4103     TreePanel tp = null;
4104
4105     try
4106     {
4107       nf.parse();
4108
4109       if (nf.getTree() != null)
4110       {
4111         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4112
4113         tp.setSize(w, h);
4114
4115         if (x > 0 && y > 0)
4116         {
4117           tp.setLocation(x, y);
4118         }
4119
4120         Desktop.addInternalFrame(tp, title, w, h);
4121       }
4122     } catch (Exception ex)
4123     {
4124       ex.printStackTrace();
4125     }
4126
4127     return tp;
4128   }
4129
4130   private boolean buildingMenu = false;
4131
4132   /**
4133    * Generates menu items and listener event actions for web service clients
4134    *
4135    */
4136   public void BuildWebServiceMenu()
4137   {
4138     while (buildingMenu)
4139     {
4140       try
4141       {
4142         System.err.println("Waiting for building menu to finish.");
4143         Thread.sleep(10);
4144       } catch (Exception e)
4145       {
4146       }
4147     }
4148     final AlignFrame me = this;
4149     buildingMenu = true;
4150     new Thread(new Runnable()
4151     {
4152       @Override
4153       public void run()
4154       {
4155         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4156         try
4157         {
4158           // System.err.println("Building ws menu again "
4159           // + Thread.currentThread());
4160           // TODO: add support for context dependent disabling of services based
4161           // on
4162           // alignment and current selection
4163           // TODO: add additional serviceHandle parameter to specify abstract
4164           // handler
4165           // class independently of AbstractName
4166           // TODO: add in rediscovery GUI function to restart discoverer
4167           // TODO: group services by location as well as function and/or
4168           // introduce
4169           // object broker mechanism.
4170           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4171           final IProgressIndicator af = me;
4172
4173           /*
4174            * do not i18n these strings - they are hard-coded in class
4175            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4176            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4177            */
4178           final JMenu msawsmenu = new JMenu("Alignment");
4179           final JMenu secstrmenu = new JMenu(
4180                   "Secondary Structure Prediction");
4181           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4182           final JMenu analymenu = new JMenu("Analysis");
4183           final JMenu dismenu = new JMenu("Protein Disorder");
4184           // JAL-940 - only show secondary structure prediction services from
4185           // the legacy server
4186           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4187               // &&
4188           Discoverer.services != null && (Discoverer.services.size() > 0))
4189           {
4190             // TODO: refactor to allow list of AbstractName/Handler bindings to
4191             // be
4192             // stored or retrieved from elsewhere
4193             // No MSAWS used any more:
4194             // Vector msaws = null; // (Vector)
4195             // Discoverer.services.get("MsaWS");
4196             Vector secstrpr = (Vector) Discoverer.services
4197                     .get("SecStrPred");
4198             if (secstrpr != null)
4199             {
4200               // Add any secondary structure prediction services
4201               for (int i = 0, j = secstrpr.size(); i < j; i++)
4202               {
4203                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4204                         .get(i);
4205                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4206                         .getServiceClient(sh);
4207                 int p = secstrmenu.getItemCount();
4208                 impl.attachWSMenuEntry(secstrmenu, me);
4209                 int q = secstrmenu.getItemCount();
4210                 for (int litm = p; litm < q; litm++)
4211                 {
4212                   legacyItems.add(secstrmenu.getItem(litm));
4213                 }
4214               }
4215             }
4216           }
4217
4218           // Add all submenus in the order they should appear on the web
4219           // services menu
4220           wsmenu.add(msawsmenu);
4221           wsmenu.add(secstrmenu);
4222           wsmenu.add(dismenu);
4223           wsmenu.add(analymenu);
4224           // No search services yet
4225           // wsmenu.add(seqsrchmenu);
4226
4227           javax.swing.SwingUtilities.invokeLater(new Runnable()
4228           {
4229             @Override
4230             public void run()
4231             {
4232               try
4233               {
4234                 webService.removeAll();
4235                 // first, add discovered services onto the webservices menu
4236                 if (wsmenu.size() > 0)
4237                 {
4238                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4239                   {
4240                     webService.add(wsmenu.get(i));
4241                   }
4242                 }
4243                 else
4244                 {
4245                   webService.add(me.webServiceNoServices);
4246                 }
4247                 // TODO: move into separate menu builder class.
4248                 boolean new_sspred = false;
4249                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4250                 {
4251                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4252                   if (jws2servs != null)
4253                   {
4254                     if (jws2servs.hasServices())
4255                     {
4256                       jws2servs.attachWSMenuEntry(webService, me);
4257                       for (Jws2Instance sv : jws2servs.getServices())
4258                       {
4259                         if (sv.description.toLowerCase().contains("jpred"))
4260                         {
4261                           for (JMenuItem jmi : legacyItems)
4262                           {
4263                             jmi.setVisible(false);
4264                           }
4265                         }
4266                       }
4267
4268                     }
4269                     if (jws2servs.isRunning())
4270                     {
4271                       JMenuItem tm = new JMenuItem(
4272                               "Still discovering JABA Services");
4273                       tm.setEnabled(false);
4274                       webService.add(tm);
4275                     }
4276                   }
4277                 }
4278                 build_urlServiceMenu(me.webService);
4279                 build_fetchdbmenu(webService);
4280                 for (JMenu item : wsmenu)
4281                 {
4282                   if (item.getItemCount() == 0)
4283                   {
4284                     item.setEnabled(false);
4285                   }
4286                   else
4287                   {
4288                     item.setEnabled(true);
4289                   }
4290                 }
4291               } catch (Exception e)
4292               {
4293                 Cache.log
4294                         .debug("Exception during web service menu building process.",
4295                                 e);
4296               }
4297             }
4298           });
4299         } catch (Exception e)
4300         {
4301         }
4302         buildingMenu = false;
4303       }
4304     }).start();
4305
4306   }
4307
4308   /**
4309    * construct any groupURL type service menu entries.
4310    *
4311    * @param webService
4312    */
4313   private void build_urlServiceMenu(JMenu webService)
4314   {
4315     // TODO: remove this code when 2.7 is released
4316     // DEBUG - alignmentView
4317     /*
4318      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4319      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4320      *
4321      * @Override public void actionPerformed(ActionEvent e) {
4322      * jalview.datamodel.AlignmentView
4323      * .testSelectionViews(af.viewport.getAlignment(),
4324      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4325      *
4326      * }); webService.add(testAlView);
4327      */
4328     // TODO: refactor to RestClient discoverer and merge menu entries for
4329     // rest-style services with other types of analysis/calculation service
4330     // SHmmr test client - still being implemented.
4331     // DEBUG - alignmentView
4332
4333     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4334             .getRestClients())
4335     {
4336       client.attachWSMenuEntry(
4337               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4338               this);
4339     }
4340   }
4341
4342   /**
4343    * Searches the alignment sequences for xRefs and builds the Show
4344    * Cross-References menu (formerly called Show Products), with database
4345    * sources for which cross-references are found (protein sources for a
4346    * nucleotide alignment and vice versa)
4347    *
4348    * @return true if Show Cross-references menu should be enabled
4349    */
4350   public boolean canShowProducts()
4351   {
4352     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4353     AlignmentI dataset = viewport.getAlignment().getDataset();
4354
4355     showProducts.removeAll();
4356     final boolean dna = viewport.getAlignment().isNucleotide();
4357
4358     if (seqs == null || seqs.length == 0)
4359     {
4360       // nothing to see here.
4361       return false;
4362     }
4363
4364     boolean showp = false;
4365     try
4366     {
4367       List<String> ptypes = new CrossRef(seqs, dataset)
4368               .findXrefSourcesForSequences(dna);
4369
4370       for (final String source : ptypes)
4371       {
4372         showp = true;
4373         final AlignFrame af = this;
4374         JMenuItem xtype = new JMenuItem(source);
4375         xtype.addActionListener(new ActionListener()
4376         {
4377           @Override
4378           public void actionPerformed(ActionEvent e)
4379           {
4380             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4381           }
4382         });
4383         showProducts.add(xtype);
4384       }
4385       showProducts.setVisible(showp);
4386       showProducts.setEnabled(showp);
4387     } catch (Exception e)
4388     {
4389       Cache.log
4390               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4391                       e);
4392       return false;
4393     }
4394     return showp;
4395   }
4396
4397   /**
4398    * Finds and displays cross-references for the selected sequences (protein
4399    * products for nucleotide sequences, dna coding sequences for peptides).
4400    *
4401    * @param sel
4402    *          the sequences to show cross-references for
4403    * @param dna
4404    *          true if from a nucleotide alignment (so showing proteins)
4405    * @param source
4406    *          the database to show cross-references for
4407    */
4408   protected void showProductsFor(final SequenceI[] sel,
4409           final boolean _odna, final String source)
4410   {
4411     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4412             .start();
4413   }
4414
4415   /**
4416    * Construct and display a new frame containing the translation of this
4417    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4418    */
4419   @Override
4420   public void showTranslation_actionPerformed(ActionEvent e)
4421   {
4422     AlignmentI al = null;
4423     try
4424     {
4425       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4426
4427       al = dna.translateCdna();
4428     } catch (Exception ex)
4429     {
4430       jalview.bin.Cache.log.error(
4431               "Exception during translation. Please report this !", ex);
4432       final String msg = MessageManager
4433               .getString("label.error_when_translating_sequences_submit_bug_report");
4434       final String errorTitle = MessageManager
4435               .getString("label.implementation_error")
4436               + MessageManager.getString("label.translation_failed");
4437       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4438               JvOptionPane.ERROR_MESSAGE);
4439       return;
4440     }
4441     if (al == null || al.getHeight() == 0)
4442     {
4443       final String msg = MessageManager
4444               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4445       final String errorTitle = MessageManager
4446               .getString("label.translation_failed");
4447       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4448               JvOptionPane.WARNING_MESSAGE);
4449     }
4450     else
4451     {
4452       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4453       af.setFileFormat(this.currentFileFormat);
4454       final String newTitle = MessageManager.formatMessage(
4455               "label.translation_of_params",
4456               new Object[] { this.getTitle() });
4457       af.setTitle(newTitle);
4458       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4459       {
4460         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4461         viewport.openSplitFrame(af, new Alignment(seqs));
4462       }
4463       else
4464       {
4465         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4466                 DEFAULT_HEIGHT);
4467       }
4468     }
4469   }
4470
4471   /**
4472    * Set the file format
4473    *
4474    * @param format
4475    */
4476   public void setFileFormat(FileFormatI format)
4477   {
4478     this.currentFileFormat = format;
4479   }
4480
4481   /**
4482    * Try to load a features file onto the alignment.
4483    *
4484    * @param file
4485    *          contents or path to retrieve file
4486    * @param sourceType
4487    *          access mode of file (see jalview.io.AlignFile)
4488    * @return true if features file was parsed correctly.
4489    */
4490   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4491   {
4492     return avc.parseFeaturesFile(file, sourceType,
4493             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4494
4495   }
4496
4497   @Override
4498   public void refreshFeatureUI(boolean enableIfNecessary)
4499   {
4500     // note - currently this is only still here rather than in the controller
4501     // because of the featureSettings hard reference that is yet to be
4502     // abstracted
4503     if (enableIfNecessary)
4504     {
4505       viewport.setShowSequenceFeatures(true);
4506       showSeqFeatures.setSelected(true);
4507     }
4508
4509   }
4510
4511   @Override
4512   public void dragEnter(DropTargetDragEvent evt)
4513   {
4514   }
4515
4516   @Override
4517   public void dragExit(DropTargetEvent evt)
4518   {
4519   }
4520
4521   @Override
4522   public void dragOver(DropTargetDragEvent evt)
4523   {
4524   }
4525
4526   @Override
4527   public void dropActionChanged(DropTargetDragEvent evt)
4528   {
4529   }
4530
4531   @Override
4532   public void drop(DropTargetDropEvent evt)
4533   {
4534     // JAL-1552 - acceptDrop required before getTransferable call for
4535     // Java's Transferable for native dnd
4536     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4537     Transferable t = evt.getTransferable();
4538     List<String> files = new ArrayList<String>();
4539     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4540
4541     try
4542     {
4543       Desktop.transferFromDropTarget(files, protocols, evt, t);
4544     } catch (Exception e)
4545     {
4546       e.printStackTrace();
4547     }
4548     if (files != null)
4549     {
4550       try
4551       {
4552         // check to see if any of these files have names matching sequences in
4553         // the alignment
4554         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4555                 .getAlignment().getSequencesArray());
4556         /**
4557          * Object[] { String,SequenceI}
4558          */
4559         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4560         ArrayList<String> filesnotmatched = new ArrayList<String>();
4561         for (int i = 0; i < files.size(); i++)
4562         {
4563           String file = files.get(i).toString();
4564           String pdbfn = "";
4565           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4566           if (protocol == DataSourceType.FILE)
4567           {
4568             File fl = new File(file);
4569             pdbfn = fl.getName();
4570           }
4571           else if (protocol == DataSourceType.URL)
4572           {
4573             URL url = new URL(file);
4574             pdbfn = url.getFile();
4575           }
4576           if (pdbfn.length() > 0)
4577           {
4578             // attempt to find a match in the alignment
4579             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4580             int l = 0, c = pdbfn.indexOf(".");
4581             while (mtch == null && c != -1)
4582             {
4583               do
4584               {
4585                 l = c;
4586               } while ((c = pdbfn.indexOf(".", l)) > l);
4587               if (l > -1)
4588               {
4589                 pdbfn = pdbfn.substring(0, l);
4590               }
4591               mtch = idm.findAllIdMatches(pdbfn);
4592             }
4593             if (mtch != null)
4594             {
4595               FileFormatI type = null;
4596               try
4597               {
4598                 type = new IdentifyFile().identify(file, protocol);
4599               } catch (Exception ex)
4600               {
4601                 type = null;
4602               }
4603               if (type != null && type.isStructureFile())
4604               {
4605                 filesmatched.add(new Object[] { file, protocol, mtch });
4606                 continue;
4607               }
4608             }
4609             // File wasn't named like one of the sequences or wasn't a PDB file.
4610             filesnotmatched.add(file);
4611           }
4612         }
4613         int assocfiles = 0;
4614         if (filesmatched.size() > 0)
4615         {
4616           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4617                   || JvOptionPane
4618                           .showConfirmDialog(
4619                                   this,
4620                                   MessageManager
4621                                           .formatMessage(
4622                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4623                                                   new Object[] { Integer
4624                                                           .valueOf(
4625                                                                   filesmatched
4626                                                                           .size())
4627                                                           .toString() }),
4628                                   MessageManager
4629                                           .getString("label.automatically_associate_structure_files_by_name"),
4630                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4631
4632           {
4633             for (Object[] fm : filesmatched)
4634             {
4635               // try and associate
4636               // TODO: may want to set a standard ID naming formalism for
4637               // associating PDB files which have no IDs.
4638               for (SequenceI toassoc : (SequenceI[]) fm[2])
4639               {
4640                 PDBEntry pe = new AssociatePdbFileWithSeq()
4641                         .associatePdbWithSeq((String) fm[0],
4642                                 (DataSourceType) fm[1], toassoc, false,
4643                                 Desktop.instance);
4644                 if (pe != null)
4645                 {
4646                   System.err.println("Associated file : "
4647                           + ((String) fm[0]) + " with "
4648                           + toassoc.getDisplayId(true));
4649                   assocfiles++;
4650                 }
4651               }
4652               alignPanel.paintAlignment(true);
4653             }
4654           }
4655         }
4656         if (filesnotmatched.size() > 0)
4657         {
4658           if (assocfiles > 0
4659                   && (Cache.getDefault(
4660                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4661                           .showConfirmDialog(
4662                                   this,
4663                                   "<html>"
4664                                           + MessageManager
4665                                                   .formatMessage(
4666                                                           "label.ignore_unmatched_dropped_files_info",
4667                                                           new Object[] { Integer
4668                                                                   .valueOf(
4669                                                                           filesnotmatched
4670                                                                                   .size())
4671                                                                   .toString() })
4672                                           + "</html>",
4673                                   MessageManager
4674                                           .getString("label.ignore_unmatched_dropped_files"),
4675                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4676           {
4677             return;
4678           }
4679           for (String fn : filesnotmatched)
4680           {
4681             loadJalviewDataFile(fn, null, null, null);
4682           }
4683
4684         }
4685       } catch (Exception ex)
4686       {
4687         ex.printStackTrace();
4688       }
4689     }
4690   }
4691
4692   /**
4693    * Attempt to load a "dropped" file or URL string: First by testing whether
4694    * it's an Annotation file, then a JNet file, and finally a features file. If
4695    * all are false then the user may have dropped an alignment file onto this
4696    * AlignFrame.
4697    *
4698    * @param file
4699    *          either a filename or a URL string.
4700    */
4701   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4702           FileFormatI format, SequenceI assocSeq)
4703   {
4704     try
4705     {
4706       if (sourceType == null)
4707       {
4708         sourceType = FormatAdapter.checkProtocol(file);
4709       }
4710       // if the file isn't identified, or not positively identified as some
4711       // other filetype (PFAM is default unidentified alignment file type) then
4712       // try to parse as annotation.
4713       boolean isAnnotation = (format == null || FileFormat.Pfam
4714               .equals(format)) ? new AnnotationFile()
4715               .annotateAlignmentView(viewport, file, sourceType) : false;
4716
4717       if (!isAnnotation)
4718       {
4719         // first see if its a T-COFFEE score file
4720         TCoffeeScoreFile tcf = null;
4721         try
4722         {
4723           tcf = new TCoffeeScoreFile(file, sourceType);
4724           if (tcf.isValid())
4725           {
4726             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4727             {
4728               buildColourMenu();
4729               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4730               isAnnotation = true;
4731               statusBar
4732                       .setText(MessageManager
4733                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4734             }
4735             else
4736             {
4737               // some problem - if no warning its probable that the ID matching
4738               // process didn't work
4739               JvOptionPane
4740                       .showMessageDialog(
4741                               Desktop.desktop,
4742                               tcf.getWarningMessage() == null ? MessageManager
4743                                       .getString("label.check_file_matches_sequence_ids_alignment")
4744                                       : tcf.getWarningMessage(),
4745                               MessageManager
4746                                       .getString("label.problem_reading_tcoffee_score_file"),
4747                               JvOptionPane.WARNING_MESSAGE);
4748             }
4749           }
4750           else
4751           {
4752             tcf = null;
4753           }
4754         } catch (Exception x)
4755         {
4756           Cache.log
4757                   .debug("Exception when processing data source as T-COFFEE score file",
4758                           x);
4759           tcf = null;
4760         }
4761         if (tcf == null)
4762         {
4763           // try to see if its a JNet 'concise' style annotation file *before*
4764           // we
4765           // try to parse it as a features file
4766           if (format == null)
4767           {
4768             format = new IdentifyFile().identify(file, sourceType);
4769           }
4770           if (FileFormat.Jnet.equals(format))
4771           {
4772             JPredFile predictions = new JPredFile(file, sourceType);
4773             new JnetAnnotationMaker();
4774             JnetAnnotationMaker.add_annotation(predictions,
4775                     viewport.getAlignment(), 0, false);
4776             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4777             viewport.getAlignment().setSeqrep(repseq);
4778             ColumnSelection cs = new ColumnSelection();
4779             cs.hideInsertionsFor(repseq);
4780             viewport.setColumnSelection(cs);
4781             isAnnotation = true;
4782           }
4783           // else if (IdentifyFile.FeaturesFile.equals(format))
4784           else if (FileFormat.Features.equals(format))
4785           {
4786             if (parseFeaturesFile(file, sourceType))
4787             {
4788               alignPanel.paintAlignment(true);
4789             }
4790           }
4791           else
4792           {
4793             new FileLoader().LoadFile(viewport, file, sourceType, format);
4794           }
4795         }
4796       }
4797       if (isAnnotation)
4798       {
4799
4800         alignPanel.adjustAnnotationHeight();
4801         viewport.updateSequenceIdColours();
4802         buildSortByAnnotationScoresMenu();
4803         alignPanel.paintAlignment(true);
4804       }
4805     } catch (Exception ex)
4806     {
4807       ex.printStackTrace();
4808     } catch (OutOfMemoryError oom)
4809     {
4810       try
4811       {
4812         System.gc();
4813       } catch (Exception x)
4814       {
4815       }
4816       new OOMWarning(
4817               "loading data "
4818                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4819                               : "using " + sourceType + " from " + file)
4820                               : ".")
4821                       + (format != null ? "(parsing as '" + format
4822                               + "' file)" : ""), oom, Desktop.desktop);
4823     }
4824   }
4825
4826   /**
4827    * Method invoked by the ChangeListener on the tabbed pane, in other words
4828    * when a different tabbed pane is selected by the user or programmatically.
4829    */
4830   @Override
4831   public void tabSelectionChanged(int index)
4832   {
4833     if (index > -1)
4834     {
4835       alignPanel = alignPanels.get(index);
4836       viewport = alignPanel.av;
4837       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4838       setMenusFromViewport(viewport);
4839     }
4840
4841     /*
4842      * 'focus' any colour slider that is open to the selected viewport
4843      */
4844     if (viewport.getConservationSelected())
4845     {
4846       SliderPanel.setConservationSlider(alignPanel,
4847               viewport.getResidueShading(), alignPanel.getViewName());
4848     }
4849     else
4850     {
4851       SliderPanel.hideConservationSlider();
4852     }
4853     if (viewport.getAbovePIDThreshold())
4854     {
4855       SliderPanel.setPIDSliderSource(alignPanel,
4856               viewport.getResidueShading(), alignPanel.getViewName());
4857     }
4858     else
4859     {
4860       SliderPanel.hidePIDSlider();
4861     }
4862
4863     /*
4864      * If there is a frame linked to this one in a SplitPane, switch it to the
4865      * same view tab index. No infinite recursion of calls should happen, since
4866      * tabSelectionChanged() should not get invoked on setting the selected
4867      * index to an unchanged value. Guard against setting an invalid index
4868      * before the new view peer tab has been created.
4869      */
4870     final AlignViewportI peer = viewport.getCodingComplement();
4871     if (peer != null)
4872     {
4873       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4874       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4875       {
4876         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4877       }
4878     }
4879   }
4880
4881   /**
4882    * On right mouse click on view tab, prompt for and set new view name.
4883    */
4884   @Override
4885   public void tabbedPane_mousePressed(MouseEvent e)
4886   {
4887     if (e.isPopupTrigger())
4888     {
4889       String msg = MessageManager.getString("label.enter_view_name");
4890       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4891               JvOptionPane.QUESTION_MESSAGE);
4892
4893       if (reply != null)
4894       {
4895         viewport.viewName = reply;
4896         // TODO warn if reply is in getExistingViewNames()?
4897         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4898       }
4899     }
4900   }
4901
4902   public AlignViewport getCurrentView()
4903   {
4904     return viewport;
4905   }
4906
4907   /**
4908    * Open the dialog for regex description parsing.
4909    */
4910   @Override
4911   protected void extractScores_actionPerformed(ActionEvent e)
4912   {
4913     ParseProperties pp = new jalview.analysis.ParseProperties(
4914             viewport.getAlignment());
4915     // TODO: verify regex and introduce GUI dialog for version 2.5
4916     // if (pp.getScoresFromDescription("col", "score column ",
4917     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4918     // true)>0)
4919     if (pp.getScoresFromDescription("description column",
4920             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4921     {
4922       buildSortByAnnotationScoresMenu();
4923     }
4924   }
4925
4926   /*
4927    * (non-Javadoc)
4928    *
4929    * @see
4930    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4931    * )
4932    */
4933   @Override
4934   protected void showDbRefs_actionPerformed(ActionEvent e)
4935   {
4936     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4937   }
4938
4939   /*
4940    * (non-Javadoc)
4941    *
4942    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4943    * ActionEvent)
4944    */
4945   @Override
4946   protected void showNpFeats_actionPerformed(ActionEvent e)
4947   {
4948     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4949   }
4950
4951   /**
4952    * find the viewport amongst the tabs in this alignment frame and close that
4953    * tab
4954    *
4955    * @param av
4956    */
4957   public boolean closeView(AlignViewportI av)
4958   {
4959     if (viewport == av)
4960     {
4961       this.closeMenuItem_actionPerformed(false);
4962       return true;
4963     }
4964     Component[] comp = tabbedPane.getComponents();
4965     for (int i = 0; comp != null && i < comp.length; i++)
4966     {
4967       if (comp[i] instanceof AlignmentPanel)
4968       {
4969         if (((AlignmentPanel) comp[i]).av == av)
4970         {
4971           // close the view.
4972           closeView((AlignmentPanel) comp[i]);
4973           return true;
4974         }
4975       }
4976     }
4977     return false;
4978   }
4979
4980   protected void build_fetchdbmenu(JMenu webService)
4981   {
4982     // Temporary hack - DBRef Fetcher always top level ws entry.
4983     // TODO We probably want to store a sequence database checklist in
4984     // preferences and have checkboxes.. rather than individual sources selected
4985     // here
4986     final JMenu rfetch = new JMenu(
4987             MessageManager.getString("action.fetch_db_references"));
4988     rfetch.setToolTipText(MessageManager
4989             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4990     webService.add(rfetch);
4991
4992     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4993             MessageManager.getString("option.trim_retrieved_seqs"));
4994     trimrs.setToolTipText(MessageManager
4995             .getString("label.trim_retrieved_sequences"));
4996     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4997     trimrs.addActionListener(new ActionListener()
4998     {
4999       @Override
5000       public void actionPerformed(ActionEvent e)
5001       {
5002         trimrs.setSelected(trimrs.isSelected());
5003         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5004                 Boolean.valueOf(trimrs.isSelected()).toString());
5005       };
5006     });
5007     rfetch.add(trimrs);
5008     JMenuItem fetchr = new JMenuItem(
5009             MessageManager.getString("label.standard_databases"));
5010     fetchr.setToolTipText(MessageManager
5011             .getString("label.fetch_embl_uniprot"));
5012     fetchr.addActionListener(new ActionListener()
5013     {
5014
5015       @Override
5016       public void actionPerformed(ActionEvent e)
5017       {
5018         new Thread(new Runnable()
5019         {
5020           @Override
5021           public void run()
5022           {
5023             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5024                     .getAlignment().isNucleotide();
5025             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5026                     .getSequenceSelection(), alignPanel.alignFrame, null,
5027                     alignPanel.alignFrame.featureSettings, isNucleotide);
5028             dbRefFetcher.addListener(new FetchFinishedListenerI()
5029             {
5030               @Override
5031               public void finished()
5032               {
5033                 AlignFrame.this.setMenusForViewport();
5034               }
5035             });
5036             dbRefFetcher.fetchDBRefs(false);
5037           }
5038         }).start();
5039
5040       }
5041
5042     });
5043     rfetch.add(fetchr);
5044     final AlignFrame me = this;
5045     new Thread(new Runnable()
5046     {
5047       @Override
5048       public void run()
5049       {
5050         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5051                 .getSequenceFetcherSingleton(me);
5052         javax.swing.SwingUtilities.invokeLater(new Runnable()
5053         {
5054           @Override
5055           public void run()
5056           {
5057             String[] dbclasses = sf.getOrderedSupportedSources();
5058             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5059             // jalview.util.QuickSort.sort(otherdb, otherdb);
5060             List<DbSourceProxy> otherdb;
5061             JMenu dfetch = new JMenu();
5062             JMenu ifetch = new JMenu();
5063             JMenuItem fetchr = null;
5064             int comp = 0, icomp = 0, mcomp = 15;
5065             String mname = null;
5066             int dbi = 0;
5067             for (String dbclass : dbclasses)
5068             {
5069               otherdb = sf.getSourceProxy(dbclass);
5070               // add a single entry for this class, or submenu allowing 'fetch
5071               // all' or pick one
5072               if (otherdb == null || otherdb.size() < 1)
5073               {
5074                 continue;
5075               }
5076               // List<DbSourceProxy> dbs=otherdb;
5077               // otherdb=new ArrayList<DbSourceProxy>();
5078               // for (DbSourceProxy db:dbs)
5079               // {
5080               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5081               // }
5082               if (mname == null)
5083               {
5084                 mname = "From " + dbclass;
5085               }
5086               if (otherdb.size() == 1)
5087               {
5088                 final DbSourceProxy[] dassource = otherdb
5089                         .toArray(new DbSourceProxy[0]);
5090                 DbSourceProxy src = otherdb.get(0);
5091                 fetchr = new JMenuItem(src.getDbSource());
5092                 fetchr.addActionListener(new ActionListener()
5093                 {
5094
5095                   @Override
5096                   public void actionPerformed(ActionEvent e)
5097                   {
5098                     new Thread(new Runnable()
5099                     {
5100
5101                       @Override
5102                       public void run()
5103                       {
5104                         boolean isNucleotide = alignPanel.alignFrame
5105                                 .getViewport().getAlignment()
5106                                 .isNucleotide();
5107                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5108                                 alignPanel.av.getSequenceSelection(),
5109                                 alignPanel.alignFrame, dassource,
5110                                 alignPanel.alignFrame.featureSettings,
5111                                 isNucleotide);
5112                         dbRefFetcher
5113                                 .addListener(new FetchFinishedListenerI()
5114                                 {
5115                                   @Override
5116                                   public void finished()
5117                                   {
5118                                     AlignFrame.this.setMenusForViewport();
5119                                   }
5120                                 });
5121                         dbRefFetcher.fetchDBRefs(false);
5122                       }
5123                     }).start();
5124                   }
5125
5126                 });
5127                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5128                         MessageManager.formatMessage(
5129                                 "label.fetch_retrieve_from",
5130                                 new Object[] { src.getDbName() })));
5131                 dfetch.add(fetchr);
5132                 comp++;
5133               }
5134               else
5135               {
5136                 final DbSourceProxy[] dassource = otherdb
5137                         .toArray(new DbSourceProxy[0]);
5138                 // fetch all entry
5139                 DbSourceProxy src = otherdb.get(0);
5140                 fetchr = new JMenuItem(MessageManager.formatMessage(
5141                         "label.fetch_all_param",
5142                         new Object[] { src.getDbSource() }));
5143                 fetchr.addActionListener(new ActionListener()
5144                 {
5145                   @Override
5146                   public void actionPerformed(ActionEvent e)
5147                   {
5148                     new Thread(new Runnable()
5149                     {
5150
5151                       @Override
5152                       public void run()
5153                       {
5154                         boolean isNucleotide = alignPanel.alignFrame
5155                                 .getViewport().getAlignment()
5156                                 .isNucleotide();
5157                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5158                                 alignPanel.av.getSequenceSelection(),
5159                                 alignPanel.alignFrame, dassource,
5160                                 alignPanel.alignFrame.featureSettings,
5161                                 isNucleotide);
5162                         dbRefFetcher
5163                                 .addListener(new FetchFinishedListenerI()
5164                                 {
5165                                   @Override
5166                                   public void finished()
5167                                   {
5168                                     AlignFrame.this.setMenusForViewport();
5169                                   }
5170                                 });
5171                         dbRefFetcher.fetchDBRefs(false);
5172                       }
5173                     }).start();
5174                   }
5175                 });
5176
5177                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5178                         MessageManager.formatMessage(
5179                                 "label.fetch_retrieve_from_all_sources",
5180                                 new Object[] {
5181                                     Integer.valueOf(otherdb.size())
5182                                             .toString(), src.getDbSource(),
5183                                     src.getDbName() })));
5184                 dfetch.add(fetchr);
5185                 comp++;
5186                 // and then build the rest of the individual menus
5187                 ifetch = new JMenu(MessageManager.formatMessage(
5188                         "label.source_from_db_source",
5189                         new Object[] { src.getDbSource() }));
5190                 icomp = 0;
5191                 String imname = null;
5192                 int i = 0;
5193                 for (DbSourceProxy sproxy : otherdb)
5194                 {
5195                   String dbname = sproxy.getDbName();
5196                   String sname = dbname.length() > 5 ? dbname.substring(0,
5197                           5) + "..." : dbname;
5198                   String msname = dbname.length() > 10 ? dbname.substring(
5199                           0, 10) + "..." : dbname;
5200                   if (imname == null)
5201                   {
5202                     imname = MessageManager.formatMessage(
5203                             "label.from_msname", new Object[] { sname });
5204                   }
5205                   fetchr = new JMenuItem(msname);
5206                   final DbSourceProxy[] dassrc = { sproxy };
5207                   fetchr.addActionListener(new ActionListener()
5208                   {
5209
5210                     @Override
5211                     public void actionPerformed(ActionEvent e)
5212                     {
5213                       new Thread(new Runnable()
5214                       {
5215
5216                         @Override
5217                         public void run()
5218                         {
5219                           boolean isNucleotide = alignPanel.alignFrame
5220                                   .getViewport().getAlignment()
5221                                   .isNucleotide();
5222                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5223                                   alignPanel.av.getSequenceSelection(),
5224                                   alignPanel.alignFrame, dassrc,
5225                                   alignPanel.alignFrame.featureSettings,
5226                                   isNucleotide);
5227                           dbRefFetcher
5228                                   .addListener(new FetchFinishedListenerI()
5229                                   {
5230                                     @Override
5231                                     public void finished()
5232                                     {
5233                                       AlignFrame.this.setMenusForViewport();
5234                                     }
5235                                   });
5236                           dbRefFetcher.fetchDBRefs(false);
5237                         }
5238                       }).start();
5239                     }
5240
5241                   });
5242                   fetchr.setToolTipText("<html>"
5243                           + MessageManager.formatMessage(
5244                                   "label.fetch_retrieve_from", new Object[]
5245                                   { dbname }));
5246                   ifetch.add(fetchr);
5247                   ++i;
5248                   if (++icomp >= mcomp || i == (otherdb.size()))
5249                   {
5250                     ifetch.setText(MessageManager.formatMessage(
5251                             "label.source_to_target", imname, sname));
5252                     dfetch.add(ifetch);
5253                     ifetch = new JMenu();
5254                     imname = null;
5255                     icomp = 0;
5256                     comp++;
5257                   }
5258                 }
5259               }
5260               ++dbi;
5261               if (comp >= mcomp || dbi >= (dbclasses.length))
5262               {
5263                 dfetch.setText(MessageManager.formatMessage(
5264                         "label.source_to_target", mname, dbclass));
5265                 rfetch.add(dfetch);
5266                 dfetch = new JMenu();
5267                 mname = null;
5268                 comp = 0;
5269               }
5270             }
5271           }
5272         });
5273       }
5274     }).start();
5275
5276   }
5277
5278   /**
5279    * Left justify the whole alignment.
5280    */
5281   @Override
5282   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5283   {
5284     AlignmentI al = viewport.getAlignment();
5285     al.justify(false);
5286     viewport.firePropertyChange("alignment", null, al);
5287   }
5288
5289   /**
5290    * Right justify the whole alignment.
5291    */
5292   @Override
5293   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5294   {
5295     AlignmentI al = viewport.getAlignment();
5296     al.justify(true);
5297     viewport.firePropertyChange("alignment", null, al);
5298   }
5299
5300   @Override
5301   public void setShowSeqFeatures(boolean b)
5302   {
5303     showSeqFeatures.setSelected(b);
5304     viewport.setShowSequenceFeatures(b);
5305   }
5306
5307   /*
5308    * (non-Javadoc)
5309    *
5310    * @see
5311    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5312    * awt.event.ActionEvent)
5313    */
5314   @Override
5315   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5316   {
5317     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5318     alignPanel.paintAlignment(true);
5319   }
5320
5321   /*
5322    * (non-Javadoc)
5323    *
5324    * @see
5325    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5326    * .ActionEvent)
5327    */
5328   @Override
5329   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5330   {
5331     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5332     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5333
5334   }
5335
5336   /*
5337    * (non-Javadoc)
5338    *
5339    * @see
5340    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5341    * .event.ActionEvent)
5342    */
5343   @Override
5344   protected void showGroupConservation_actionPerformed(ActionEvent e)
5345   {
5346     viewport.setShowGroupConservation(showGroupConservation.getState());
5347     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5348   }
5349
5350   /*
5351    * (non-Javadoc)
5352    *
5353    * @see
5354    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5355    * .event.ActionEvent)
5356    */
5357   @Override
5358   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5359   {
5360     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5361     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5362   }
5363
5364   /*
5365    * (non-Javadoc)
5366    *
5367    * @see
5368    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5369    * .event.ActionEvent)
5370    */
5371   @Override
5372   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5373   {
5374     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5375     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5376   }
5377
5378   @Override
5379   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5380   {
5381     showSequenceLogo.setState(true);
5382     viewport.setShowSequenceLogo(true);
5383     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5384     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5385   }
5386
5387   @Override
5388   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5389   {
5390     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5391   }
5392
5393   /*
5394    * (non-Javadoc)
5395    *
5396    * @see
5397    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5398    * .event.ActionEvent)
5399    */
5400   @Override
5401   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5402   {
5403     if (avc.makeGroupsFromSelection())
5404     {
5405       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5406       alignPanel.updateAnnotation();
5407       alignPanel.paintAlignment(true);
5408     }
5409   }
5410
5411   public void clearAlignmentSeqRep()
5412   {
5413     // TODO refactor alignmentseqrep to controller
5414     if (viewport.getAlignment().hasSeqrep())
5415     {
5416       viewport.getAlignment().setSeqrep(null);
5417       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5418       alignPanel.updateAnnotation();
5419       alignPanel.paintAlignment(true);
5420     }
5421   }
5422
5423   @Override
5424   protected void createGroup_actionPerformed(ActionEvent e)
5425   {
5426     if (avc.createGroup())
5427     {
5428       alignPanel.alignmentChanged();
5429     }
5430   }
5431
5432   @Override
5433   protected void unGroup_actionPerformed(ActionEvent e)
5434   {
5435     if (avc.unGroup())
5436     {
5437       alignPanel.alignmentChanged();
5438     }
5439   }
5440
5441   /**
5442    * make the given alignmentPanel the currently selected tab
5443    *
5444    * @param alignmentPanel
5445    */
5446   public void setDisplayedView(AlignmentPanel alignmentPanel)
5447   {
5448     if (!viewport.getSequenceSetId().equals(
5449             alignmentPanel.av.getSequenceSetId()))
5450     {
5451       throw new Error(
5452               MessageManager
5453                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5454     }
5455     if (tabbedPane != null
5456             && tabbedPane.getTabCount() > 0
5457             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5458                     .getSelectedIndex())
5459     {
5460       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5461     }
5462   }
5463
5464   /**
5465    * Action on selection of menu options to Show or Hide annotations.
5466    *
5467    * @param visible
5468    * @param forSequences
5469    *          update sequence-related annotations
5470    * @param forAlignment
5471    *          update non-sequence-related annotations
5472    */
5473   @Override
5474   protected void setAnnotationsVisibility(boolean visible,
5475           boolean forSequences, boolean forAlignment)
5476   {
5477     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5478             .getAlignmentAnnotation();
5479     if (anns == null)
5480     {
5481       return;
5482     }
5483     for (AlignmentAnnotation aa : anns)
5484     {
5485       /*
5486        * don't display non-positional annotations on an alignment
5487        */
5488       if (aa.annotations == null)
5489       {
5490         continue;
5491       }
5492       boolean apply = (aa.sequenceRef == null && forAlignment)
5493               || (aa.sequenceRef != null && forSequences);
5494       if (apply)
5495       {
5496         aa.visible = visible;
5497       }
5498     }
5499     alignPanel.validateAnnotationDimensions(true);
5500     alignPanel.alignmentChanged();
5501   }
5502
5503   /**
5504    * Store selected annotation sort order for the view and repaint.
5505    */
5506   @Override
5507   protected void sortAnnotations_actionPerformed()
5508   {
5509     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5510     this.alignPanel.av
5511             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5512     alignPanel.paintAlignment(true);
5513   }
5514
5515   /**
5516    *
5517    * @return alignment panels in this alignment frame
5518    */
5519   public List<? extends AlignmentViewPanel> getAlignPanels()
5520   {
5521     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5522   }
5523
5524   /**
5525    * Open a new alignment window, with the cDNA associated with this (protein)
5526    * alignment, aligned as is the protein.
5527    */
5528   protected void viewAsCdna_actionPerformed()
5529   {
5530     // TODO no longer a menu action - refactor as required
5531     final AlignmentI alignment = getViewport().getAlignment();
5532     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5533     if (mappings == null)
5534     {
5535       return;
5536     }
5537     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5538     for (SequenceI aaSeq : alignment.getSequences())
5539     {
5540       for (AlignedCodonFrame acf : mappings)
5541       {
5542         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5543         if (dnaSeq != null)
5544         {
5545           /*
5546            * There is a cDNA mapping for this protein sequence - add to new
5547            * alignment. It will share the same dataset sequence as other mapped
5548            * cDNA (no new mappings need to be created).
5549            */
5550           final Sequence newSeq = new Sequence(dnaSeq);
5551           newSeq.setDatasetSequence(dnaSeq);
5552           cdnaSeqs.add(newSeq);
5553         }
5554       }
5555     }
5556     if (cdnaSeqs.size() == 0)
5557     {
5558       // show a warning dialog no mapped cDNA
5559       return;
5560     }
5561     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5562             .size()]));
5563     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5564             AlignFrame.DEFAULT_HEIGHT);
5565     cdna.alignAs(alignment);
5566     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5567             + this.title;
5568     Desktop.addInternalFrame(alignFrame, newtitle,
5569             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5570   }
5571
5572   /**
5573    * Set visibility of dna/protein complement view (available when shown in a
5574    * split frame).
5575    *
5576    * @param show
5577    */
5578   @Override
5579   protected void showComplement_actionPerformed(boolean show)
5580   {
5581     SplitContainerI sf = getSplitViewContainer();
5582     if (sf != null)
5583     {
5584       sf.setComplementVisible(this, show);
5585     }
5586   }
5587
5588   /**
5589    * Generate the reverse (optionally complemented) of the selected sequences,
5590    * and add them to the alignment
5591    */
5592   @Override
5593   protected void showReverse_actionPerformed(boolean complement)
5594   {
5595     AlignmentI al = null;
5596     try
5597     {
5598       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5599       al = dna.reverseCdna(complement);
5600       viewport.addAlignment(al, "");
5601       addHistoryItem(new EditCommand(
5602               MessageManager.getString("label.add_sequences"),
5603               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5604               viewport.getAlignment()));
5605     } catch (Exception ex)
5606     {
5607       System.err.println(ex.getMessage());
5608       return;
5609     }
5610   }
5611
5612   /**
5613    * Try to run a script in the Groovy console, having first ensured that this
5614    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5615    * be targeted at this alignment.
5616    */
5617   @Override
5618   protected void runGroovy_actionPerformed()
5619   {
5620     Jalview.setCurrentAlignFrame(this);
5621     groovy.ui.Console console = Desktop.getGroovyConsole();
5622     if (console != null)
5623     {
5624       try
5625       {
5626         console.runScript();
5627       } catch (Exception ex)
5628       {
5629         System.err.println((ex.toString()));
5630         JvOptionPane
5631                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5632                         .getString("label.couldnt_run_groovy_script"),
5633                         MessageManager
5634                                 .getString("label.groovy_support_failed"),
5635                         JvOptionPane.ERROR_MESSAGE);
5636       }
5637     }
5638     else
5639     {
5640       System.err.println("Can't run Groovy script as console not found");
5641     }
5642   }
5643
5644   /**
5645    * Hides columns containing (or not containing) a specified feature, provided
5646    * that would not leave all columns hidden
5647    *
5648    * @param featureType
5649    * @param columnsContaining
5650    * @return
5651    */
5652   public boolean hideFeatureColumns(String featureType,
5653           boolean columnsContaining)
5654   {
5655     boolean notForHiding = avc.markColumnsContainingFeatures(
5656             columnsContaining, false, false, featureType);
5657     if (notForHiding)
5658     {
5659       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5660               false, featureType))
5661       {
5662         getViewport().hideSelectedColumns();
5663         return true;
5664       }
5665     }
5666     return false;
5667   }
5668
5669   @Override
5670   protected void selectHighlightedColumns_actionPerformed(
5671           ActionEvent actionEvent)
5672   {
5673     // include key modifier check in case user selects from menu
5674     avc.markHighlightedColumns(
5675             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5676             true,
5677             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5678   }
5679
5680   /**
5681    * Rebuilds the Colour menu, including any user-defined colours which have
5682    * been loaded either on startup or during the session
5683    */
5684   public void buildColourMenu()
5685   {
5686     colourMenu.removeAll();
5687
5688     colourMenu.add(applyToAllGroups);
5689     colourMenu.add(textColour);
5690     colourMenu.addSeparator();
5691
5692     ColourMenuHelper.addMenuItems(colourMenu, this,
5693             viewport.getAlignment(), false);
5694
5695     colourMenu.addSeparator();
5696     colourMenu.add(conservationMenuItem);
5697     colourMenu.add(modifyConservation);
5698     colourMenu.add(abovePIDThreshold);
5699     colourMenu.add(modifyPID);
5700     colourMenu.add(annotationColour);
5701
5702     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5703     String schemeName = colourScheme == null ? null : colourScheme
5704             .getSchemeName();
5705
5706     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5707   }
5708
5709   /**
5710    * Disable inapplicable items in the Select menu when it is clicked
5711    */
5712   @Override
5713   protected void configureSelectMenu()
5714   {
5715     createGroup.setEnabled(false);
5716     unGroup.setEnabled(false);
5717     SequenceGroup sg = viewport.getSelectionGroup();
5718     if (sg != null)
5719     {
5720       List<SequenceGroup> groups = viewport.getAlignment().getGroups();
5721       createGroup.setEnabled(groups == null || !groups.contains(sg));
5722       unGroup.setEnabled(groups != null && groups.contains(sg));
5723     }
5724   }
5725 }
5726
5727 class PrintThread extends Thread
5728 {
5729   AlignmentPanel ap;
5730
5731   public PrintThread(AlignmentPanel ap)
5732   {
5733     this.ap = ap;
5734   }
5735
5736   static PageFormat pf;
5737
5738   @Override
5739   public void run()
5740   {
5741     PrinterJob printJob = PrinterJob.getPrinterJob();
5742
5743     if (pf != null)
5744     {
5745       printJob.setPrintable(ap, pf);
5746     }
5747     else
5748     {
5749       printJob.setPrintable(ap);
5750     }
5751
5752     if (printJob.printDialog())
5753     {
5754       try
5755       {
5756         printJob.print();
5757       } catch (Exception PrintException)
5758       {
5759         PrintException.printStackTrace();
5760       }
5761     }
5762   }
5763 }