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.ws.DBRefFetcher;
  90 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  91 import jalview.ws.jws1.Discoverer;
  92 import jalview.ws.jws2.Jws2Discoverer;
  93 import jalview.ws.jws2.jabaws2.Jws2Instance;
  94 import jalview.ws.seqfetcher.DbSourceProxy;
  95
  96 import java.awt.BorderLayout;
  97 import java.awt.Component;
  98 import java.awt.Rectangle;
  99 import java.awt.Toolkit;
 100 import java.awt.datatransfer.Clipboard;
 101 import java.awt.datatransfer.DataFlavor;
 102 import java.awt.datatransfer.StringSelection;
 103 import java.awt.datatransfer.Transferable;
 104 import java.awt.dnd.DnDConstants;
 105 import java.awt.dnd.DropTargetDragEvent;
 106 import java.awt.dnd.DropTargetDropEvent;
 107 import java.awt.dnd.DropTargetEvent;
 108 import java.awt.dnd.DropTargetListener;
 109 import java.awt.event.ActionEvent;
 110 import java.awt.event.ActionListener;
 111 import java.awt.event.FocusAdapter;
 112 import java.awt.event.FocusEvent;
 113 import java.awt.event.ItemEvent;
 114 import java.awt.event.ItemListener;
 115 import java.awt.event.KeyAdapter;
 116 import java.awt.event.KeyEvent;
 117 import java.awt.event.MouseEvent;
 118 import java.awt.print.PageFormat;
 119 import java.awt.print.PrinterJob;
 120 import java.beans.PropertyChangeEvent;
 121 import java.io.File;
 122 import java.io.FileWriter;
 123 import java.io.PrintWriter;
 124 import java.net.URL;
 125 import java.util.ArrayList;
 126 import java.util.Arrays;
 127 import java.util.Deque;
 128 import java.util.Enumeration;
 129 import java.util.Hashtable;
 130 import java.util.List;
 131 import java.util.Vector;
 132
 133 import javax.swing.JCheckBoxMenuItem;
 134 import javax.swing.JEditorPane;
 135 import javax.swing.JInternalFrame;
 136 import javax.swing.JLayeredPane;
 137 import javax.swing.JMenu;
 138 import javax.swing.JMenuItem;
 139 import javax.swing.JScrollPane;
 140 import javax.swing.SwingUtilities;
 141
 142 /**
 143  * DOCUMENT ME!
 144  *
 145  * @author $author$
 146  * @version $Revision$
 147  */
 148 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 149         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 150 {
 151
 152   public static final int DEFAULT_WIDTH = 700;
 153
 154   public static final int DEFAULT_HEIGHT = 500;
 155
 156   /*
 157    * The currently displayed panel (selected tabbed view if more than one)
 158    */
 159   public AlignmentPanel alignPanel;
 160
 161   AlignViewport viewport;
 162
 163   public AlignViewControllerI avc;
 164
 165   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 166
 167   /**
 168    * Last format used to load or save alignments in this window
 169    */
 170   FileFormatI currentFileFormat = null;
 171
 172   /**
 173    * Current filename for this alignment
 174    */
 175   String fileName = null;
 176
 177   /**
 178    * Creates a new AlignFrame object with specific width and height.
 179    *
 180    * @param al
 181    * @param width
 182    * @param height
 183    */
 184   public AlignFrame(AlignmentI al, int width, int height)
 185   {
 186     this(al, null, width, height);
 187   }
 188
 189   /**
 190    * Creates a new AlignFrame object with specific width, height and
 191    * sequenceSetId
 192    *
 193    * @param al
 194    * @param width
 195    * @param height
 196    * @param sequenceSetId
 197    */
 198   public AlignFrame(AlignmentI al, int width, int height,
 199           String sequenceSetId)
 200   {
 201     this(al, null, width, height, sequenceSetId);
 202   }
 203
 204   /**
 205    * Creates a new AlignFrame object with specific width, height and
 206    * sequenceSetId
 207    *
 208    * @param al
 209    * @param width
 210    * @param height
 211    * @param sequenceSetId
 212    * @param viewId
 213    */
 214   public AlignFrame(AlignmentI al, int width, int height,
 215           String sequenceSetId, String viewId)
 216   {
 217     this(al, null, width, height, sequenceSetId, viewId);
 218   }
 219
 220   /**
 221    * new alignment window with hidden columns
 222    *
 223    * @param al
 224    *          AlignmentI
 225    * @param hiddenColumns
 226    *          ColumnSelection or null
 227    * @param width
 228    *          Width of alignment frame
 229    * @param height
 230    *          height of frame.
 231    */
 232   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 233           int width, int height)
 234   {
 235     this(al, hiddenColumns, width, height, null);
 236   }
 237
 238   /**
 239    * Create alignment frame for al with hiddenColumns, a specific width and
 240    * height, and specific sequenceId
 241    *
 242    * @param al
 243    * @param hiddenColumns
 244    * @param width
 245    * @param height
 246    * @param sequenceSetId
 247    *          (may be null)
 248    */
 249   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 250           int width, int height, String sequenceSetId)
 251   {
 252     this(al, hiddenColumns, width, height, sequenceSetId, null);
 253   }
 254
 255   /**
 256    * Create alignment frame for al with hiddenColumns, a specific width and
 257    * height, and specific sequenceId
 258    *
 259    * @param al
 260    * @param hiddenColumns
 261    * @param width
 262    * @param height
 263    * @param sequenceSetId
 264    *          (may be null)
 265    * @param viewId
 266    *          (may be null)
 267    */
 268   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 269           int width, int height, String sequenceSetId, String viewId)
 270   {
 271     setSize(width, height);
 272
 273     if (al.getDataset() == null)
 274     {
 275       al.setDataset(null);
 276     }
 277
 278     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 279
 280     alignPanel = new AlignmentPanel(this, viewport);
 281
 282     addAlignmentPanel(alignPanel, true);
 283     init();
 284   }
 285
 286   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 287           ColumnSelection hiddenColumns, int width, int height)
 288   {
 289     setSize(width, height);
 290
 291     if (al.getDataset() == null)
 292     {
 293       al.setDataset(null);
 294     }
 295
 296     viewport = new AlignViewport(al, hiddenColumns);
 297
 298     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 299     {
 300       viewport.hideSequence(hiddenSeqs);
 301     }
 302     alignPanel = new AlignmentPanel(this, viewport);
 303     addAlignmentPanel(alignPanel, true);
 304     init();
 305   }
 306
 307   /**
 308    * Make a new AlignFrame from existing alignmentPanels
 309    *
 310    * @param ap
 311    *          AlignmentPanel
 312    * @param av
 313    *          AlignViewport
 314    */
 315   public AlignFrame(AlignmentPanel ap)
 316   {
 317     viewport = ap.av;
 318     alignPanel = ap;
 319     addAlignmentPanel(ap, false);
 320     init();
 321   }
 322
 323   /**
 324    * initalise the alignframe from the underlying viewport data and the
 325    * configurations
 326    */
 327   void init()
 328   {
 329     if (!Jalview.isHeadlessMode())
 330     {
 331       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 332     }
 333
 334     avc = new jalview.controller.AlignViewController(this, viewport,
 335             alignPanel);
 336     if (viewport.getAlignmentConservationAnnotation() == null)
 337     {
 338       // BLOSUM62Colour.setEnabled(false);
 339       conservationMenuItem.setEnabled(false);
 340       modifyConservation.setEnabled(false);
 341       // PIDColour.setEnabled(false);
 342       // abovePIDThreshold.setEnabled(false);
 343       // modifyPID.setEnabled(false);
 344     }
 345
 346     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 347             "No sort");
 348
 349     if (sortby.equals("Id"))
 350     {
 351       sortIDMenuItem_actionPerformed(null);
 352     }
 353     else if (sortby.equals("Pairwise Identity"))
 354     {
 355       sortPairwiseMenuItem_actionPerformed(null);
 356     }
 357
 358     this.alignPanel.av
 359             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 360
 361     setMenusFromViewport(viewport);
 362     buildSortByAnnotationScoresMenu();
 363     buildTreeMenu();
 364     buildColourMenu();
 365
 366     if (Desktop.desktop != null)
 367     {
 368       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 369       addServiceListeners();
 370       setGUINucleotide();
 371     }
 372
 373     if (viewport.getWrapAlignment())
 374     {
 375       wrapMenuItem_actionPerformed(null);
 376     }
 377
 378     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 379     {
 380       this.overviewMenuItem_actionPerformed(null);
 381     }
 382
 383     addKeyListener();
 384
 385     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 386     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 387     final String menuLabel = MessageManager
 388             .getString("label.copy_format_from");
 389     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 390             new ViewSetProvider()
 391             {
 392
 393               @Override
 394               public AlignmentPanel[] getAllAlignmentPanels()
 395               {
 396                 origview.clear();
 397                 origview.add(alignPanel);
 398                 // make an array of all alignment panels except for this one
 399                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 400                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 401                 aps.remove(AlignFrame.this.alignPanel);
 402                 return aps.toArray(new AlignmentPanel[aps.size()]);
 403               }
 404             }, selviews, new ItemListener()
 405             {
 406
 407               @Override
 408               public void itemStateChanged(ItemEvent e)
 409               {
 410                 if (origview.size() > 0)
 411                 {
 412                   final AlignmentPanel ap = origview.get(0);
 413
 414                   /*
 415                    * Copy the ViewStyle of the selected panel to 'this one'.
 416                    * Don't change value of 'scaleProteinAsCdna' unless copying
 417                    * from a SplitFrame.
 418                    */
 419                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 420                           .getViewStyle();
 421                   boolean fromSplitFrame = selviews.get(0)
 422                           .getAlignViewport().getCodingComplement() != null;
 423                   if (!fromSplitFrame)
 424                   {
 425                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 426                             .getViewStyle().isScaleProteinAsCdna());
 427                   }
 428                   ap.getAlignViewport().setViewStyle(vs);
 429
 430                   /*
 431                    * Also rescale ViewStyle of SplitFrame complement if there is
 432                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 433                    * the whole ViewStyle (allow cDNA protein to have different
 434                    * fonts)
 435                    */
 436                   AlignViewportI complement = ap.getAlignViewport()
 437                           .getCodingComplement();
 438                   if (complement != null && vs.isScaleProteinAsCdna())
 439                   {
 440                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 441                     ((SplitFrame) af.getSplitViewContainer())
 442                             .adjustLayout();
 443                     af.setMenusForViewport();
 444                   }
 445
 446                   ap.updateLayout();
 447                   ap.setSelected(true);
 448                   ap.alignFrame.setMenusForViewport();
 449
 450                 }
 451               }
 452             });
 453     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 454             .indexOf("devel") > -1
 455             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 456                     .indexOf("test") > -1)
 457     {
 458       formatMenu.add(vsel);
 459     }
 460     addFocusListener(new FocusAdapter()
 461     {
 462       @Override
 463       public void focusGained(FocusEvent e)
 464       {
 465         Jalview.setCurrentAlignFrame(AlignFrame.this);
 466       }
 467     });
 468
 469   }
 470
 471   /**
 472    * Change the filename and format for the alignment, and enable the 'reload'
 473    * button functionality.
 474    *
 475    * @param file
 476    *          valid filename
 477    * @param format
 478    *          format of file
 479    */
 480   public void setFileName(String file, FileFormatI format)
 481   {
 482     fileName = file;
 483     setFileFormat(format);
 484     reload.setEnabled(true);
 485   }
 486
 487   /**
 488    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 489    * events
 490    */
 491   void addKeyListener()
 492   {
 493     addKeyListener(new KeyAdapter()
 494     {
 495       @Override
 496       public void keyPressed(KeyEvent evt)
 497       {
 498         if (viewport.cursorMode
 499                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 500                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 501                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 502                 && Character.isDigit(evt.getKeyChar()))
 503         {
 504           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 505         }
 506
 507         switch (evt.getKeyCode())
 508         {
 509
 510         case 27: // escape key
 511           deselectAllSequenceMenuItem_actionPerformed(null);
 512
 513           break;
 514
 515         case KeyEvent.VK_DOWN:
 516           if (evt.isAltDown() || !viewport.cursorMode)
 517           {
 518             moveSelectedSequences(false);
 519           }
 520           if (viewport.cursorMode)
 521           {
 522             alignPanel.getSeqPanel().moveCursor(0, 1);
 523           }
 524           break;
 525
 526         case KeyEvent.VK_UP:
 527           if (evt.isAltDown() || !viewport.cursorMode)
 528           {
 529             moveSelectedSequences(true);
 530           }
 531           if (viewport.cursorMode)
 532           {
 533             alignPanel.getSeqPanel().moveCursor(0, -1);
 534           }
 535
 536           break;
 537
 538         case KeyEvent.VK_LEFT:
 539           if (evt.isAltDown() || !viewport.cursorMode)
 540           {
 541             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 542           }
 543           else
 544           {
 545             alignPanel.getSeqPanel().moveCursor(-1, 0);
 546           }
 547
 548           break;
 549
 550         case KeyEvent.VK_RIGHT:
 551           if (evt.isAltDown() || !viewport.cursorMode)
 552           {
 553             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 554           }
 555           else
 556           {
 557             alignPanel.getSeqPanel().moveCursor(1, 0);
 558           }
 559           break;
 560
 561         case KeyEvent.VK_SPACE:
 562           if (viewport.cursorMode)
 563           {
 564             alignPanel.getSeqPanel().insertGapAtCursor(
 565                     evt.isControlDown() || evt.isShiftDown()
 566                             || evt.isAltDown());
 567           }
 568           break;
 569
 570         // case KeyEvent.VK_A:
 571         // if (viewport.cursorMode)
 572         // {
 573         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 574         // //System.out.println("A");
 575         // }
 576         // break;
 577         /*
 578          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 579          * System.out.println("closing bracket"); } break;
 580          */
 581         case KeyEvent.VK_DELETE:
 582         case KeyEvent.VK_BACK_SPACE:
 583           if (!viewport.cursorMode)
 584           {
 585             cut_actionPerformed(null);
 586           }
 587           else
 588           {
 589             alignPanel.getSeqPanel().deleteGapAtCursor(
 590                     evt.isControlDown() || evt.isShiftDown()
 591                             || evt.isAltDown());
 592           }
 593
 594           break;
 595
 596         case KeyEvent.VK_S:
 597           if (viewport.cursorMode)
 598           {
 599             alignPanel.getSeqPanel().setCursorRow();
 600           }
 601           break;
 602         case KeyEvent.VK_C:
 603           if (viewport.cursorMode && !evt.isControlDown())
 604           {
 605             alignPanel.getSeqPanel().setCursorColumn();
 606           }
 607           break;
 608         case KeyEvent.VK_P:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().setCursorPosition();
 612           }
 613           break;
 614
 615         case KeyEvent.VK_ENTER:
 616         case KeyEvent.VK_COMMA:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorRowAndColumn();
 620           }
 621           break;
 622
 623         case KeyEvent.VK_Q:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 627           }
 628           break;
 629         case KeyEvent.VK_M:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 633           }
 634           break;
 635
 636         case KeyEvent.VK_F2:
 637           viewport.cursorMode = !viewport.cursorMode;
 638           statusBar.setText(MessageManager.formatMessage(
 639                   "label.keyboard_editing_mode",
 640                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 644             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 645           }
 646           alignPanel.getSeqPanel().seqCanvas.repaint();
 647           break;
 648
 649         case KeyEvent.VK_F1:
 650           try
 651           {
 652             Help.showHelpWindow();
 653           } catch (Exception ex)
 654           {
 655             ex.printStackTrace();
 656           }
 657           break;
 658         case KeyEvent.VK_H:
 659         {
 660           boolean toggleSeqs = !evt.isControlDown();
 661           boolean toggleCols = !evt.isShiftDown();
 662           toggleHiddenRegions(toggleSeqs, toggleCols);
 663           break;
 664         }
 665         case KeyEvent.VK_B:
 666         {
 667           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 668           boolean modifyExisting = true; // always modify, don't clear
 669                                          // evt.isShiftDown();
 670           boolean invertHighlighted = evt.isAltDown();
 671           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 672                   toggleSel);
 673           break;
 674         }
 675         case KeyEvent.VK_PAGE_UP:
 676           if (viewport.getWrapAlignment())
 677           {
 678             alignPanel.scrollUp(true);
 679           }
 680           else
 681           {
 682             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 683                     - viewport.endSeq + viewport.startSeq);
 684           }
 685           break;
 686         case KeyEvent.VK_PAGE_DOWN:
 687           if (viewport.getWrapAlignment())
 688           {
 689             alignPanel.scrollUp(false);
 690           }
 691           else
 692           {
 693             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 694                     + viewport.endSeq - viewport.startSeq);
 695           }
 696           break;
 697         }
 698       }
 699
 700       @Override
 701       public void keyReleased(KeyEvent evt)
 702       {
 703         switch (evt.getKeyCode())
 704         {
 705         case KeyEvent.VK_LEFT:
 706           if (evt.isAltDown() || !viewport.cursorMode)
 707           {
 708             viewport.firePropertyChange("alignment", null, viewport
 709                     .getAlignment().getSequences());
 710           }
 711           break;
 712
 713         case KeyEvent.VK_RIGHT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null, viewport
 717                     .getAlignment().getSequences());
 718           }
 719           break;
 720         }
 721       }
 722     });
 723   }
 724
 725   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 726   {
 727     ap.alignFrame = this;
 728     avc = new jalview.controller.AlignViewController(this, viewport,
 729             alignPanel);
 730
 731     alignPanels.add(ap);
 732
 733     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 734
 735     int aSize = alignPanels.size();
 736
 737     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 738
 739     if (aSize == 1 && ap.av.viewName == null)
 740     {
 741       this.getContentPane().add(ap, BorderLayout.CENTER);
 742     }
 743     else
 744     {
 745       if (aSize == 2)
 746       {
 747         setInitialTabVisible();
 748       }
 749
 750       expandViews.setEnabled(true);
 751       gatherViews.setEnabled(true);
 752       tabbedPane.addTab(ap.av.viewName, ap);
 753
 754       ap.setVisible(false);
 755     }
 756
 757     if (newPanel)
 758     {
 759       if (ap.av.isPadGaps())
 760       {
 761         ap.av.getAlignment().padGaps();
 762       }
 763       ap.av.updateConservation(ap);
 764       ap.av.updateConsensus(ap);
 765       ap.av.updateStrucConsensus(ap);
 766     }
 767   }
 768
 769   public void setInitialTabVisible()
 770   {
 771     expandViews.setEnabled(true);
 772     gatherViews.setEnabled(true);
 773     tabbedPane.setVisible(true);
 774     AlignmentPanel first = alignPanels.get(0);
 775     tabbedPane.addTab(first.av.viewName, first);
 776     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 777   }
 778
 779   public AlignViewport getViewport()
 780   {
 781     return viewport;
 782   }
 783
 784   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 785   private void addServiceListeners()
 786   {
 787     final java.beans.PropertyChangeListener thisListener;
 788     Desktop.instance.addJalviewPropertyChangeListener("services",
 789             thisListener = new java.beans.PropertyChangeListener()
 790             {
 791               @Override
 792               public void propertyChange(PropertyChangeEvent evt)
 793               {
 794                 // // System.out.println("Discoverer property change.");
 795                 // if (evt.getPropertyName().equals("services"))
 796                 {
 797                   SwingUtilities.invokeLater(new Runnable()
 798                   {
 799
 800                     @Override
 801                     public void run()
 802                     {
 803                       System.err
 804                               .println("Rebuild WS Menu for service change");
 805                       BuildWebServiceMenu();
 806                     }
 807
 808                   });
 809                 }
 810               }
 811             });
 812     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 813     {
 814       @Override
 815       public void internalFrameClosed(
 816               javax.swing.event.InternalFrameEvent evt)
 817       {
 818         // System.out.println("deregistering discoverer listener");
 819         Desktop.instance.removeJalviewPropertyChangeListener("services",
 820                 thisListener);
 821         closeMenuItem_actionPerformed(true);
 822       };
 823     });
 824     // Finally, build the menu once to get current service state
 825     new Thread(new Runnable()
 826     {
 827       @Override
 828       public void run()
 829       {
 830         BuildWebServiceMenu();
 831       }
 832     }).start();
 833   }
 834
 835   /**
 836    * Configure menu items that vary according to whether the alignment is
 837    * nucleotide or protein
 838    */
 839   public void setGUINucleotide()
 840   {
 841     AlignmentI al = getViewport().getAlignment();
 842     boolean nucleotide = al.isNucleotide();
 843
 844     showTranslation.setVisible(nucleotide);
 845     showReverse.setVisible(nucleotide);
 846     showReverseComplement.setVisible(nucleotide);
 847     conservationMenuItem.setEnabled(!nucleotide);
 848     modifyConservation.setEnabled(!nucleotide);
 849     showGroupConservation.setEnabled(!nucleotide);
 850
 851     showComplementMenuItem.setText(nucleotide ? MessageManager
 852             .getString("label.protein") : MessageManager
 853             .getString("label.nucleotide"));
 854   }
 855
 856   /**
 857    * set up menus for the current viewport. This may be called after any
 858    * operation that affects the data in the current view (selection changed,
 859    * etc) to update the menus to reflect the new state.
 860    */
 861   @Override
 862   public void setMenusForViewport()
 863   {
 864     setMenusFromViewport(viewport);
 865   }
 866
 867   /**
 868    * Need to call this method when tabs are selected for multiple views, or when
 869    * loading from Jalview2XML.java
 870    *
 871    * @param av
 872    *          AlignViewport
 873    */
 874   void setMenusFromViewport(AlignViewport av)
 875   {
 876     padGapsMenuitem.setSelected(av.isPadGaps());
 877     colourTextMenuItem.setSelected(av.isShowColourText());
 878     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 879     conservationMenuItem.setSelected(av.getConservationSelected());
 880     seqLimits.setSelected(av.getShowJVSuffix());
 881     idRightAlign.setSelected(av.isRightAlignIds());
 882     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 883     renderGapsMenuItem.setSelected(av.isRenderGaps());
 884     wrapMenuItem.setSelected(av.getWrapAlignment());
 885     scaleAbove.setVisible(av.getWrapAlignment());
 886     scaleLeft.setVisible(av.getWrapAlignment());
 887     scaleRight.setVisible(av.getWrapAlignment());
 888     annotationPanelMenuItem.setState(av.isShowAnnotation());
 889     /*
 890      * Show/hide annotations only enabled if annotation panel is shown
 891      */
 892     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 893     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 894     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 895     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 897     viewTextMenuItem.setSelected(av.getShowText());
 898     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 899     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 900     showGroupConservation.setSelected(av.isShowGroupConservation());
 901     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 902     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 903     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 904
 905     ColourMenuHelper.setColourSelected(colourMenu,
 906             av.getGlobalColourScheme());
 907
 908     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 909     hiddenMarkers.setState(av.getShowHiddenMarkers());
 910     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 911     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 912     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 913     autoCalculate.setSelected(av.autoCalculateConsensus);
 914     sortByTree.setSelected(av.sortByTree);
 915     listenToViewSelections.setSelected(av.followSelection);
 916
 917     showProducts.setEnabled(canShowProducts());
 918     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 919
 920     updateEditMenuBar();
 921   }
 922
 923   /**
 924    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 925    *
 926    * @param b
 927    */
 928   public void setGroovyEnabled(boolean b)
 929   {
 930     runGroovy.setEnabled(b);
 931   }
 932
 933   private IProgressIndicator progressBar;
 934
 935   /*
 936    * (non-Javadoc)
 937    *
 938    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 939    */
 940   @Override
 941   public void setProgressBar(String message, long id)
 942   {
 943     progressBar.setProgressBar(message, id);
 944   }
 945
 946   @Override
 947   public void registerHandler(final long id,
 948           final IProgressIndicatorHandler handler)
 949   {
 950     progressBar.registerHandler(id, handler);
 951   }
 952
 953   /**
 954    *
 955    * @return true if any progress bars are still active
 956    */
 957   @Override
 958   public boolean operationInProgress()
 959   {
 960     return progressBar.operationInProgress();
 961   }
 962
 963   @Override
 964   public void setStatus(String text)
 965   {
 966     statusBar.setText(text);
 967   }
 968
 969   /*
 970    * Added so Castor Mapping file can obtain Jalview Version
 971    */
 972   public String getVersion()
 973   {
 974     return jalview.bin.Cache.getProperty("VERSION");
 975   }
 976
 977   public FeatureRenderer getFeatureRenderer()
 978   {
 979     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 980   }
 981
 982   @Override
 983   public void fetchSequence_actionPerformed(ActionEvent e)
 984   {
 985     new jalview.gui.SequenceFetcher(this);
 986   }
 987
 988   @Override
 989   public void addFromFile_actionPerformed(ActionEvent e)
 990   {
 991     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 992   }
 993
 994   @Override
 995   public void reload_actionPerformed(ActionEvent e)
 996   {
 997     if (fileName != null)
 998     {
 999       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1000       // originating file's format
1001       // TODO: work out how to recover feature settings for correct view(s) when
1002       // file is reloaded.
1003       if (FileFormat.Jalview.equals(currentFileFormat))
1004       {
1005         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1006         for (int i = 0; i < frames.length; i++)
1007         {
1008           if (frames[i] instanceof AlignFrame && frames[i] != this
1009                   && ((AlignFrame) frames[i]).fileName != null
1010                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1011           {
1012             try
1013             {
1014               frames[i].setSelected(true);
1015               Desktop.instance.closeAssociatedWindows();
1016             } catch (java.beans.PropertyVetoException ex)
1017             {
1018             }
1019           }
1020
1021         }
1022         Desktop.instance.closeAssociatedWindows();
1023
1024         FileLoader loader = new FileLoader();
1025         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1026                 : DataSourceType.FILE;
1027         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1028       }
1029       else
1030       {
1031         Rectangle bounds = this.getBounds();
1032
1033         FileLoader loader = new FileLoader();
1034         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1035                 : DataSourceType.FILE;
1036         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1037                 protocol, currentFileFormat);
1038
1039         newframe.setBounds(bounds);
1040         if (featureSettings != null && featureSettings.isShowing())
1041         {
1042           final Rectangle fspos = featureSettings.frame.getBounds();
1043           // TODO: need a 'show feature settings' function that takes bounds -
1044           // need to refactor Desktop.addFrame
1045           newframe.featureSettings_actionPerformed(null);
1046           final FeatureSettings nfs = newframe.featureSettings;
1047           SwingUtilities.invokeLater(new Runnable()
1048           {
1049             @Override
1050             public void run()
1051             {
1052               nfs.frame.setBounds(fspos);
1053             }
1054           });
1055           this.featureSettings.close();
1056           this.featureSettings = null;
1057         }
1058         this.closeMenuItem_actionPerformed(true);
1059       }
1060     }
1061   }
1062
1063   @Override
1064   public void addFromText_actionPerformed(ActionEvent e)
1065   {
1066     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1067             .getAlignPanel());
1068   }
1069
1070   @Override
1071   public void addFromURL_actionPerformed(ActionEvent e)
1072   {
1073     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1074   }
1075
1076   @Override
1077   public void save_actionPerformed(ActionEvent e)
1078   {
1079     if (fileName == null || (currentFileFormat == null)
1080             || fileName.startsWith("http"))
1081     {
1082       saveAs_actionPerformed(null);
1083     }
1084     else
1085     {
1086       saveAlignment(fileName, currentFileFormat);
1087     }
1088   }
1089
1090   /**
1091    * DOCUMENT ME!
1092    *
1093    * @param e
1094    *          DOCUMENT ME!
1095    */
1096   @Override
1097   public void saveAs_actionPerformed(ActionEvent e)
1098   {
1099     String format = currentFileFormat == null ? null : currentFileFormat
1100             .getName();
1101     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1102             Cache.getProperty("LAST_DIRECTORY"), format);
1103
1104     chooser.setFileView(new JalviewFileView());
1105     chooser.setDialogTitle(MessageManager
1106             .getString("label.save_alignment_to_file"));
1107     chooser.setToolTipText(MessageManager.getString("action.save"));
1108
1109     int value = chooser.showSaveDialog(this);
1110
1111     if (value == JalviewFileChooser.APPROVE_OPTION)
1112     {
1113       currentFileFormat = chooser.getSelectedFormat();
1114       while (currentFileFormat == null)
1115       {
1116         JvOptionPane
1117                 .showInternalMessageDialog(
1118                         Desktop.desktop,
1119                         MessageManager
1120                                 .getString("label.select_file_format_before_saving"),
1121                         MessageManager
1122                                 .getString("label.file_format_not_specified"),
1123                         JvOptionPane.WARNING_MESSAGE);
1124         currentFileFormat = chooser.getSelectedFormat();
1125         value = chooser.showSaveDialog(this);
1126         if (value != JalviewFileChooser.APPROVE_OPTION)
1127         {
1128           return;
1129         }
1130       }
1131
1132       fileName = chooser.getSelectedFile().getPath();
1133
1134       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1135
1136       Cache.setProperty("LAST_DIRECTORY", fileName);
1137       saveAlignment(fileName, currentFileFormat);
1138     }
1139   }
1140
1141   public boolean saveAlignment(String file, FileFormatI format)
1142   {
1143     boolean success = true;
1144
1145     if (FileFormat.Jalview.equals(format))
1146     {
1147       String shortName = title;
1148
1149       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1150       {
1151         shortName = shortName.substring(shortName
1152                 .lastIndexOf(java.io.File.separatorChar) + 1);
1153       }
1154
1155       success = new Jalview2XML().saveAlignment(this, file, shortName);
1156
1157       statusBar.setText(MessageManager.formatMessage(
1158               "label.successfully_saved_to_file_in_format", new Object[] {
1159                   fileName, format }));
1160
1161     }
1162     else
1163     {
1164       AlignmentExportData exportData = getAlignmentForExport(format,
1165               viewport, null);
1166       if (exportData.getSettings().isCancelled())
1167       {
1168         return false;
1169       }
1170       FormatAdapter f = new FormatAdapter(alignPanel,
1171               exportData.getSettings());
1172       String output = f.formatSequences(
1173               format,
1174               exportData.getAlignment(), // class cast exceptions will
1175               // occur in the distant future
1176               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1177               f.getCacheSuffixDefault(format),
1178               viewport.getColumnSelection());
1179
1180       if (output == null)
1181       {
1182         success = false;
1183       }
1184       else
1185       {
1186         try
1187         {
1188           PrintWriter out = new PrintWriter(new FileWriter(file));
1189
1190           out.print(output);
1191           out.close();
1192           this.setTitle(file);
1193           statusBar.setText(MessageManager.formatMessage(
1194                   "label.successfully_saved_to_file_in_format",
1195                   new Object[] { fileName, format.getName() }));
1196         } catch (Exception ex)
1197         {
1198           success = false;
1199           ex.printStackTrace();
1200         }
1201       }
1202     }
1203
1204     if (!success)
1205     {
1206       JvOptionPane.showInternalMessageDialog(this, MessageManager
1207               .formatMessage("label.couldnt_save_file",
1208                       new Object[] { fileName }), MessageManager
1209               .getString("label.error_saving_file"),
1210               JvOptionPane.WARNING_MESSAGE);
1211     }
1212
1213     return success;
1214   }
1215
1216   private void warningMessage(String warning, String title)
1217   {
1218     if (new jalview.util.Platform().isHeadless())
1219     {
1220       System.err.println("Warning: " + title + "\nWarning: " + warning);
1221
1222     }
1223     else
1224     {
1225       JvOptionPane.showInternalMessageDialog(this, warning, title,
1226               JvOptionPane.WARNING_MESSAGE);
1227     }
1228     return;
1229   }
1230
1231   /**
1232    * DOCUMENT ME!
1233    *
1234    * @param e
1235    *          DOCUMENT ME!
1236    */
1237   @Override
1238   protected void outputText_actionPerformed(ActionEvent e)
1239   {
1240     FileFormatI fileFormat = FileFormats.getInstance().forName(
1241             e.getActionCommand());
1242     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1243             viewport, null);
1244     if (exportData.getSettings().isCancelled())
1245     {
1246       return;
1247     }
1248     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1249     cap.setForInput(null);
1250     try
1251     {
1252       FileFormatI format = fileFormat;
1253       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1254               .formatSequences(format,
1255                       exportData.getAlignment(),
1256                       exportData.getOmitHidden(),
1257                       exportData.getStartEndPostions(),
1258                       viewport.getColumnSelection()));
1259       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1260               "label.alignment_output_command",
1261               new Object[] { e.getActionCommand() }), 600, 500);
1262     } catch (OutOfMemoryError oom)
1263     {
1264       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1265       cap.dispose();
1266     }
1267
1268   }
1269
1270   public static AlignmentExportData getAlignmentForExport(
1271           FileFormatI format, AlignViewportI viewport,
1272           AlignExportSettingI exportSettings)
1273   {
1274     AlignmentI alignmentToExport = null;
1275     AlignExportSettingI settings = exportSettings;
1276     String[] omitHidden = null;
1277
1278     HiddenSequences hiddenSeqs = viewport.getAlignment()
1279             .getHiddenSequences();
1280
1281     alignmentToExport = viewport.getAlignment();
1282
1283     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1284     if (settings == null)
1285     {
1286       settings = new AlignExportSettings(hasHiddenSeqs,
1287               viewport.hasHiddenColumns(), format);
1288     }
1289     // settings.isExportAnnotations();
1290
1291     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1292     {
1293       omitHidden = viewport.getViewAsString(false,
1294               settings.isExportHiddenSequences());
1295     }
1296
1297     int[] alignmentStartEnd = new int[2];
1298     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1299     {
1300       alignmentToExport = hiddenSeqs.getFullAlignment();
1301     }
1302     else
1303     {
1304       alignmentToExport = viewport.getAlignment();
1305     }
1306     alignmentStartEnd = alignmentToExport
1307             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1308                     .getHiddenColumns());
1309     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1310             omitHidden, alignmentStartEnd, settings);
1311     return ed;
1312   }
1313
1314   /**
1315    * DOCUMENT ME!
1316    *
1317    * @param e
1318    *          DOCUMENT ME!
1319    */
1320   @Override
1321   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1322   {
1323     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1324     htmlSVG.exportHTML(null);
1325   }
1326
1327   @Override
1328   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1329   {
1330     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1331     bjs.exportHTML(null);
1332   }
1333
1334   public void createImageMap(File file, String image)
1335   {
1336     alignPanel.makePNGImageMap(file, image);
1337   }
1338
1339   /**
1340    * DOCUMENT ME!
1341    *
1342    * @param e
1343    *          DOCUMENT ME!
1344    */
1345   @Override
1346   public void createPNG(File f)
1347   {
1348     alignPanel.makePNG(f);
1349   }
1350
1351   /**
1352    * DOCUMENT ME!
1353    *
1354    * @param e
1355    *          DOCUMENT ME!
1356    */
1357   @Override
1358   public void createEPS(File f)
1359   {
1360     alignPanel.makeEPS(f);
1361   }
1362
1363   @Override
1364   public void createSVG(File f)
1365   {
1366     alignPanel.makeSVG(f);
1367   }
1368
1369   @Override
1370   public void pageSetup_actionPerformed(ActionEvent e)
1371   {
1372     PrinterJob printJob = PrinterJob.getPrinterJob();
1373     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1374   }
1375
1376   /**
1377    * DOCUMENT ME!
1378    *
1379    * @param e
1380    *          DOCUMENT ME!
1381    */
1382   @Override
1383   public void printMenuItem_actionPerformed(ActionEvent e)
1384   {
1385     // Putting in a thread avoids Swing painting problems
1386     PrintThread thread = new PrintThread(alignPanel);
1387     thread.start();
1388   }
1389
1390   @Override
1391   public void exportFeatures_actionPerformed(ActionEvent e)
1392   {
1393     new AnnotationExporter().exportFeatures(alignPanel);
1394   }
1395
1396   @Override
1397   public void exportAnnotations_actionPerformed(ActionEvent e)
1398   {
1399     new AnnotationExporter().exportAnnotations(alignPanel);
1400   }
1401
1402   @Override
1403   public void associatedData_actionPerformed(ActionEvent e)
1404   {
1405     // Pick the tree file
1406     JalviewFileChooser chooser = new JalviewFileChooser(
1407             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1408     chooser.setFileView(new JalviewFileView());
1409     chooser.setDialogTitle(MessageManager
1410             .getString("label.load_jalview_annotations"));
1411     chooser.setToolTipText(MessageManager
1412             .getString("label.load_jalview_annotations"));
1413
1414     int value = chooser.showOpenDialog(null);
1415
1416     if (value == JalviewFileChooser.APPROVE_OPTION)
1417     {
1418       String choice = chooser.getSelectedFile().getPath();
1419       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1420       loadJalviewDataFile(choice, null, null, null);
1421     }
1422
1423   }
1424
1425   /**
1426    * Close the current view or all views in the alignment frame. If the frame
1427    * only contains one view then the alignment will be removed from memory.
1428    *
1429    * @param closeAllTabs
1430    */
1431   @Override
1432   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1433   {
1434     if (alignPanels != null && alignPanels.size() < 2)
1435     {
1436       closeAllTabs = true;
1437     }
1438
1439     try
1440     {
1441       if (alignPanels != null)
1442       {
1443         if (closeAllTabs)
1444         {
1445           if (this.isClosed())
1446           {
1447             // really close all the windows - otherwise wait till
1448             // setClosed(true) is called
1449             for (int i = 0; i < alignPanels.size(); i++)
1450             {
1451               AlignmentPanel ap = alignPanels.get(i);
1452               ap.closePanel();
1453             }
1454           }
1455         }
1456         else
1457         {
1458           closeView(alignPanel);
1459         }
1460       }
1461
1462       if (closeAllTabs)
1463       {
1464         /*
1465          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1466          * be called recursively, with the frame now in 'closed' state
1467          */
1468         this.setClosed(true);
1469       }
1470     } catch (Exception ex)
1471     {
1472       ex.printStackTrace();
1473     }
1474   }
1475
1476   /**
1477    * Close the specified panel and close up tabs appropriately.
1478    *
1479    * @param panelToClose
1480    */
1481   public void closeView(AlignmentPanel panelToClose)
1482   {
1483     int index = tabbedPane.getSelectedIndex();
1484     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1485     alignPanels.remove(panelToClose);
1486     panelToClose.closePanel();
1487     panelToClose = null;
1488
1489     tabbedPane.removeTabAt(closedindex);
1490     tabbedPane.validate();
1491
1492     if (index > closedindex || index == tabbedPane.getTabCount())
1493     {
1494       // modify currently selected tab index if necessary.
1495       index--;
1496     }
1497
1498     this.tabSelectionChanged(index);
1499   }
1500
1501   /**
1502    * DOCUMENT ME!
1503    */
1504   void updateEditMenuBar()
1505   {
1506
1507     if (viewport.getHistoryList().size() > 0)
1508     {
1509       undoMenuItem.setEnabled(true);
1510       CommandI command = viewport.getHistoryList().peek();
1511       undoMenuItem.setText(MessageManager.formatMessage(
1512               "label.undo_command",
1513               new Object[] { command.getDescription() }));
1514     }
1515     else
1516     {
1517       undoMenuItem.setEnabled(false);
1518       undoMenuItem.setText(MessageManager.getString("action.undo"));
1519     }
1520
1521     if (viewport.getRedoList().size() > 0)
1522     {
1523       redoMenuItem.setEnabled(true);
1524
1525       CommandI command = viewport.getRedoList().peek();
1526       redoMenuItem.setText(MessageManager.formatMessage(
1527               "label.redo_command",
1528               new Object[] { command.getDescription() }));
1529     }
1530     else
1531     {
1532       redoMenuItem.setEnabled(false);
1533       redoMenuItem.setText(MessageManager.getString("action.redo"));
1534     }
1535   }
1536
1537   @Override
1538   public void addHistoryItem(CommandI command)
1539   {
1540     if (command.getSize() > 0)
1541     {
1542       viewport.addToHistoryList(command);
1543       viewport.clearRedoList();
1544       updateEditMenuBar();
1545       viewport.updateHiddenColumns();
1546       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1547       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1548       // viewport.getColumnSelection()
1549       // .getHiddenColumns().size() > 0);
1550     }
1551   }
1552
1553   /**
1554    *
1555    * @return alignment objects for all views
1556    */
1557   AlignmentI[] getViewAlignments()
1558   {
1559     if (alignPanels != null)
1560     {
1561       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1562       int i = 0;
1563       for (AlignmentPanel ap : alignPanels)
1564       {
1565         als[i++] = ap.av.getAlignment();
1566       }
1567       return als;
1568     }
1569     if (viewport != null)
1570     {
1571       return new AlignmentI[] { viewport.getAlignment() };
1572     }
1573     return null;
1574   }
1575
1576   /**
1577    * DOCUMENT ME!
1578    *
1579    * @param e
1580    *          DOCUMENT ME!
1581    */
1582   @Override
1583   protected void undoMenuItem_actionPerformed(ActionEvent e)
1584   {
1585     if (viewport.getHistoryList().isEmpty())
1586     {
1587       return;
1588     }
1589     CommandI command = viewport.getHistoryList().pop();
1590     viewport.addToRedoList(command);
1591     command.undoCommand(getViewAlignments());
1592
1593     AlignmentViewport originalSource = getOriginatingSource(command);
1594     updateEditMenuBar();
1595
1596     if (originalSource != null)
1597     {
1598       if (originalSource != viewport)
1599       {
1600         Cache.log
1601                 .warn("Implementation worry: mismatch of viewport origin for undo");
1602       }
1603       originalSource.updateHiddenColumns();
1604       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1605       // null
1606       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1607       // viewport.getColumnSelection()
1608       // .getHiddenColumns().size() > 0);
1609       originalSource.firePropertyChange("alignment", null, originalSource
1610               .getAlignment().getSequences());
1611     }
1612   }
1613
1614   /**
1615    * DOCUMENT ME!
1616    *
1617    * @param e
1618    *          DOCUMENT ME!
1619    */
1620   @Override
1621   protected void redoMenuItem_actionPerformed(ActionEvent e)
1622   {
1623     if (viewport.getRedoList().size() < 1)
1624     {
1625       return;
1626     }
1627
1628     CommandI command = viewport.getRedoList().pop();
1629     viewport.addToHistoryList(command);
1630     command.doCommand(getViewAlignments());
1631
1632     AlignmentViewport originalSource = getOriginatingSource(command);
1633     updateEditMenuBar();
1634
1635     if (originalSource != null)
1636     {
1637
1638       if (originalSource != viewport)
1639       {
1640         Cache.log
1641                 .warn("Implementation worry: mismatch of viewport origin for redo");
1642       }
1643       originalSource.updateHiddenColumns();
1644       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1645       // null
1646       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1647       // viewport.getColumnSelection()
1648       // .getHiddenColumns().size() > 0);
1649       originalSource.firePropertyChange("alignment", null, originalSource
1650               .getAlignment().getSequences());
1651     }
1652   }
1653
1654   AlignmentViewport getOriginatingSource(CommandI command)
1655   {
1656     AlignmentViewport originalSource = null;
1657     // For sequence removal and addition, we need to fire
1658     // the property change event FROM the viewport where the
1659     // original alignment was altered
1660     AlignmentI al = null;
1661     if (command instanceof EditCommand)
1662     {
1663       EditCommand editCommand = (EditCommand) command;
1664       al = editCommand.getAlignment();
1665       List<Component> comps = PaintRefresher.components.get(viewport
1666               .getSequenceSetId());
1667
1668       for (Component comp : comps)
1669       {
1670         if (comp instanceof AlignmentPanel)
1671         {
1672           if (al == ((AlignmentPanel) comp).av.getAlignment())
1673           {
1674             originalSource = ((AlignmentPanel) comp).av;
1675             break;
1676           }
1677         }
1678       }
1679     }
1680
1681     if (originalSource == null)
1682     {
1683       // The original view is closed, we must validate
1684       // the current view against the closed view first
1685       if (al != null)
1686       {
1687         PaintRefresher.validateSequences(al, viewport.getAlignment());
1688       }
1689
1690       originalSource = viewport;
1691     }
1692
1693     return originalSource;
1694   }
1695
1696   /**
1697    * DOCUMENT ME!
1698    *
1699    * @param up
1700    *          DOCUMENT ME!
1701    */
1702   public void moveSelectedSequences(boolean up)
1703   {
1704     SequenceGroup sg = viewport.getSelectionGroup();
1705
1706     if (sg == null)
1707     {
1708       return;
1709     }
1710     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1711             viewport.getHiddenRepSequences(), up);
1712     alignPanel.paintAlignment(true);
1713   }
1714
1715   synchronized void slideSequences(boolean right, int size)
1716   {
1717     List<SequenceI> sg = new ArrayList<SequenceI>();
1718     if (viewport.cursorMode)
1719     {
1720       sg.add(viewport.getAlignment().getSequenceAt(
1721               alignPanel.getSeqPanel().seqCanvas.cursorY));
1722     }
1723     else if (viewport.getSelectionGroup() != null
1724             && viewport.getSelectionGroup().getSize() != viewport
1725                     .getAlignment().getHeight())
1726     {
1727       sg = viewport.getSelectionGroup().getSequences(
1728               viewport.getHiddenRepSequences());
1729     }
1730
1731     if (sg.size() < 1)
1732     {
1733       return;
1734     }
1735
1736     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1737
1738     for (SequenceI seq : viewport.getAlignment().getSequences())
1739     {
1740       if (!sg.contains(seq))
1741       {
1742         invertGroup.add(seq);
1743       }
1744     }
1745
1746     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1747
1748     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1749     for (int i = 0; i < invertGroup.size(); i++)
1750     {
1751       seqs2[i] = invertGroup.get(i);
1752     }
1753
1754     SlideSequencesCommand ssc;
1755     if (right)
1756     {
1757       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1758               size, viewport.getGapCharacter());
1759     }
1760     else
1761     {
1762       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1763               size, viewport.getGapCharacter());
1764     }
1765
1766     int groupAdjustment = 0;
1767     if (ssc.getGapsInsertedBegin() && right)
1768     {
1769       if (viewport.cursorMode)
1770       {
1771         alignPanel.getSeqPanel().moveCursor(size, 0);
1772       }
1773       else
1774       {
1775         groupAdjustment = size;
1776       }
1777     }
1778     else if (!ssc.getGapsInsertedBegin() && !right)
1779     {
1780       if (viewport.cursorMode)
1781       {
1782         alignPanel.getSeqPanel().moveCursor(-size, 0);
1783       }
1784       else
1785       {
1786         groupAdjustment = -size;
1787       }
1788     }
1789
1790     if (groupAdjustment != 0)
1791     {
1792       viewport.getSelectionGroup().setStartRes(
1793               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1794       viewport.getSelectionGroup().setEndRes(
1795               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1796     }
1797
1798     /*
1799      * just extend the last slide command if compatible; but not if in
1800      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1801      */
1802     boolean appendHistoryItem = false;
1803     Deque<CommandI> historyList = viewport.getHistoryList();
1804     boolean inSplitFrame = getSplitViewContainer() != null;
1805     if (!inSplitFrame && historyList != null && historyList.size() > 0
1806             && historyList.peek() instanceof SlideSequencesCommand)
1807     {
1808       appendHistoryItem = ssc
1809               .appendSlideCommand((SlideSequencesCommand) historyList
1810                       .peek());
1811     }
1812
1813     if (!appendHistoryItem)
1814     {
1815       addHistoryItem(ssc);
1816     }
1817
1818     repaint();
1819   }
1820
1821   /**
1822    * DOCUMENT ME!
1823    *
1824    * @param e
1825    *          DOCUMENT ME!
1826    */
1827   @Override
1828   protected void copy_actionPerformed(ActionEvent e)
1829   {
1830     System.gc();
1831     if (viewport.getSelectionGroup() == null)
1832     {
1833       return;
1834     }
1835     // TODO: preserve the ordering of displayed alignment annotation in any
1836     // internal paste (particularly sequence associated annotation)
1837     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1838     String[] omitHidden = null;
1839
1840     if (viewport.hasHiddenColumns())
1841     {
1842       omitHidden = viewport.getViewAsString(true);
1843     }
1844
1845     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1846             seqs,
1847             omitHidden, null);
1848
1849     StringSelection ss = new StringSelection(output);
1850
1851     try
1852     {
1853       jalview.gui.Desktop.internalCopy = true;
1854       // Its really worth setting the clipboard contents
1855       // to empty before setting the large StringSelection!!
1856       Toolkit.getDefaultToolkit().getSystemClipboard()
1857               .setContents(new StringSelection(""), null);
1858
1859       Toolkit.getDefaultToolkit().getSystemClipboard()
1860               .setContents(ss, Desktop.instance);
1861     } catch (OutOfMemoryError er)
1862     {
1863       new OOMWarning("copying region", er);
1864       return;
1865     }
1866
1867     ArrayList<int[]> hiddenColumns = null;
1868     if (viewport.hasHiddenColumns())
1869     {
1870       hiddenColumns = new ArrayList<int[]>();
1871       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1872               .getSelectionGroup().getEndRes();
1873       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1874       {
1875         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1876         {
1877           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1878               region[1] - hiddenOffset });
1879         }
1880       }
1881     }
1882
1883     Desktop.jalviewClipboard = new Object[] { seqs,
1884         viewport.getAlignment().getDataset(), hiddenColumns };
1885     statusBar.setText(MessageManager.formatMessage(
1886             "label.copied_sequences_to_clipboard", new Object[] { Integer
1887                     .valueOf(seqs.length).toString() }));
1888   }
1889
1890   /**
1891    * DOCUMENT ME!
1892    *
1893    * @param e
1894    *          DOCUMENT ME!
1895    */
1896   @Override
1897   protected void pasteNew_actionPerformed(ActionEvent e)
1898   {
1899     paste(true);
1900   }
1901
1902   /**
1903    * DOCUMENT ME!
1904    *
1905    * @param e
1906    *          DOCUMENT ME!
1907    */
1908   @Override
1909   protected void pasteThis_actionPerformed(ActionEvent e)
1910   {
1911     paste(false);
1912   }
1913
1914   /**
1915    * Paste contents of Jalview clipboard
1916    *
1917    * @param newAlignment
1918    *          true to paste to a new alignment, otherwise add to this.
1919    */
1920   void paste(boolean newAlignment)
1921   {
1922     boolean externalPaste = true;
1923     try
1924     {
1925       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1926       Transferable contents = c.getContents(this);
1927
1928       if (contents == null)
1929       {
1930         return;
1931       }
1932
1933       String str;
1934       FileFormatI format;
1935       try
1936       {
1937         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1938         if (str.length() < 1)
1939         {
1940           return;
1941         }
1942
1943         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1944
1945       } catch (OutOfMemoryError er)
1946       {
1947         new OOMWarning("Out of memory pasting sequences!!", er);
1948         return;
1949       }
1950
1951       SequenceI[] sequences;
1952       boolean annotationAdded = false;
1953       AlignmentI alignment = null;
1954
1955       if (Desktop.jalviewClipboard != null)
1956       {
1957         // The clipboard was filled from within Jalview, we must use the
1958         // sequences
1959         // And dataset from the copied alignment
1960         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1961         // be doubly sure that we create *new* sequence objects.
1962         sequences = new SequenceI[newseq.length];
1963         for (int i = 0; i < newseq.length; i++)
1964         {
1965           sequences[i] = new Sequence(newseq[i]);
1966         }
1967         alignment = new Alignment(sequences);
1968         externalPaste = false;
1969       }
1970       else
1971       {
1972         // parse the clipboard as an alignment.
1973         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1974                 format);
1975         sequences = alignment.getSequencesArray();
1976       }
1977
1978       int alwidth = 0;
1979       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1980       int fgroup = -1;
1981
1982       if (newAlignment)
1983       {
1984
1985         if (Desktop.jalviewClipboard != null)
1986         {
1987           // dataset is inherited
1988           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1989         }
1990         else
1991         {
1992           // new dataset is constructed
1993           alignment.setDataset(null);
1994         }
1995         alwidth = alignment.getWidth() + 1;
1996       }
1997       else
1998       {
1999         AlignmentI pastedal = alignment; // preserve pasted alignment object
2000         // Add pasted sequences and dataset into existing alignment.
2001         alignment = viewport.getAlignment();
2002         alwidth = alignment.getWidth() + 1;
2003         // decide if we need to import sequences from an existing dataset
2004         boolean importDs = Desktop.jalviewClipboard != null
2005                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2006         // importDs==true instructs us to copy over new dataset sequences from
2007         // an existing alignment
2008         Vector newDs = (importDs) ? new Vector() : null; // used to create
2009         // minimum dataset set
2010
2011         for (int i = 0; i < sequences.length; i++)
2012         {
2013           if (importDs)
2014           {
2015             newDs.addElement(null);
2016           }
2017           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2018           // paste
2019           if (importDs && ds != null)
2020           {
2021             if (!newDs.contains(ds))
2022             {
2023               newDs.setElementAt(ds, i);
2024               ds = new Sequence(ds);
2025               // update with new dataset sequence
2026               sequences[i].setDatasetSequence(ds);
2027             }
2028             else
2029             {
2030               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2031             }
2032           }
2033           else
2034           {
2035             // copy and derive new dataset sequence
2036             sequences[i] = sequences[i].deriveSequence();
2037             alignment.getDataset().addSequence(
2038                     sequences[i].getDatasetSequence());
2039             // TODO: avoid creation of duplicate dataset sequences with a
2040             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2041           }
2042           alignment.addSequence(sequences[i]); // merges dataset
2043         }
2044         if (newDs != null)
2045         {
2046           newDs.clear(); // tidy up
2047         }
2048         if (alignment.getAlignmentAnnotation() != null)
2049         {
2050           for (AlignmentAnnotation alan : alignment
2051                   .getAlignmentAnnotation())
2052           {
2053             if (alan.graphGroup > fgroup)
2054             {
2055               fgroup = alan.graphGroup;
2056             }
2057           }
2058         }
2059         if (pastedal.getAlignmentAnnotation() != null)
2060         {
2061           // Add any annotation attached to alignment.
2062           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2063           for (int i = 0; i < alann.length; i++)
2064           {
2065             annotationAdded = true;
2066             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2067             {
2068               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2069               if (newann.graphGroup > -1)
2070               {
2071                 if (newGraphGroups.size() <= newann.graphGroup
2072                         || newGraphGroups.get(newann.graphGroup) == null)
2073                 {
2074                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2075                   {
2076                     newGraphGroups.add(q, null);
2077                   }
2078                   newGraphGroups.set(newann.graphGroup, new Integer(
2079                           ++fgroup));
2080                 }
2081                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2082                         .intValue();
2083               }
2084
2085               newann.padAnnotation(alwidth);
2086               alignment.addAnnotation(newann);
2087             }
2088           }
2089         }
2090       }
2091       if (!newAlignment)
2092       {
2093         // /////
2094         // ADD HISTORY ITEM
2095         //
2096         addHistoryItem(new EditCommand(
2097                 MessageManager.getString("label.add_sequences"),
2098                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2099       }
2100       // Add any annotations attached to sequences
2101       for (int i = 0; i < sequences.length; i++)
2102       {
2103         if (sequences[i].getAnnotation() != null)
2104         {
2105           AlignmentAnnotation newann;
2106           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2107           {
2108             annotationAdded = true;
2109             newann = sequences[i].getAnnotation()[a];
2110             newann.adjustForAlignment();
2111             newann.padAnnotation(alwidth);
2112             if (newann.graphGroup > -1)
2113             {
2114               if (newann.graphGroup > -1)
2115               {
2116                 if (newGraphGroups.size() <= newann.graphGroup
2117                         || newGraphGroups.get(newann.graphGroup) == null)
2118                 {
2119                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2120                   {
2121                     newGraphGroups.add(q, null);
2122                   }
2123                   newGraphGroups.set(newann.graphGroup, new Integer(
2124                           ++fgroup));
2125                 }
2126                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2127                         .intValue();
2128               }
2129             }
2130             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2131             // was
2132             // duplicated
2133             // earlier
2134             alignment
2135                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2136           }
2137         }
2138       }
2139       if (!newAlignment)
2140       {
2141
2142         // propagate alignment changed.
2143         viewport.setEndSeq(alignment.getHeight());
2144         if (annotationAdded)
2145         {
2146           // Duplicate sequence annotation in all views.
2147           AlignmentI[] alview = this.getViewAlignments();
2148           for (int i = 0; i < sequences.length; i++)
2149           {
2150             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2151             if (sann == null)
2152             {
2153               continue;
2154             }
2155             for (int avnum = 0; avnum < alview.length; avnum++)
2156             {
2157               if (alview[avnum] != alignment)
2158               {
2159                 // duplicate in a view other than the one with input focus
2160                 int avwidth = alview[avnum].getWidth() + 1;
2161                 // this relies on sann being preserved after we
2162                 // modify the sequence's annotation array for each duplication
2163                 for (int a = 0; a < sann.length; a++)
2164                 {
2165                   AlignmentAnnotation newann = new AlignmentAnnotation(
2166                           sann[a]);
2167                   sequences[i].addAlignmentAnnotation(newann);
2168                   newann.padAnnotation(avwidth);
2169                   alview[avnum].addAnnotation(newann); // annotation was
2170                   // duplicated earlier
2171                   // TODO JAL-1145 graphGroups are not updated for sequence
2172                   // annotation added to several views. This may cause
2173                   // strangeness
2174                   alview[avnum].setAnnotationIndex(newann, a);
2175                 }
2176               }
2177             }
2178           }
2179           buildSortByAnnotationScoresMenu();
2180         }
2181         viewport.firePropertyChange("alignment", null,
2182                 alignment.getSequences());
2183         if (alignPanels != null)
2184         {
2185           for (AlignmentPanel ap : alignPanels)
2186           {
2187             ap.validateAnnotationDimensions(false);
2188           }
2189         }
2190         else
2191         {
2192           alignPanel.validateAnnotationDimensions(false);
2193         }
2194
2195       }
2196       else
2197       {
2198         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2199                 DEFAULT_HEIGHT);
2200         String newtitle = new String("Copied sequences");
2201
2202         if (Desktop.jalviewClipboard != null
2203                 && Desktop.jalviewClipboard[2] != null)
2204         {
2205           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2206           for (int[] region : hc)
2207           {
2208             af.viewport.hideColumns(region[0], region[1]);
2209           }
2210         }
2211
2212         // >>>This is a fix for the moment, until a better solution is
2213         // found!!<<<
2214         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2215                 .transferSettings(
2216                         alignPanel.getSeqPanel().seqCanvas
2217                                 .getFeatureRenderer());
2218
2219         // TODO: maintain provenance of an alignment, rather than just make the
2220         // title a concatenation of operations.
2221         if (!externalPaste)
2222         {
2223           if (title.startsWith("Copied sequences"))
2224           {
2225             newtitle = title;
2226           }
2227           else
2228           {
2229             newtitle = newtitle.concat("- from " + title);
2230           }
2231         }
2232         else
2233         {
2234           newtitle = new String("Pasted sequences");
2235         }
2236
2237         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2238                 DEFAULT_HEIGHT);
2239
2240       }
2241
2242     } catch (Exception ex)
2243     {
2244       ex.printStackTrace();
2245       System.out.println("Exception whilst pasting: " + ex);
2246       // could be anything being pasted in here
2247     }
2248
2249   }
2250
2251   @Override
2252   protected void expand_newalign(ActionEvent e)
2253   {
2254     try
2255     {
2256       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2257               .getAlignment(), -1);
2258       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2259               DEFAULT_HEIGHT);
2260       String newtitle = new String("Flanking alignment");
2261
2262       if (Desktop.jalviewClipboard != null
2263               && Desktop.jalviewClipboard[2] != null)
2264       {
2265         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2266         for (int region[] : hc)
2267         {
2268           af.viewport.hideColumns(region[0], region[1]);
2269         }
2270       }
2271
2272       // >>>This is a fix for the moment, until a better solution is
2273       // found!!<<<
2274       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2275               .transferSettings(
2276                       alignPanel.getSeqPanel().seqCanvas
2277                               .getFeatureRenderer());
2278
2279       // TODO: maintain provenance of an alignment, rather than just make the
2280       // title a concatenation of operations.
2281       {
2282         if (title.startsWith("Copied sequences"))
2283         {
2284           newtitle = title;
2285         }
2286         else
2287         {
2288           newtitle = newtitle.concat("- from " + title);
2289         }
2290       }
2291
2292       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2293
2294     } catch (Exception ex)
2295     {
2296       ex.printStackTrace();
2297       System.out.println("Exception whilst pasting: " + ex);
2298       // could be anything being pasted in here
2299     } catch (OutOfMemoryError oom)
2300     {
2301       new OOMWarning("Viewing flanking region of alignment", oom);
2302     }
2303   }
2304
2305   /**
2306    * DOCUMENT ME!
2307    *
2308    * @param e
2309    *          DOCUMENT ME!
2310    */
2311   @Override
2312   protected void cut_actionPerformed(ActionEvent e)
2313   {
2314     copy_actionPerformed(null);
2315     delete_actionPerformed(null);
2316   }
2317
2318   /**
2319    * DOCUMENT ME!
2320    *
2321    * @param e
2322    *          DOCUMENT ME!
2323    */
2324   @Override
2325   protected void delete_actionPerformed(ActionEvent evt)
2326   {
2327
2328     SequenceGroup sg = viewport.getSelectionGroup();
2329     if (sg == null)
2330     {
2331       return;
2332     }
2333
2334     /*
2335      * If the cut affects all sequences, warn, remove highlighted columns
2336      */
2337     if (sg.getSize() == viewport.getAlignment().getHeight())
2338     {
2339       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2340               .getAlignment().getWidth()) ? true : false;
2341       if (isEntireAlignWidth)
2342       {
2343         int confirm = JvOptionPane.showConfirmDialog(this,
2344                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2345                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2346                 JvOptionPane.OK_CANCEL_OPTION);
2347
2348         if (confirm == JvOptionPane.CANCEL_OPTION
2349                 || confirm == JvOptionPane.CLOSED_OPTION)
2350         {
2351           return;
2352         }
2353       }
2354       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2355               sg.getEndRes() + 1);
2356     }
2357     SequenceI[] cut = sg.getSequences()
2358             .toArray(new SequenceI[sg.getSize()]);
2359
2360     addHistoryItem(new EditCommand(
2361             MessageManager.getString("label.cut_sequences"), Action.CUT,
2362             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2363             viewport.getAlignment()));
2364
2365     viewport.setSelectionGroup(null);
2366     viewport.sendSelection();
2367     viewport.getAlignment().deleteGroup(sg);
2368
2369     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2370             .getSequences());
2371     if (viewport.getAlignment().getHeight() < 1)
2372     {
2373       try
2374       {
2375         this.setClosed(true);
2376       } catch (Exception ex)
2377       {
2378       }
2379     }
2380   }
2381
2382   /**
2383    * DOCUMENT ME!
2384    *
2385    * @param e
2386    *          DOCUMENT ME!
2387    */
2388   @Override
2389   protected void deleteGroups_actionPerformed(ActionEvent e)
2390   {
2391     if (avc.deleteGroups())
2392     {
2393       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2394       alignPanel.updateAnnotation();
2395       alignPanel.paintAlignment(true);
2396     }
2397   }
2398
2399   /**
2400    * DOCUMENT ME!
2401    *
2402    * @param e
2403    *          DOCUMENT ME!
2404    */
2405   @Override
2406   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2407   {
2408     SequenceGroup sg = new SequenceGroup();
2409
2410     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2411     {
2412       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2413     }
2414
2415     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2416     viewport.setSelectionGroup(sg);
2417     viewport.sendSelection();
2418     // JAL-2034 - should delegate to
2419     // alignPanel to decide if overview needs
2420     // updating.
2421     alignPanel.paintAlignment(false);
2422     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2423   }
2424
2425   /**
2426    * DOCUMENT ME!
2427    *
2428    * @param e
2429    *          DOCUMENT ME!
2430    */
2431   @Override
2432   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2433   {
2434     if (viewport.cursorMode)
2435     {
2436       alignPanel.getSeqPanel().keyboardNo1 = null;
2437       alignPanel.getSeqPanel().keyboardNo2 = null;
2438     }
2439     viewport.setSelectionGroup(null);
2440     viewport.getColumnSelection().clear();
2441     viewport.setSelectionGroup(null);
2442     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2443     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2444     // JAL-2034 - should delegate to
2445     // alignPanel to decide if overview needs
2446     // updating.
2447     alignPanel.paintAlignment(false);
2448     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449     viewport.sendSelection();
2450   }
2451
2452   /**
2453    * DOCUMENT ME!
2454    *
2455    * @param e
2456    *          DOCUMENT ME!
2457    */
2458   @Override
2459   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2460   {
2461     SequenceGroup sg = viewport.getSelectionGroup();
2462
2463     if (sg == null)
2464     {
2465       selectAllSequenceMenuItem_actionPerformed(null);
2466
2467       return;
2468     }
2469
2470     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2471     {
2472       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2473     }
2474     // JAL-2034 - should delegate to
2475     // alignPanel to decide if overview needs
2476     // updating.
2477
2478     alignPanel.paintAlignment(true);
2479     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2480     viewport.sendSelection();
2481   }
2482
2483   @Override
2484   public void invertColSel_actionPerformed(ActionEvent e)
2485   {
2486     viewport.invertColumnSelection();
2487     alignPanel.paintAlignment(true);
2488     viewport.sendSelection();
2489   }
2490
2491   /**
2492    * DOCUMENT ME!
2493    *
2494    * @param e
2495    *          DOCUMENT ME!
2496    */
2497   @Override
2498   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2499   {
2500     trimAlignment(true);
2501   }
2502
2503   /**
2504    * DOCUMENT ME!
2505    *
2506    * @param e
2507    *          DOCUMENT ME!
2508    */
2509   @Override
2510   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2511   {
2512     trimAlignment(false);
2513   }
2514
2515   void trimAlignment(boolean trimLeft)
2516   {
2517     ColumnSelection colSel = viewport.getColumnSelection();
2518     int column;
2519
2520     if (!colSel.isEmpty())
2521     {
2522       if (trimLeft)
2523       {
2524         column = colSel.getMin();
2525       }
2526       else
2527       {
2528         column = colSel.getMax();
2529       }
2530
2531       SequenceI[] seqs;
2532       if (viewport.getSelectionGroup() != null)
2533       {
2534         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2535                 viewport.getHiddenRepSequences());
2536       }
2537       else
2538       {
2539         seqs = viewport.getAlignment().getSequencesArray();
2540       }
2541
2542       TrimRegionCommand trimRegion;
2543       if (trimLeft)
2544       {
2545         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2546                 column, viewport.getAlignment());
2547         viewport.setStartRes(0);
2548       }
2549       else
2550       {
2551         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2552                 column, viewport.getAlignment());
2553       }
2554
2555       statusBar.setText(MessageManager.formatMessage(
2556               "label.removed_columns",
2557               new String[] { Integer.valueOf(trimRegion.getSize())
2558                       .toString() }));
2559
2560       addHistoryItem(trimRegion);
2561
2562       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2563       {
2564         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2565                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2566         {
2567           viewport.getAlignment().deleteGroup(sg);
2568         }
2569       }
2570
2571       viewport.firePropertyChange("alignment", null, viewport
2572               .getAlignment().getSequences());
2573     }
2574   }
2575
2576   /**
2577    * DOCUMENT ME!
2578    *
2579    * @param e
2580    *          DOCUMENT ME!
2581    */
2582   @Override
2583   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2584   {
2585     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2586
2587     SequenceI[] seqs;
2588     if (viewport.getSelectionGroup() != null)
2589     {
2590       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2591               viewport.getHiddenRepSequences());
2592       start = viewport.getSelectionGroup().getStartRes();
2593       end = viewport.getSelectionGroup().getEndRes();
2594     }
2595     else
2596     {
2597       seqs = viewport.getAlignment().getSequencesArray();
2598     }
2599
2600     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2601             "Remove Gapped Columns", seqs, start, end,
2602             viewport.getAlignment());
2603
2604     addHistoryItem(removeGapCols);
2605
2606     statusBar.setText(MessageManager.formatMessage(
2607             "label.removed_empty_columns",
2608             new Object[] { Integer.valueOf(removeGapCols.getSize())
2609                     .toString() }));
2610
2611     // This is to maintain viewport position on first residue
2612     // of first sequence
2613     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2614     int startRes = seq.findPosition(viewport.startRes);
2615     // ShiftList shifts;
2616     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2617     // edit.alColumnChanges=shifts.getInverse();
2618     // if (viewport.hasHiddenColumns)
2619     // viewport.getColumnSelection().compensateForEdits(shifts);
2620     viewport.setStartRes(seq.findIndex(startRes) - 1);
2621     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2622             .getSequences());
2623
2624   }
2625
2626   /**
2627    * DOCUMENT ME!
2628    *
2629    * @param e
2630    *          DOCUMENT ME!
2631    */
2632   @Override
2633   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2634   {
2635     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2636
2637     SequenceI[] seqs;
2638     if (viewport.getSelectionGroup() != null)
2639     {
2640       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2641               viewport.getHiddenRepSequences());
2642       start = viewport.getSelectionGroup().getStartRes();
2643       end = viewport.getSelectionGroup().getEndRes();
2644     }
2645     else
2646     {
2647       seqs = viewport.getAlignment().getSequencesArray();
2648     }
2649
2650     // This is to maintain viewport position on first residue
2651     // of first sequence
2652     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2653     int startRes = seq.findPosition(viewport.startRes);
2654
2655     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2656             viewport.getAlignment()));
2657
2658     viewport.setStartRes(seq.findIndex(startRes) - 1);
2659
2660     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2661             .getSequences());
2662
2663   }
2664
2665   /**
2666    * DOCUMENT ME!
2667    *
2668    * @param e
2669    *          DOCUMENT ME!
2670    */
2671   @Override
2672   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2673   {
2674     viewport.setPadGaps(padGapsMenuitem.isSelected());
2675     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2676             .getSequences());
2677   }
2678
2679   /**
2680    * DOCUMENT ME!
2681    *
2682    * @param e
2683    *          DOCUMENT ME!
2684    */
2685   @Override
2686   public void findMenuItem_actionPerformed(ActionEvent e)
2687   {
2688     new Finder();
2689   }
2690
2691   /**
2692    * Create a new view of the current alignment.
2693    */
2694   @Override
2695   public void newView_actionPerformed(ActionEvent e)
2696   {
2697     newView(null, true);
2698   }
2699
2700   /**
2701    * Creates and shows a new view of the current alignment.
2702    *
2703    * @param viewTitle
2704    *          title of newly created view; if null, one will be generated
2705    * @param copyAnnotation
2706    *          if true then duplicate all annnotation, groups and settings
2707    * @return new alignment panel, already displayed.
2708    */
2709   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2710   {
2711     /*
2712      * Create a new AlignmentPanel (with its own, new Viewport)
2713      */
2714     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2715             true);
2716     if (!copyAnnotation)
2717     {
2718       /*
2719        * remove all groups and annotation except for the automatic stuff
2720        */
2721       newap.av.getAlignment().deleteAllGroups();
2722       newap.av.getAlignment().deleteAllAnnotations(false);
2723     }
2724
2725     newap.av.setGatherViewsHere(false);
2726
2727     if (viewport.viewName == null)
2728     {
2729       viewport.viewName = MessageManager
2730               .getString("label.view_name_original");
2731     }
2732
2733     /*
2734      * Views share the same edits undo and redo stacks
2735      */
2736     newap.av.setHistoryList(viewport.getHistoryList());
2737     newap.av.setRedoList(viewport.getRedoList());
2738
2739     /*
2740      * Views share the same mappings; need to deregister any new mappings
2741      * created by copyAlignPanel, and register the new reference to the shared
2742      * mappings
2743      */
2744     newap.av.replaceMappings(viewport.getAlignment());
2745
2746     newap.av.viewName = getNewViewName(viewTitle);
2747
2748     addAlignmentPanel(newap, true);
2749     newap.alignmentChanged();
2750
2751     if (alignPanels.size() == 2)
2752     {
2753       viewport.setGatherViewsHere(true);
2754     }
2755     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2756     return newap;
2757   }
2758
2759   /**
2760    * Make a new name for the view, ensuring it is unique within the current
2761    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2762    * these now use viewId. Unique view names are still desirable for usability.)
2763    *
2764    * @param viewTitle
2765    * @return
2766    */
2767   protected String getNewViewName(String viewTitle)
2768   {
2769     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2770     boolean addFirstIndex = false;
2771     if (viewTitle == null || viewTitle.trim().length() == 0)
2772     {
2773       viewTitle = MessageManager.getString("action.view");
2774       addFirstIndex = true;
2775     }
2776     else
2777     {
2778       index = 1;// we count from 1 if given a specific name
2779     }
2780     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2781
2782     List<Component> comps = PaintRefresher.components.get(viewport
2783             .getSequenceSetId());
2784
2785     List<String> existingNames = getExistingViewNames(comps);
2786
2787     while (existingNames.contains(newViewName))
2788     {
2789       newViewName = viewTitle + " " + (++index);
2790     }
2791     return newViewName;
2792   }
2793
2794   /**
2795    * Returns a list of distinct view names found in the given list of
2796    * components. View names are held on the viewport of an AlignmentPanel.
2797    *
2798    * @param comps
2799    * @return
2800    */
2801   protected List<String> getExistingViewNames(List<Component> comps)
2802   {
2803     List<String> existingNames = new ArrayList<String>();
2804     for (Component comp : comps)
2805     {
2806       if (comp instanceof AlignmentPanel)
2807       {
2808         AlignmentPanel ap = (AlignmentPanel) comp;
2809         if (!existingNames.contains(ap.av.viewName))
2810         {
2811           existingNames.add(ap.av.viewName);
2812         }
2813       }
2814     }
2815     return existingNames;
2816   }
2817
2818   /**
2819    * Explode tabbed views into separate windows.
2820    */
2821   @Override
2822   public void expandViews_actionPerformed(ActionEvent e)
2823   {
2824     Desktop.explodeViews(this);
2825   }
2826
2827   /**
2828    * Gather views in separate windows back into a tabbed presentation.
2829    */
2830   @Override
2831   public void gatherViews_actionPerformed(ActionEvent e)
2832   {
2833     Desktop.instance.gatherViews(this);
2834   }
2835
2836   /**
2837    * DOCUMENT ME!
2838    *
2839    * @param e
2840    *          DOCUMENT ME!
2841    */
2842   @Override
2843   public void font_actionPerformed(ActionEvent e)
2844   {
2845     new FontChooser(alignPanel);
2846   }
2847
2848   /**
2849    * DOCUMENT ME!
2850    *
2851    * @param e
2852    *          DOCUMENT ME!
2853    */
2854   @Override
2855   protected void seqLimit_actionPerformed(ActionEvent e)
2856   {
2857     viewport.setShowJVSuffix(seqLimits.isSelected());
2858
2859     alignPanel.getIdPanel().getIdCanvas()
2860             .setPreferredSize(alignPanel.calculateIdWidth());
2861     alignPanel.paintAlignment(true);
2862   }
2863
2864   @Override
2865   public void idRightAlign_actionPerformed(ActionEvent e)
2866   {
2867     viewport.setRightAlignIds(idRightAlign.isSelected());
2868     alignPanel.paintAlignment(true);
2869   }
2870
2871   @Override
2872   public void centreColumnLabels_actionPerformed(ActionEvent e)
2873   {
2874     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2875     alignPanel.paintAlignment(true);
2876   }
2877
2878   /*
2879    * (non-Javadoc)
2880    *
2881    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2882    */
2883   @Override
2884   protected void followHighlight_actionPerformed()
2885   {
2886     /*
2887      * Set the 'follow' flag on the Viewport (and scroll to position if now
2888      * true).
2889      */
2890     final boolean state = this.followHighlightMenuItem.getState();
2891     viewport.setFollowHighlight(state);
2892     if (state)
2893     {
2894       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2895     }
2896   }
2897
2898   /**
2899    * DOCUMENT ME!
2900    *
2901    * @param e
2902    *          DOCUMENT ME!
2903    */
2904   @Override
2905   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2906   {
2907     viewport.setColourText(colourTextMenuItem.isSelected());
2908     alignPanel.paintAlignment(true);
2909   }
2910
2911   /**
2912    * DOCUMENT ME!
2913    *
2914    * @param e
2915    *          DOCUMENT ME!
2916    */
2917   @Override
2918   public void wrapMenuItem_actionPerformed(ActionEvent e)
2919   {
2920     scaleAbove.setVisible(wrapMenuItem.isSelected());
2921     scaleLeft.setVisible(wrapMenuItem.isSelected());
2922     scaleRight.setVisible(wrapMenuItem.isSelected());
2923     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2924     alignPanel.updateLayout();
2925   }
2926
2927   @Override
2928   public void showAllSeqs_actionPerformed(ActionEvent e)
2929   {
2930     viewport.showAllHiddenSeqs();
2931   }
2932
2933   @Override
2934   public void showAllColumns_actionPerformed(ActionEvent e)
2935   {
2936     viewport.showAllHiddenColumns();
2937     repaint();
2938     viewport.sendSelection();
2939   }
2940
2941   @Override
2942   public void hideSelSequences_actionPerformed(ActionEvent e)
2943   {
2944     viewport.hideAllSelectedSeqs();
2945     // alignPanel.paintAlignment(true);
2946   }
2947
2948   /**
2949    * called by key handler and the hide all/show all menu items
2950    *
2951    * @param toggleSeqs
2952    * @param toggleCols
2953    */
2954   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2955   {
2956
2957     boolean hide = false;
2958     SequenceGroup sg = viewport.getSelectionGroup();
2959     if (!toggleSeqs && !toggleCols)
2960     {
2961       // Hide everything by the current selection - this is a hack - we do the
2962       // invert and then hide
2963       // first check that there will be visible columns after the invert.
2964       if (viewport.hasSelectedColumns()
2965               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2966                       .getEndRes()))
2967       {
2968         // now invert the sequence set, if required - empty selection implies
2969         // that no hiding is required.
2970         if (sg != null)
2971         {
2972           invertSequenceMenuItem_actionPerformed(null);
2973           sg = viewport.getSelectionGroup();
2974           toggleSeqs = true;
2975
2976         }
2977         viewport.expandColSelection(sg, true);
2978         // finally invert the column selection and get the new sequence
2979         // selection.
2980         invertColSel_actionPerformed(null);
2981         toggleCols = true;
2982       }
2983     }
2984
2985     if (toggleSeqs)
2986     {
2987       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2988       {
2989         hideSelSequences_actionPerformed(null);
2990         hide = true;
2991       }
2992       else if (!(toggleCols && viewport.hasSelectedColumns()))
2993       {
2994         showAllSeqs_actionPerformed(null);
2995       }
2996     }
2997
2998     if (toggleCols)
2999     {
3000       if (viewport.hasSelectedColumns())
3001       {
3002         hideSelColumns_actionPerformed(null);
3003         if (!toggleSeqs)
3004         {
3005           viewport.setSelectionGroup(sg);
3006         }
3007       }
3008       else if (!hide)
3009       {
3010         showAllColumns_actionPerformed(null);
3011       }
3012     }
3013   }
3014
3015   /*
3016    * (non-Javadoc)
3017    *
3018    * @see
3019    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3020    * event.ActionEvent)
3021    */
3022   @Override
3023   public void hideAllButSelection_actionPerformed(ActionEvent e)
3024   {
3025     toggleHiddenRegions(false, false);
3026     viewport.sendSelection();
3027   }
3028
3029   /*
3030    * (non-Javadoc)
3031    *
3032    * @see
3033    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3034    * .ActionEvent)
3035    */
3036   @Override
3037   public void hideAllSelection_actionPerformed(ActionEvent e)
3038   {
3039     SequenceGroup sg = viewport.getSelectionGroup();
3040     viewport.expandColSelection(sg, false);
3041     viewport.hideAllSelectedSeqs();
3042     viewport.hideSelectedColumns();
3043     alignPanel.paintAlignment(true);
3044     viewport.sendSelection();
3045   }
3046
3047   /*
3048    * (non-Javadoc)
3049    *
3050    * @see
3051    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3052    * ActionEvent)
3053    */
3054   @Override
3055   public void showAllhidden_actionPerformed(ActionEvent e)
3056   {
3057     viewport.showAllHiddenColumns();
3058     viewport.showAllHiddenSeqs();
3059     alignPanel.paintAlignment(true);
3060     viewport.sendSelection();
3061   }
3062
3063   @Override
3064   public void hideSelColumns_actionPerformed(ActionEvent e)
3065   {
3066     viewport.hideSelectedColumns();
3067     alignPanel.paintAlignment(true);
3068     viewport.sendSelection();
3069   }
3070
3071   @Override
3072   public void hiddenMarkers_actionPerformed(ActionEvent e)
3073   {
3074     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3075     repaint();
3076   }
3077
3078   /**
3079    * DOCUMENT ME!
3080    *
3081    * @param e
3082    *          DOCUMENT ME!
3083    */
3084   @Override
3085   protected void scaleAbove_actionPerformed(ActionEvent e)
3086   {
3087     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3088     alignPanel.paintAlignment(true);
3089   }
3090
3091   /**
3092    * DOCUMENT ME!
3093    *
3094    * @param e
3095    *          DOCUMENT ME!
3096    */
3097   @Override
3098   protected void scaleLeft_actionPerformed(ActionEvent e)
3099   {
3100     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3101     alignPanel.paintAlignment(true);
3102   }
3103
3104   /**
3105    * DOCUMENT ME!
3106    *
3107    * @param e
3108    *          DOCUMENT ME!
3109    */
3110   @Override
3111   protected void scaleRight_actionPerformed(ActionEvent e)
3112   {
3113     viewport.setScaleRightWrapped(scaleRight.isSelected());
3114     alignPanel.paintAlignment(true);
3115   }
3116
3117   /**
3118    * DOCUMENT ME!
3119    *
3120    * @param e
3121    *          DOCUMENT ME!
3122    */
3123   @Override
3124   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3125   {
3126     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3127     alignPanel.paintAlignment(true);
3128   }
3129
3130   /**
3131    * DOCUMENT ME!
3132    *
3133    * @param e
3134    *          DOCUMENT ME!
3135    */
3136   @Override
3137   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3138   {
3139     viewport.setShowText(viewTextMenuItem.isSelected());
3140     alignPanel.paintAlignment(true);
3141   }
3142
3143   /**
3144    * DOCUMENT ME!
3145    *
3146    * @param e
3147    *          DOCUMENT ME!
3148    */
3149   @Override
3150   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3151   {
3152     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3153     alignPanel.paintAlignment(true);
3154   }
3155
3156   public FeatureSettings featureSettings;
3157
3158   @Override
3159   public FeatureSettingsControllerI getFeatureSettingsUI()
3160   {
3161     return featureSettings;
3162   }
3163
3164   @Override
3165   public void featureSettings_actionPerformed(ActionEvent e)
3166   {
3167     if (featureSettings != null)
3168     {
3169       featureSettings.close();
3170       featureSettings = null;
3171     }
3172     if (!showSeqFeatures.isSelected())
3173     {
3174       // make sure features are actually displayed
3175       showSeqFeatures.setSelected(true);
3176       showSeqFeatures_actionPerformed(null);
3177     }
3178     featureSettings = new FeatureSettings(this);
3179   }
3180
3181   /**
3182    * Set or clear 'Show Sequence Features'
3183    *
3184    * @param evt
3185    *          DOCUMENT ME!
3186    */
3187   @Override
3188   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3189   {
3190     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3191     alignPanel.paintAlignment(true);
3192     if (alignPanel.getOverviewPanel() != null)
3193     {
3194       alignPanel.getOverviewPanel().updateOverviewImage();
3195     }
3196   }
3197
3198   /**
3199    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3200    * the annotations panel as a whole.
3201    *
3202    * The options to show/hide all annotations should be enabled when the panel
3203    * is shown, and disabled when the panel is hidden.
3204    *
3205    * @param e
3206    */
3207   @Override
3208   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3209   {
3210     final boolean setVisible = annotationPanelMenuItem.isSelected();
3211     viewport.setShowAnnotation(setVisible);
3212     this.showAllSeqAnnotations.setEnabled(setVisible);
3213     this.hideAllSeqAnnotations.setEnabled(setVisible);
3214     this.showAllAlAnnotations.setEnabled(setVisible);
3215     this.hideAllAlAnnotations.setEnabled(setVisible);
3216     alignPanel.updateLayout();
3217   }
3218
3219   @Override
3220   public void alignmentProperties()
3221   {
3222     JEditorPane editPane = new JEditorPane("text/html", "");
3223     editPane.setEditable(false);
3224     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3225             .formatAsHtml();
3226     editPane.setText(MessageManager.formatMessage("label.html_content",
3227             new Object[] { contents.toString() }));
3228     JInternalFrame frame = new JInternalFrame();
3229     frame.getContentPane().add(new JScrollPane(editPane));
3230
3231     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3232             "label.alignment_properties", new Object[] { getTitle() }),
3233             500, 400);
3234   }
3235
3236   /**
3237    * DOCUMENT ME!
3238    *
3239    * @param e
3240    *          DOCUMENT ME!
3241    */
3242   @Override
3243   public void overviewMenuItem_actionPerformed(ActionEvent e)
3244   {
3245     if (alignPanel.overviewPanel != null)
3246     {
3247       return;
3248     }
3249
3250     JInternalFrame frame = new JInternalFrame();
3251     OverviewPanel overview = new OverviewPanel(alignPanel);
3252     frame.setContentPane(overview);
3253     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3254             "label.overview_params", new Object[] { this.getTitle() }),
3255             frame.getWidth(), frame.getHeight());
3256     frame.pack();
3257     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3258     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3259     {
3260       @Override
3261       public void internalFrameClosed(
3262               javax.swing.event.InternalFrameEvent evt)
3263       {
3264         alignPanel.setOverviewPanel(null);
3265       };
3266     });
3267
3268     alignPanel.setOverviewPanel(overview);
3269   }
3270
3271   @Override
3272   public void textColour_actionPerformed()
3273   {
3274     new TextColourChooser().chooseColour(alignPanel, null);
3275   }
3276
3277   /*
3278    * public void covariationColour_actionPerformed() {
3279    * changeColour(new
3280    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3281    * ()[0])); }
3282    */
3283   @Override
3284   public void annotationColour_actionPerformed()
3285   {
3286     new AnnotationColourChooser(viewport, alignPanel);
3287   }
3288
3289   @Override
3290   public void annotationColumn_actionPerformed(ActionEvent e)
3291   {
3292     new AnnotationColumnChooser(viewport, alignPanel);
3293   }
3294
3295   /**
3296    * Action on the user checking or unchecking the option to apply the selected
3297    * colour scheme to all groups. If unchecked, groups may have their own
3298    * independent colour schemes.
3299    *
3300    */
3301   @Override
3302   protected void applyToAllGroups_actionPerformed()
3303   {
3304     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3305   }
3306
3307   /**
3308    * Action on user selecting a colour from the colour menu
3309    *
3310    * @param name
3311    *          the name (not the menu item label!) of the colour scheme
3312    */
3313   @Override
3314   public void changeColour_actionPerformed(String name)
3315   {
3316     /*
3317      * 'User Defined' opens a panel to configure or load a
3318      * user-defined colour scheme
3319      */
3320     if (ResidueColourScheme.USER_DEFINED.equals(name))
3321     {
3322       new UserDefinedColours(alignPanel, null);
3323       return;
3324     }
3325
3326     /*
3327      * otherwise set the chosen colour scheme (or null for 'None')
3328      */
3329     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3330             viewport.getAlignment(), viewport.getHiddenRepSequences());
3331     changeColour(cs);
3332   }
3333
3334   /**
3335    * Actions on setting or changing the alignment colour scheme
3336    *
3337    * @param cs
3338    */
3339   @Override
3340   public void changeColour(ColourSchemeI cs)
3341   {
3342     // TODO: pull up to controller method
3343     if (cs != null)
3344     {
3345       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3346       // Make sure viewport is up to date w.r.t. any sliders
3347       if (viewport.getAbovePIDThreshold())
3348       {
3349         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3350                 "Background");
3351         viewport.setThreshold(threshold);
3352       }
3353
3354       if (viewport.getConservationSelected())
3355       {
3356         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3357                 cs, "Background"));
3358       }
3359     }
3360
3361     viewport.setGlobalColourScheme(cs);
3362
3363     alignPanel.paintAlignment(true);
3364   }
3365
3366   /**
3367    * DOCUMENT ME!
3368    *
3369    * @param e
3370    *          DOCUMENT ME!
3371    */
3372   @Override
3373   protected void modifyPID_actionPerformed()
3374   {
3375     if (viewport.getAbovePIDThreshold()
3376             && viewport.getGlobalColourScheme() != null)
3377     {
3378       SliderPanel.setPIDSliderSource(alignPanel,
3379               viewport.getGlobalColourScheme(), "Background");
3380       SliderPanel.showPIDSlider();
3381     }
3382   }
3383
3384   /**
3385    * DOCUMENT ME!
3386    *
3387    * @param e
3388    *          DOCUMENT ME!
3389    */
3390   @Override
3391   protected void modifyConservation_actionPerformed()
3392   {
3393     if (viewport.getConservationSelected()
3394             && viewport.getGlobalColourScheme() != null)
3395     {
3396       SliderPanel.setConservationSlider(alignPanel,
3397               viewport.getGlobalColourScheme(), "Background");
3398       SliderPanel.showConservationSlider();
3399     }
3400   }
3401
3402   /**
3403    * DOCUMENT ME!
3404    *
3405    * @param e
3406    *          DOCUMENT ME!
3407    */
3408   @Override
3409   protected void conservationMenuItem_actionPerformed()
3410   {
3411     viewport.setConservationSelected(conservationMenuItem.isSelected());
3412
3413     viewport.setAbovePIDThreshold(false);
3414     abovePIDThreshold.setSelected(false);
3415
3416     changeColour(viewport.getGlobalColourScheme());
3417
3418     modifyConservation_actionPerformed();
3419   }
3420
3421   /**
3422    * DOCUMENT ME!
3423    *
3424    * @param e
3425    *          DOCUMENT ME!
3426    */
3427   @Override
3428   public void abovePIDThreshold_actionPerformed()
3429   {
3430     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3431
3432     conservationMenuItem.setSelected(false);
3433     viewport.setConservationSelected(false);
3434
3435     changeColour(viewport.getGlobalColourScheme());
3436
3437     modifyPID_actionPerformed();
3438   }
3439
3440   /**
3441    * DOCUMENT ME!
3442    *
3443    * @param e
3444    *          DOCUMENT ME!
3445    */
3446   @Override
3447   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3448   {
3449     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3450     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3451             .getAlignment().getSequenceAt(0), null);
3452     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3453             viewport.getAlignment()));
3454     alignPanel.paintAlignment(true);
3455   }
3456
3457   /**
3458    * DOCUMENT ME!
3459    *
3460    * @param e
3461    *          DOCUMENT ME!
3462    */
3463   @Override
3464   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3465   {
3466     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3467     AlignmentSorter.sortByID(viewport.getAlignment());
3468     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3469             viewport.getAlignment()));
3470     alignPanel.paintAlignment(true);
3471   }
3472
3473   /**
3474    * DOCUMENT ME!
3475    *
3476    * @param e
3477    *          DOCUMENT ME!
3478    */
3479   @Override
3480   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3481   {
3482     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3483     AlignmentSorter.sortByLength(viewport.getAlignment());
3484     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3485             viewport.getAlignment()));
3486     alignPanel.paintAlignment(true);
3487   }
3488
3489   /**
3490    * DOCUMENT ME!
3491    *
3492    * @param e
3493    *          DOCUMENT ME!
3494    */
3495   @Override
3496   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3497   {
3498     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3499     AlignmentSorter.sortByGroup(viewport.getAlignment());
3500     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3501             viewport.getAlignment()));
3502
3503     alignPanel.paintAlignment(true);
3504   }
3505
3506   /**
3507    * DOCUMENT ME!
3508    *
3509    * @param e
3510    *          DOCUMENT ME!
3511    */
3512   @Override
3513   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3514   {
3515     new RedundancyPanel(alignPanel, this);
3516   }
3517
3518   /**
3519    * DOCUMENT ME!
3520    *
3521    * @param e
3522    *          DOCUMENT ME!
3523    */
3524   @Override
3525   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3526   {
3527     if ((viewport.getSelectionGroup() == null)
3528             || (viewport.getSelectionGroup().getSize() < 2))
3529     {
3530       JvOptionPane.showInternalMessageDialog(this, MessageManager
3531               .getString("label.you_must_select_least_two_sequences"),
3532               MessageManager.getString("label.invalid_selection"),
3533               JvOptionPane.WARNING_MESSAGE);
3534     }
3535     else
3536     {
3537       JInternalFrame frame = new JInternalFrame();
3538       frame.setContentPane(new PairwiseAlignPanel(viewport));
3539       Desktop.addInternalFrame(frame,
3540               MessageManager.getString("action.pairwise_alignment"), 600,
3541               500);
3542     }
3543   }
3544
3545   /**
3546    * DOCUMENT ME!
3547    *
3548    * @param e
3549    *          DOCUMENT ME!
3550    */
3551   @Override
3552   public void PCAMenuItem_actionPerformed(ActionEvent e)
3553   {
3554     if (((viewport.getSelectionGroup() != null)
3555             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3556             .getSelectionGroup().getSize() > 0))
3557             || (viewport.getAlignment().getHeight() < 4))
3558     {
3559       JvOptionPane
3560               .showInternalMessageDialog(
3561                       this,
3562                       MessageManager
3563                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3564                       MessageManager
3565                               .getString("label.sequence_selection_insufficient"),
3566                       JvOptionPane.WARNING_MESSAGE);
3567
3568       return;
3569     }
3570
3571     new PCAPanel(alignPanel);
3572   }
3573
3574   @Override
3575   public void autoCalculate_actionPerformed(ActionEvent e)
3576   {
3577     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3578     if (viewport.autoCalculateConsensus)
3579     {
3580       viewport.firePropertyChange("alignment", null, viewport
3581               .getAlignment().getSequences());
3582     }
3583   }
3584
3585   @Override
3586   public void sortByTreeOption_actionPerformed(ActionEvent e)
3587   {
3588     viewport.sortByTree = sortByTree.isSelected();
3589   }
3590
3591   @Override
3592   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3593   {
3594     viewport.followSelection = listenToViewSelections.isSelected();
3595   }
3596
3597   /**
3598    * DOCUMENT ME!
3599    *
3600    * @param e
3601    *          DOCUMENT ME!
3602    */
3603   @Override
3604   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3605   {
3606     newTreePanel("AV", "PID", "Average distance tree using PID");
3607   }
3608
3609   /**
3610    * DOCUMENT ME!
3611    *
3612    * @param e
3613    *          DOCUMENT ME!
3614    */
3615   @Override
3616   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3617   {
3618     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3619   }
3620
3621   /**
3622    * DOCUMENT ME!
3623    *
3624    * @param e
3625    *          DOCUMENT ME!
3626    */
3627   @Override
3628   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3629   {
3630     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3631   }
3632
3633   /**
3634    * DOCUMENT ME!
3635    *
3636    * @param e
3637    *          DOCUMENT ME!
3638    */
3639   @Override
3640   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3641   {
3642     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3643   }
3644
3645   /**
3646    * DOCUMENT ME!
3647    *
3648    * @param type
3649    *          DOCUMENT ME!
3650    * @param pwType
3651    *          DOCUMENT ME!
3652    * @param title
3653    *          DOCUMENT ME!
3654    */
3655   void newTreePanel(String type, String pwType, String title)
3656   {
3657     TreePanel tp;
3658
3659     if (viewport.getSelectionGroup() != null
3660             && viewport.getSelectionGroup().getSize() > 0)
3661     {
3662       if (viewport.getSelectionGroup().getSize() < 3)
3663       {
3664         JvOptionPane
3665                 .showMessageDialog(
3666                         Desktop.desktop,
3667                         MessageManager
3668                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3669                         MessageManager
3670                                 .getString("label.not_enough_sequences"),
3671                         JvOptionPane.WARNING_MESSAGE);
3672         return;
3673       }
3674
3675       SequenceGroup sg = viewport.getSelectionGroup();
3676
3677       /* Decide if the selection is a column region */
3678       for (SequenceI _s : sg.getSequences())
3679       {
3680         if (_s.getLength() < sg.getEndRes())
3681         {
3682           JvOptionPane
3683                   .showMessageDialog(
3684                           Desktop.desktop,
3685                           MessageManager
3686                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3687                           MessageManager
3688                                   .getString("label.sequences_selection_not_aligned"),
3689                           JvOptionPane.WARNING_MESSAGE);
3690
3691           return;
3692         }
3693       }
3694
3695       title = title + " on region";
3696       tp = new TreePanel(alignPanel, type, pwType);
3697     }
3698     else
3699     {
3700       // are the visible sequences aligned?
3701       if (!viewport.getAlignment().isAligned(false))
3702       {
3703         JvOptionPane
3704                 .showMessageDialog(
3705                         Desktop.desktop,
3706                         MessageManager
3707                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3708                         MessageManager
3709                                 .getString("label.sequences_not_aligned"),
3710                         JvOptionPane.WARNING_MESSAGE);
3711
3712         return;
3713       }
3714
3715       if (viewport.getAlignment().getHeight() < 2)
3716       {
3717         return;
3718       }
3719
3720       tp = new TreePanel(alignPanel, type, pwType);
3721     }
3722
3723     title += " from ";
3724
3725     if (viewport.viewName != null)
3726     {
3727       title += viewport.viewName + " of ";
3728     }
3729
3730     title += this.title;
3731
3732     Desktop.addInternalFrame(tp, title, 600, 500);
3733   }
3734
3735   /**
3736    * DOCUMENT ME!
3737    *
3738    * @param title
3739    *          DOCUMENT ME!
3740    * @param order
3741    *          DOCUMENT ME!
3742    */
3743   public void addSortByOrderMenuItem(String title,
3744           final AlignmentOrder order)
3745   {
3746     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3747             "action.by_title_param", new Object[] { title }));
3748     sort.add(item);
3749     item.addActionListener(new java.awt.event.ActionListener()
3750     {
3751       @Override
3752       public void actionPerformed(ActionEvent e)
3753       {
3754         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3755
3756         // TODO: JBPNote - have to map order entries to curent SequenceI
3757         // pointers
3758         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3759
3760         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3761                 .getAlignment()));
3762
3763         alignPanel.paintAlignment(true);
3764       }
3765     });
3766   }
3767
3768   /**
3769    * Add a new sort by annotation score menu item
3770    *
3771    * @param sort
3772    *          the menu to add the option to
3773    * @param scoreLabel
3774    *          the label used to retrieve scores for each sequence on the
3775    *          alignment
3776    */
3777   public void addSortByAnnotScoreMenuItem(JMenu sort,
3778           final String scoreLabel)
3779   {
3780     final JMenuItem item = new JMenuItem(scoreLabel);
3781     sort.add(item);
3782     item.addActionListener(new java.awt.event.ActionListener()
3783     {
3784       @Override
3785       public void actionPerformed(ActionEvent e)
3786       {
3787         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3788         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3789                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3790         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3791                 viewport.getAlignment()));
3792         alignPanel.paintAlignment(true);
3793       }
3794     });
3795   }
3796
3797   /**
3798    * last hash for alignment's annotation array - used to minimise cost of
3799    * rebuild.
3800    */
3801   protected int _annotationScoreVectorHash;
3802
3803   /**
3804    * search the alignment and rebuild the sort by annotation score submenu the
3805    * last alignment annotation vector hash is stored to minimize cost of
3806    * rebuilding in subsequence calls.
3807    *
3808    */
3809   @Override
3810   public void buildSortByAnnotationScoresMenu()
3811   {
3812     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3813     {
3814       return;
3815     }
3816
3817     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3818     {
3819       sortByAnnotScore.removeAll();
3820       // almost certainly a quicker way to do this - but we keep it simple
3821       Hashtable scoreSorts = new Hashtable();
3822       AlignmentAnnotation aann[];
3823       for (SequenceI sqa : viewport.getAlignment().getSequences())
3824       {
3825         aann = sqa.getAnnotation();
3826         for (int i = 0; aann != null && i < aann.length; i++)
3827         {
3828           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3829           {
3830             scoreSorts.put(aann[i].label, aann[i].label);
3831           }
3832         }
3833       }
3834       Enumeration labels = scoreSorts.keys();
3835       while (labels.hasMoreElements())
3836       {
3837         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3838                 (String) labels.nextElement());
3839       }
3840       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3841       scoreSorts.clear();
3842
3843       _annotationScoreVectorHash = viewport.getAlignment()
3844               .getAlignmentAnnotation().hashCode();
3845     }
3846   }
3847
3848   /**
3849    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3850    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3851    * call. Listeners are added to remove the menu item when the treePanel is
3852    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3853    * modified.
3854    *
3855    * @param treePanel
3856    *          Displayed tree window.
3857    * @param title
3858    *          SortBy menu item title.
3859    */
3860   @Override
3861   public void buildTreeMenu()
3862   {
3863     calculateTree.removeAll();
3864     // build the calculate menu
3865
3866     for (final String type : new String[] { "NJ", "AV" })
3867     {
3868       String treecalcnm = MessageManager.getString("label.tree_calc_"
3869               + type.toLowerCase());
3870       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3871       {
3872         JMenuItem tm = new JMenuItem();
3873         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3874         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3875                 || sm.isProtein() == !viewport.getAlignment()
3876                         .isNucleotide())
3877         {
3878           String smn = MessageManager.getStringOrReturn(
3879                   "label.score_model_", sm.getName());
3880           final String title = MessageManager.formatMessage(
3881                   "label.treecalc_title", treecalcnm, smn);
3882           tm.setText(title);//
3883           tm.addActionListener(new java.awt.event.ActionListener()
3884           {
3885             @Override
3886             public void actionPerformed(ActionEvent e)
3887             {
3888               newTreePanel(type, pwtype, title);
3889             }
3890           });
3891           calculateTree.add(tm);
3892         }
3893
3894       }
3895     }
3896     sortByTreeMenu.removeAll();
3897
3898     List<Component> comps = PaintRefresher.components.get(viewport
3899             .getSequenceSetId());
3900     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3901     for (Component comp : comps)
3902     {
3903       if (comp instanceof TreePanel)
3904       {
3905         treePanels.add((TreePanel) comp);
3906       }
3907     }
3908
3909     if (treePanels.size() < 1)
3910     {
3911       sortByTreeMenu.setVisible(false);
3912       return;
3913     }
3914
3915     sortByTreeMenu.setVisible(true);
3916
3917     for (final TreePanel tp : treePanels)
3918     {
3919       final JMenuItem item = new JMenuItem(tp.getTitle());
3920       item.addActionListener(new java.awt.event.ActionListener()
3921       {
3922         @Override
3923         public void actionPerformed(ActionEvent e)
3924         {
3925           tp.sortByTree_actionPerformed();
3926           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3927
3928         }
3929       });
3930
3931       sortByTreeMenu.add(item);
3932     }
3933   }
3934
3935   public boolean sortBy(AlignmentOrder alorder, String undoname)
3936   {
3937     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3938     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3939     if (undoname != null)
3940     {
3941       addHistoryItem(new OrderCommand(undoname, oldOrder,
3942               viewport.getAlignment()));
3943     }
3944     alignPanel.paintAlignment(true);
3945     return true;
3946   }
3947
3948   /**
3949    * Work out whether the whole set of sequences or just the selected set will
3950    * be submitted for multiple alignment.
3951    *
3952    */
3953   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3954   {
3955     // Now, check we have enough sequences
3956     AlignmentView msa = null;
3957
3958     if ((viewport.getSelectionGroup() != null)
3959             && (viewport.getSelectionGroup().getSize() > 1))
3960     {
3961       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3962       // some common interface!
3963       /*
3964        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3965        * SequenceI[sz = seqs.getSize(false)];
3966        *
3967        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3968        * seqs.getSequenceAt(i); }
3969        */
3970       msa = viewport.getAlignmentView(true);
3971     }
3972     else if (viewport.getSelectionGroup() != null
3973             && viewport.getSelectionGroup().getSize() == 1)
3974     {
3975       int option = JvOptionPane.showConfirmDialog(this,
3976               MessageManager.getString("warn.oneseq_msainput_selection"),
3977               MessageManager.getString("label.invalid_selection"),
3978               JvOptionPane.OK_CANCEL_OPTION);
3979       if (option == JvOptionPane.OK_OPTION)
3980       {
3981         msa = viewport.getAlignmentView(false);
3982       }
3983     }
3984     else
3985     {
3986       msa = viewport.getAlignmentView(false);
3987     }
3988     return msa;
3989   }
3990
3991   /**
3992    * Decides what is submitted to a secondary structure prediction service: the
3993    * first sequence in the alignment, or in the current selection, or, if the
3994    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3995    * region or the whole alignment. (where the first sequence in the set is the
3996    * one that the prediction will be for).
3997    */
3998   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3999   {
4000     AlignmentView seqs = null;
4001
4002     if ((viewport.getSelectionGroup() != null)
4003             && (viewport.getSelectionGroup().getSize() > 0))
4004     {
4005       seqs = viewport.getAlignmentView(true);
4006     }
4007     else
4008     {
4009       seqs = viewport.getAlignmentView(false);
4010     }
4011     // limit sequences - JBPNote in future - could spawn multiple prediction
4012     // jobs
4013     // TODO: viewport.getAlignment().isAligned is a global state - the local
4014     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4015     if (!viewport.getAlignment().isAligned(false))
4016     {
4017       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4018       // TODO: if seqs.getSequences().length>1 then should really have warned
4019       // user!
4020
4021     }
4022     return seqs;
4023   }
4024
4025   /**
4026    * DOCUMENT ME!
4027    *
4028    * @param e
4029    *          DOCUMENT ME!
4030    */
4031   @Override
4032   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4033   {
4034     // Pick the tree file
4035     JalviewFileChooser chooser = new JalviewFileChooser(
4036             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4037     chooser.setFileView(new JalviewFileView());
4038     chooser.setDialogTitle(MessageManager
4039             .getString("label.select_newick_like_tree_file"));
4040     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4041
4042     int value = chooser.showOpenDialog(null);
4043
4044     if (value == JalviewFileChooser.APPROVE_OPTION)
4045     {
4046       String choice = chooser.getSelectedFile().getPath();
4047       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4048       jalview.io.NewickFile fin = null;
4049       try
4050       {
4051         fin = new NewickFile(choice, DataSourceType.FILE);
4052         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4053       } catch (Exception ex)
4054       {
4055         JvOptionPane
4056                 .showMessageDialog(
4057                         Desktop.desktop,
4058                         ex.getMessage(),
4059                         MessageManager
4060                                 .getString("label.problem_reading_tree_file"),
4061                         JvOptionPane.WARNING_MESSAGE);
4062         ex.printStackTrace();
4063       }
4064       if (fin != null && fin.hasWarningMessage())
4065       {
4066         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4067                 .getWarningMessage(), MessageManager
4068                 .getString("label.possible_problem_with_tree_file"),
4069                 JvOptionPane.WARNING_MESSAGE);
4070       }
4071     }
4072   }
4073
4074   public TreePanel ShowNewickTree(NewickFile nf, String title)
4075   {
4076     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4077   }
4078
4079   public TreePanel ShowNewickTree(NewickFile nf, String title,
4080           AlignmentView input)
4081   {
4082     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4083   }
4084
4085   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4086           int h, int x, int y)
4087   {
4088     return ShowNewickTree(nf, title, null, w, h, x, y);
4089   }
4090
4091   /**
4092    * Add a treeviewer for the tree extracted from a newick file object to the
4093    * current alignment view
4094    *
4095    * @param nf
4096    *          the tree
4097    * @param title
4098    *          tree viewer title
4099    * @param input
4100    *          Associated alignment input data (or null)
4101    * @param w
4102    *          width
4103    * @param h
4104    *          height
4105    * @param x
4106    *          position
4107    * @param y
4108    *          position
4109    * @return TreePanel handle
4110    */
4111   public TreePanel ShowNewickTree(NewickFile nf, String title,
4112           AlignmentView input, int w, int h, int x, int y)
4113   {
4114     TreePanel tp = null;
4115
4116     try
4117     {
4118       nf.parse();
4119
4120       if (nf.getTree() != null)
4121       {
4122         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4123
4124         tp.setSize(w, h);
4125
4126         if (x > 0 && y > 0)
4127         {
4128           tp.setLocation(x, y);
4129         }
4130
4131         Desktop.addInternalFrame(tp, title, w, h);
4132       }
4133     } catch (Exception ex)
4134     {
4135       ex.printStackTrace();
4136     }
4137
4138     return tp;
4139   }
4140
4141   private boolean buildingMenu = false;
4142
4143   /**
4144    * Generates menu items and listener event actions for web service clients
4145    *
4146    */
4147   public void BuildWebServiceMenu()
4148   {
4149     while (buildingMenu)
4150     {
4151       try
4152       {
4153         System.err.println("Waiting for building menu to finish.");
4154         Thread.sleep(10);
4155       } catch (Exception e)
4156       {
4157       }
4158     }
4159     final AlignFrame me = this;
4160     buildingMenu = true;
4161     new Thread(new Runnable()
4162     {
4163       @Override
4164       public void run()
4165       {
4166         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4167         try
4168         {
4169           // System.err.println("Building ws menu again "
4170           // + Thread.currentThread());
4171           // TODO: add support for context dependent disabling of services based
4172           // on
4173           // alignment and current selection
4174           // TODO: add additional serviceHandle parameter to specify abstract
4175           // handler
4176           // class independently of AbstractName
4177           // TODO: add in rediscovery GUI function to restart discoverer
4178           // TODO: group services by location as well as function and/or
4179           // introduce
4180           // object broker mechanism.
4181           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4182           final IProgressIndicator af = me;
4183
4184           /*
4185            * do not i18n these strings - they are hard-coded in class
4186            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4187            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4188            */
4189           final JMenu msawsmenu = new JMenu("Alignment");
4190           final JMenu secstrmenu = new JMenu(
4191                   "Secondary Structure Prediction");
4192           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4193           final JMenu analymenu = new JMenu("Analysis");
4194           final JMenu dismenu = new JMenu("Protein Disorder");
4195           // JAL-940 - only show secondary structure prediction services from
4196           // the legacy server
4197           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4198               // &&
4199           Discoverer.services != null && (Discoverer.services.size() > 0))
4200           {
4201             // TODO: refactor to allow list of AbstractName/Handler bindings to
4202             // be
4203             // stored or retrieved from elsewhere
4204             // No MSAWS used any more:
4205             // Vector msaws = null; // (Vector)
4206             // Discoverer.services.get("MsaWS");
4207             Vector secstrpr = (Vector) Discoverer.services
4208                     .get("SecStrPred");
4209             if (secstrpr != null)
4210             {
4211               // Add any secondary structure prediction services
4212               for (int i = 0, j = secstrpr.size(); i < j; i++)
4213               {
4214                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4215                         .get(i);
4216                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4217                         .getServiceClient(sh);
4218                 int p = secstrmenu.getItemCount();
4219                 impl.attachWSMenuEntry(secstrmenu, me);
4220                 int q = secstrmenu.getItemCount();
4221                 for (int litm = p; litm < q; litm++)
4222                 {
4223                   legacyItems.add(secstrmenu.getItem(litm));
4224                 }
4225               }
4226             }
4227           }
4228
4229           // Add all submenus in the order they should appear on the web
4230           // services menu
4231           wsmenu.add(msawsmenu);
4232           wsmenu.add(secstrmenu);
4233           wsmenu.add(dismenu);
4234           wsmenu.add(analymenu);
4235           // No search services yet
4236           // wsmenu.add(seqsrchmenu);
4237
4238           javax.swing.SwingUtilities.invokeLater(new Runnable()
4239           {
4240             @Override
4241             public void run()
4242             {
4243               try
4244               {
4245                 webService.removeAll();
4246                 // first, add discovered services onto the webservices menu
4247                 if (wsmenu.size() > 0)
4248                 {
4249                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4250                   {
4251                     webService.add(wsmenu.get(i));
4252                   }
4253                 }
4254                 else
4255                 {
4256                   webService.add(me.webServiceNoServices);
4257                 }
4258                 // TODO: move into separate menu builder class.
4259                 boolean new_sspred = false;
4260                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4261                 {
4262                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4263                   if (jws2servs != null)
4264                   {
4265                     if (jws2servs.hasServices())
4266                     {
4267                       jws2servs.attachWSMenuEntry(webService, me);
4268                       for (Jws2Instance sv : jws2servs.getServices())
4269                       {
4270                         if (sv.description.toLowerCase().contains("jpred"))
4271                         {
4272                           for (JMenuItem jmi : legacyItems)
4273                           {
4274                             jmi.setVisible(false);
4275                           }
4276                         }
4277                       }
4278
4279                     }
4280                     if (jws2servs.isRunning())
4281                     {
4282                       JMenuItem tm = new JMenuItem(
4283                               "Still discovering JABA Services");
4284                       tm.setEnabled(false);
4285                       webService.add(tm);
4286                     }
4287                   }
4288                 }
4289                 build_urlServiceMenu(me.webService);
4290                 build_fetchdbmenu(webService);
4291                 for (JMenu item : wsmenu)
4292                 {
4293                   if (item.getItemCount() == 0)
4294                   {
4295                     item.setEnabled(false);
4296                   }
4297                   else
4298                   {
4299                     item.setEnabled(true);
4300                   }
4301                 }
4302               } catch (Exception e)
4303               {
4304                 Cache.log
4305                         .debug("Exception during web service menu building process.",
4306                                 e);
4307               }
4308             }
4309           });
4310         } catch (Exception e)
4311         {
4312         }
4313         buildingMenu = false;
4314       }
4315     }).start();
4316
4317   }
4318
4319   /**
4320    * construct any groupURL type service menu entries.
4321    *
4322    * @param webService
4323    */
4324   private void build_urlServiceMenu(JMenu webService)
4325   {
4326     // TODO: remove this code when 2.7 is released
4327     // DEBUG - alignmentView
4328     /*
4329      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4330      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4331      *
4332      * @Override public void actionPerformed(ActionEvent e) {
4333      * jalview.datamodel.AlignmentView
4334      * .testSelectionViews(af.viewport.getAlignment(),
4335      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4336      *
4337      * }); webService.add(testAlView);
4338      */
4339     // TODO: refactor to RestClient discoverer and merge menu entries for
4340     // rest-style services with other types of analysis/calculation service
4341     // SHmmr test client - still being implemented.
4342     // DEBUG - alignmentView
4343
4344     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4345             .getRestClients())
4346     {
4347       client.attachWSMenuEntry(
4348               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4349               this);
4350     }
4351   }
4352
4353   /**
4354    * Searches the alignment sequences for xRefs and builds the Show
4355    * Cross-References menu (formerly called Show Products), with database
4356    * sources for which cross-references are found (protein sources for a
4357    * nucleotide alignment and vice versa)
4358    *
4359    * @return true if Show Cross-references menu should be enabled
4360    */
4361   public boolean canShowProducts()
4362   {
4363     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4364     AlignmentI dataset = viewport.getAlignment().getDataset();
4365
4366     showProducts.removeAll();
4367     final boolean dna = viewport.getAlignment().isNucleotide();
4368
4369     if (seqs == null || seqs.length == 0)
4370     {
4371       // nothing to see here.
4372       return false;
4373     }
4374
4375     boolean showp = false;
4376     try
4377     {
4378       List<String> ptypes = new CrossRef(seqs, dataset)
4379               .findXrefSourcesForSequences(dna);
4380
4381       for (final String source : ptypes)
4382       {
4383         showp = true;
4384         final AlignFrame af = this;
4385         JMenuItem xtype = new JMenuItem(source);
4386         xtype.addActionListener(new ActionListener()
4387         {
4388           @Override
4389           public void actionPerformed(ActionEvent e)
4390           {
4391             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4392           }
4393         });
4394         showProducts.add(xtype);
4395       }
4396       showProducts.setVisible(showp);
4397       showProducts.setEnabled(showp);
4398     } catch (Exception e)
4399     {
4400       Cache.log
4401               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4402                       e);
4403       return false;
4404     }
4405     return showp;
4406   }
4407
4408   /**
4409    * Finds and displays cross-references for the selected sequences (protein
4410    * products for nucleotide sequences, dna coding sequences for peptides).
4411    *
4412    * @param sel
4413    *          the sequences to show cross-references for
4414    * @param dna
4415    *          true if from a nucleotide alignment (so showing proteins)
4416    * @param source
4417    *          the database to show cross-references for
4418    */
4419   protected void showProductsFor(final SequenceI[] sel,
4420           final boolean _odna, final String source)
4421   {
4422     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4423             .start();
4424   }
4425
4426   /**
4427    * Construct and display a new frame containing the translation of this
4428    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4429    */
4430   @Override
4431   public void showTranslation_actionPerformed(ActionEvent e)
4432   {
4433     AlignmentI al = null;
4434     try
4435     {
4436       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4437
4438       al = dna.translateCdna();
4439     } catch (Exception ex)
4440     {
4441       jalview.bin.Cache.log.error(
4442               "Exception during translation. Please report this !", ex);
4443       final String msg = MessageManager
4444               .getString("label.error_when_translating_sequences_submit_bug_report");
4445       final String errorTitle = MessageManager
4446               .getString("label.implementation_error")
4447               + MessageManager.getString("label.translation_failed");
4448       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4449               JvOptionPane.ERROR_MESSAGE);
4450       return;
4451     }
4452     if (al == null || al.getHeight() == 0)
4453     {
4454       final String msg = MessageManager
4455               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4456       final String errorTitle = MessageManager
4457               .getString("label.translation_failed");
4458       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4459               JvOptionPane.WARNING_MESSAGE);
4460     }
4461     else
4462     {
4463       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4464       af.setFileFormat(this.currentFileFormat);
4465       final String newTitle = MessageManager.formatMessage(
4466               "label.translation_of_params",
4467               new Object[] { this.getTitle() });
4468       af.setTitle(newTitle);
4469       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4470       {
4471         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4472         viewport.openSplitFrame(af, new Alignment(seqs));
4473       }
4474       else
4475       {
4476         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4477                 DEFAULT_HEIGHT);
4478       }
4479     }
4480   }
4481
4482   /**
4483    * Set the file format
4484    *
4485    * @param format
4486    */
4487   public void setFileFormat(FileFormatI format)
4488   {
4489     this.currentFileFormat = format;
4490   }
4491
4492   /**
4493    * Try to load a features file onto the alignment.
4494    *
4495    * @param file
4496    *          contents or path to retrieve file
4497    * @param sourceType
4498    *          access mode of file (see jalview.io.AlignFile)
4499    * @return true if features file was parsed correctly.
4500    */
4501   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4502   {
4503     return avc.parseFeaturesFile(file, sourceType,
4504             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4505
4506   }
4507
4508   @Override
4509   public void refreshFeatureUI(boolean enableIfNecessary)
4510   {
4511     // note - currently this is only still here rather than in the controller
4512     // because of the featureSettings hard reference that is yet to be
4513     // abstracted
4514     if (enableIfNecessary)
4515     {
4516       viewport.setShowSequenceFeatures(true);
4517       showSeqFeatures.setSelected(true);
4518     }
4519
4520   }
4521
4522   @Override
4523   public void dragEnter(DropTargetDragEvent evt)
4524   {
4525   }
4526
4527   @Override
4528   public void dragExit(DropTargetEvent evt)
4529   {
4530   }
4531
4532   @Override
4533   public void dragOver(DropTargetDragEvent evt)
4534   {
4535   }
4536
4537   @Override
4538   public void dropActionChanged(DropTargetDragEvent evt)
4539   {
4540   }
4541
4542   @Override
4543   public void drop(DropTargetDropEvent evt)
4544   {
4545     // JAL-1552 - acceptDrop required before getTransferable call for
4546     // Java's Transferable for native dnd
4547     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4548     Transferable t = evt.getTransferable();
4549     List<String> files = new ArrayList<String>();
4550     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4551
4552     try
4553     {
4554       Desktop.transferFromDropTarget(files, protocols, evt, t);
4555     } catch (Exception e)
4556     {
4557       e.printStackTrace();
4558     }
4559     if (files != null)
4560     {
4561       try
4562       {
4563         // check to see if any of these files have names matching sequences in
4564         // the alignment
4565         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4566                 .getAlignment().getSequencesArray());
4567         /**
4568          * Object[] { String,SequenceI}
4569          */
4570         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4571         ArrayList<String> filesnotmatched = new ArrayList<String>();
4572         for (int i = 0; i < files.size(); i++)
4573         {
4574           String file = files.get(i).toString();
4575           String pdbfn = "";
4576           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4577           if (protocol == DataSourceType.FILE)
4578           {
4579             File fl = new File(file);
4580             pdbfn = fl.getName();
4581           }
4582           else if (protocol == DataSourceType.URL)
4583           {
4584             URL url = new URL(file);
4585             pdbfn = url.getFile();
4586           }
4587           if (pdbfn.length() > 0)
4588           {
4589             // attempt to find a match in the alignment
4590             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4591             int l = 0, c = pdbfn.indexOf(".");
4592             while (mtch == null && c != -1)
4593             {
4594               do
4595               {
4596                 l = c;
4597               } while ((c = pdbfn.indexOf(".", l)) > l);
4598               if (l > -1)
4599               {
4600                 pdbfn = pdbfn.substring(0, l);
4601               }
4602               mtch = idm.findAllIdMatches(pdbfn);
4603             }
4604             if (mtch != null)
4605             {
4606               FileFormatI type = null;
4607               try
4608               {
4609                 type = new IdentifyFile().identify(file, protocol);
4610               } catch (Exception ex)
4611               {
4612                 type = null;
4613               }
4614               if (type != null && type.isStructureFile())
4615               {
4616                 filesmatched.add(new Object[] { file, protocol, mtch });
4617                 continue;
4618               }
4619             }
4620             // File wasn't named like one of the sequences or wasn't a PDB file.
4621             filesnotmatched.add(file);
4622           }
4623         }
4624         int assocfiles = 0;
4625         if (filesmatched.size() > 0)
4626         {
4627           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4628                   || JvOptionPane
4629                           .showConfirmDialog(
4630                                   this,
4631                                   MessageManager
4632                                           .formatMessage(
4633                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4634                                                   new Object[] { Integer
4635                                                           .valueOf(
4636                                                                   filesmatched
4637                                                                           .size())
4638                                                           .toString() }),
4639                                   MessageManager
4640                                           .getString("label.automatically_associate_structure_files_by_name"),
4641                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4642
4643           {
4644             for (Object[] fm : filesmatched)
4645             {
4646               // try and associate
4647               // TODO: may want to set a standard ID naming formalism for
4648               // associating PDB files which have no IDs.
4649               for (SequenceI toassoc : (SequenceI[]) fm[2])
4650               {
4651                 PDBEntry pe = new AssociatePdbFileWithSeq()
4652                         .associatePdbWithSeq((String) fm[0],
4653                                 (DataSourceType) fm[1], toassoc, false,
4654                                 Desktop.instance);
4655                 if (pe != null)
4656                 {
4657                   System.err.println("Associated file : "
4658                           + ((String) fm[0]) + " with "
4659                           + toassoc.getDisplayId(true));
4660                   assocfiles++;
4661                 }
4662               }
4663               alignPanel.paintAlignment(true);
4664             }
4665           }
4666         }
4667         if (filesnotmatched.size() > 0)
4668         {
4669           if (assocfiles > 0
4670                   && (Cache.getDefault(
4671                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4672                           .showConfirmDialog(
4673                                   this,
4674                                   "<html>"
4675                                           + MessageManager
4676                                                   .formatMessage(
4677                                                           "label.ignore_unmatched_dropped_files_info",
4678                                                           new Object[] { Integer
4679                                                                   .valueOf(
4680                                                                           filesnotmatched
4681                                                                                   .size())
4682                                                                   .toString() })
4683                                           + "</html>",
4684                                   MessageManager
4685                                           .getString("label.ignore_unmatched_dropped_files"),
4686                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4687           {
4688             return;
4689           }
4690           for (String fn : filesnotmatched)
4691           {
4692             loadJalviewDataFile(fn, null, null, null);
4693           }
4694
4695         }
4696       } catch (Exception ex)
4697       {
4698         ex.printStackTrace();
4699       }
4700     }
4701   }
4702
4703   /**
4704    * Attempt to load a "dropped" file or URL string: First by testing whether
4705    * it's an Annotation file, then a JNet file, and finally a features file. If
4706    * all are false then the user may have dropped an alignment file onto this
4707    * AlignFrame.
4708    *
4709    * @param file
4710    *          either a filename or a URL string.
4711    */
4712   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4713           FileFormatI format, SequenceI assocSeq)
4714   {
4715     try
4716     {
4717       if (sourceType == null)
4718       {
4719         sourceType = FormatAdapter.checkProtocol(file);
4720       }
4721       // if the file isn't identified, or not positively identified as some
4722       // other filetype (PFAM is default unidentified alignment file type) then
4723       // try to parse as annotation.
4724       boolean isAnnotation = (format == null || FileFormat.Pfam
4725               .equals(format)) ? new AnnotationFile()
4726               .annotateAlignmentView(viewport, file, sourceType) : false;
4727
4728       if (!isAnnotation)
4729       {
4730         // first see if its a T-COFFEE score file
4731         TCoffeeScoreFile tcf = null;
4732         try
4733         {
4734           tcf = new TCoffeeScoreFile(file, sourceType);
4735           if (tcf.isValid())
4736           {
4737             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4738             {
4739               buildColourMenu();
4740               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4741               isAnnotation = true;
4742               statusBar
4743                       .setText(MessageManager
4744                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4745             }
4746             else
4747             {
4748               // some problem - if no warning its probable that the ID matching
4749               // process didn't work
4750               JvOptionPane
4751                       .showMessageDialog(
4752                               Desktop.desktop,
4753                               tcf.getWarningMessage() == null ? MessageManager
4754                                       .getString("label.check_file_matches_sequence_ids_alignment")
4755                                       : tcf.getWarningMessage(),
4756                               MessageManager
4757                                       .getString("label.problem_reading_tcoffee_score_file"),
4758                               JvOptionPane.WARNING_MESSAGE);
4759             }
4760           }
4761           else
4762           {
4763             tcf = null;
4764           }
4765         } catch (Exception x)
4766         {
4767           Cache.log
4768                   .debug("Exception when processing data source as T-COFFEE score file",
4769                           x);
4770           tcf = null;
4771         }
4772         if (tcf == null)
4773         {
4774           // try to see if its a JNet 'concise' style annotation file *before*
4775           // we
4776           // try to parse it as a features file
4777           if (format == null)
4778           {
4779             format = new IdentifyFile().identify(file, sourceType);
4780           }
4781           if (FileFormat.Jnet.equals(format))
4782           {
4783             JPredFile predictions = new JPredFile(
4784                     file, sourceType);
4785             new JnetAnnotationMaker();
4786             JnetAnnotationMaker.add_annotation(predictions,
4787                     viewport.getAlignment(), 0, false);
4788             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4789             viewport.getAlignment().setSeqrep(repseq);
4790             ColumnSelection cs = new ColumnSelection();
4791             cs.hideInsertionsFor(repseq);
4792             viewport.setColumnSelection(cs);
4793             isAnnotation = true;
4794           }
4795           // else if (IdentifyFile.FeaturesFile.equals(format))
4796           else if (FileFormat.Features.equals(format))
4797           {
4798             if (parseFeaturesFile(file, sourceType))
4799             {
4800               alignPanel.paintAlignment(true);
4801             }
4802           }
4803           else
4804           {
4805             new FileLoader().LoadFile(viewport, file, sourceType, format);
4806           }
4807         }
4808       }
4809       if (isAnnotation)
4810       {
4811
4812         alignPanel.adjustAnnotationHeight();
4813         viewport.updateSequenceIdColours();
4814         buildSortByAnnotationScoresMenu();
4815         alignPanel.paintAlignment(true);
4816       }
4817     } catch (Exception ex)
4818     {
4819       ex.printStackTrace();
4820     } catch (OutOfMemoryError oom)
4821     {
4822       try
4823       {
4824         System.gc();
4825       } catch (Exception x)
4826       {
4827       }
4828       new OOMWarning(
4829               "loading data "
4830                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4831                               : "using " + sourceType + " from " + file)
4832                               : ".")
4833                       + (format != null ? "(parsing as '" + format
4834                               + "' file)" : ""), oom, Desktop.desktop);
4835     }
4836   }
4837
4838   /**
4839    * Method invoked by the ChangeListener on the tabbed pane, in other words
4840    * when a different tabbed pane is selected by the user or programmatically.
4841    */
4842   @Override
4843   public void tabSelectionChanged(int index)
4844   {
4845     if (index > -1)
4846     {
4847       alignPanel = alignPanels.get(index);
4848       viewport = alignPanel.av;
4849       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4850       setMenusFromViewport(viewport);
4851     }
4852
4853     /*
4854      * If there is a frame linked to this one in a SplitPane, switch it to the
4855      * same view tab index. No infinite recursion of calls should happen, since
4856      * tabSelectionChanged() should not get invoked on setting the selected
4857      * index to an unchanged value. Guard against setting an invalid index
4858      * before the new view peer tab has been created.
4859      */
4860     final AlignViewportI peer = viewport.getCodingComplement();
4861     if (peer != null)
4862     {
4863       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4864       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4865       {
4866         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4867       }
4868     }
4869   }
4870
4871   /**
4872    * On right mouse click on view tab, prompt for and set new view name.
4873    */
4874   @Override
4875   public void tabbedPane_mousePressed(MouseEvent e)
4876   {
4877     if (e.isPopupTrigger())
4878     {
4879       String msg = MessageManager.getString("label.enter_view_name");
4880       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4881               JvOptionPane.QUESTION_MESSAGE);
4882
4883       if (reply != null)
4884       {
4885         viewport.viewName = reply;
4886         // TODO warn if reply is in getExistingViewNames()?
4887         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4888       }
4889     }
4890   }
4891
4892   public AlignViewport getCurrentView()
4893   {
4894     return viewport;
4895   }
4896
4897   /**
4898    * Open the dialog for regex description parsing.
4899    */
4900   @Override
4901   protected void extractScores_actionPerformed(ActionEvent e)
4902   {
4903     ParseProperties pp = new jalview.analysis.ParseProperties(
4904             viewport.getAlignment());
4905     // TODO: verify regex and introduce GUI dialog for version 2.5
4906     // if (pp.getScoresFromDescription("col", "score column ",
4907     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4908     // true)>0)
4909     if (pp.getScoresFromDescription("description column",
4910             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4911     {
4912       buildSortByAnnotationScoresMenu();
4913     }
4914   }
4915
4916   /*
4917    * (non-Javadoc)
4918    *
4919    * @see
4920    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4921    * )
4922    */
4923   @Override
4924   protected void showDbRefs_actionPerformed(ActionEvent e)
4925   {
4926     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4927   }
4928
4929   /*
4930    * (non-Javadoc)
4931    *
4932    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4933    * ActionEvent)
4934    */
4935   @Override
4936   protected void showNpFeats_actionPerformed(ActionEvent e)
4937   {
4938     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4939   }
4940
4941   /**
4942    * find the viewport amongst the tabs in this alignment frame and close that
4943    * tab
4944    *
4945    * @param av
4946    */
4947   public boolean closeView(AlignViewportI av)
4948   {
4949     if (viewport == av)
4950     {
4951       this.closeMenuItem_actionPerformed(false);
4952       return true;
4953     }
4954     Component[] comp = tabbedPane.getComponents();
4955     for (int i = 0; comp != null && i < comp.length; i++)
4956     {
4957       if (comp[i] instanceof AlignmentPanel)
4958       {
4959         if (((AlignmentPanel) comp[i]).av == av)
4960         {
4961           // close the view.
4962           closeView((AlignmentPanel) comp[i]);
4963           return true;
4964         }
4965       }
4966     }
4967     return false;
4968   }
4969
4970   protected void build_fetchdbmenu(JMenu webService)
4971   {
4972     // Temporary hack - DBRef Fetcher always top level ws entry.
4973     // TODO We probably want to store a sequence database checklist in
4974     // preferences and have checkboxes.. rather than individual sources selected
4975     // here
4976     final JMenu rfetch = new JMenu(
4977             MessageManager.getString("action.fetch_db_references"));
4978     rfetch.setToolTipText(MessageManager
4979             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4980     webService.add(rfetch);
4981
4982     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4983             MessageManager.getString("option.trim_retrieved_seqs"));
4984     trimrs.setToolTipText(MessageManager
4985             .getString("label.trim_retrieved_sequences"));
4986     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4987     trimrs.addActionListener(new ActionListener()
4988     {
4989       @Override
4990       public void actionPerformed(ActionEvent e)
4991       {
4992         trimrs.setSelected(trimrs.isSelected());
4993         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4994                 Boolean.valueOf(trimrs.isSelected()).toString());
4995       };
4996     });
4997     rfetch.add(trimrs);
4998     JMenuItem fetchr = new JMenuItem(
4999             MessageManager.getString("label.standard_databases"));
5000     fetchr.setToolTipText(MessageManager
5001             .getString("label.fetch_embl_uniprot"));
5002     fetchr.addActionListener(new ActionListener()
5003     {
5004
5005       @Override
5006       public void actionPerformed(ActionEvent e)
5007       {
5008         new Thread(new Runnable()
5009         {
5010           @Override
5011           public void run()
5012           {
5013             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5014                     .getAlignment().isNucleotide();
5015             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5016                     .getSequenceSelection(), alignPanel.alignFrame, null,
5017                     alignPanel.alignFrame.featureSettings, isNucleotide);
5018             dbRefFetcher.addListener(new FetchFinishedListenerI()
5019             {
5020               @Override
5021               public void finished()
5022               {
5023                 AlignFrame.this.setMenusForViewport();
5024               }
5025             });
5026             dbRefFetcher.fetchDBRefs(false);
5027           }
5028         }).start();
5029
5030       }
5031
5032     });
5033     rfetch.add(fetchr);
5034     final AlignFrame me = this;
5035     new Thread(new Runnable()
5036     {
5037       @Override
5038       public void run()
5039       {
5040         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5041                 .getSequenceFetcherSingleton(me);
5042         javax.swing.SwingUtilities.invokeLater(new Runnable()
5043         {
5044           @Override
5045           public void run()
5046           {
5047             String[] dbclasses = sf.getOrderedSupportedSources();
5048             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5049             // jalview.util.QuickSort.sort(otherdb, otherdb);
5050             List<DbSourceProxy> otherdb;
5051             JMenu dfetch = new JMenu();
5052             JMenu ifetch = new JMenu();
5053             JMenuItem fetchr = null;
5054             int comp = 0, icomp = 0, mcomp = 15;
5055             String mname = null;
5056             int dbi = 0;
5057             for (String dbclass : dbclasses)
5058             {
5059               otherdb = sf.getSourceProxy(dbclass);
5060               // add a single entry for this class, or submenu allowing 'fetch
5061               // all' or pick one
5062               if (otherdb == null || otherdb.size() < 1)
5063               {
5064                 continue;
5065               }
5066               // List<DbSourceProxy> dbs=otherdb;
5067               // otherdb=new ArrayList<DbSourceProxy>();
5068               // for (DbSourceProxy db:dbs)
5069               // {
5070               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5071               // }
5072               if (mname == null)
5073               {
5074                 mname = "From " + dbclass;
5075               }
5076               if (otherdb.size() == 1)
5077               {
5078                 final DbSourceProxy[] dassource = otherdb
5079                         .toArray(new DbSourceProxy[0]);
5080                 DbSourceProxy src = otherdb.get(0);
5081                 fetchr = new JMenuItem(src.getDbSource());
5082                 fetchr.addActionListener(new ActionListener()
5083                 {
5084
5085                   @Override
5086                   public void actionPerformed(ActionEvent e)
5087                   {
5088                     new Thread(new Runnable()
5089                     {
5090
5091                       @Override
5092                       public void run()
5093                       {
5094                         boolean isNucleotide = alignPanel.alignFrame
5095                                 .getViewport().getAlignment()
5096                                 .isNucleotide();
5097                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5098                                 alignPanel.av.getSequenceSelection(),
5099                                 alignPanel.alignFrame, dassource,
5100                                 alignPanel.alignFrame.featureSettings,
5101                                 isNucleotide);
5102                         dbRefFetcher
5103                                 .addListener(new FetchFinishedListenerI()
5104                                 {
5105                                   @Override
5106                                   public void finished()
5107                                   {
5108                                     AlignFrame.this.setMenusForViewport();
5109                                   }
5110                                 });
5111                         dbRefFetcher.fetchDBRefs(false);
5112                       }
5113                     }).start();
5114                   }
5115
5116                 });
5117                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5118                         MessageManager.formatMessage(
5119                                 "label.fetch_retrieve_from",
5120                                 new Object[] { src.getDbName() })));
5121                 dfetch.add(fetchr);
5122                 comp++;
5123               }
5124               else
5125               {
5126                 final DbSourceProxy[] dassource = otherdb
5127                         .toArray(new DbSourceProxy[0]);
5128                 // fetch all entry
5129                 DbSourceProxy src = otherdb.get(0);
5130                 fetchr = new JMenuItem(MessageManager.formatMessage(
5131                         "label.fetch_all_param",
5132                         new Object[] { src.getDbSource() }));
5133                 fetchr.addActionListener(new ActionListener()
5134                 {
5135                   @Override
5136                   public void actionPerformed(ActionEvent e)
5137                   {
5138                     new Thread(new Runnable()
5139                     {
5140
5141                       @Override
5142                       public void run()
5143                       {
5144                         boolean isNucleotide = alignPanel.alignFrame
5145                                 .getViewport().getAlignment()
5146                                 .isNucleotide();
5147                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5148                                 alignPanel.av.getSequenceSelection(),
5149                                 alignPanel.alignFrame, dassource,
5150                                 alignPanel.alignFrame.featureSettings,
5151                                 isNucleotide);
5152                         dbRefFetcher
5153                                 .addListener(new FetchFinishedListenerI()
5154                                 {
5155                                   @Override
5156                                   public void finished()
5157                                   {
5158                                     AlignFrame.this.setMenusForViewport();
5159                                   }
5160                                 });
5161                         dbRefFetcher.fetchDBRefs(false);
5162                       }
5163                     }).start();
5164                   }
5165                 });
5166
5167                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5168                         MessageManager.formatMessage(
5169                                 "label.fetch_retrieve_from_all_sources",
5170                                 new Object[] {
5171                                     Integer.valueOf(otherdb.size())
5172                                             .toString(), src.getDbSource(),
5173                                     src.getDbName() })));
5174                 dfetch.add(fetchr);
5175                 comp++;
5176                 // and then build the rest of the individual menus
5177                 ifetch = new JMenu(MessageManager.formatMessage(
5178                         "label.source_from_db_source",
5179                         new Object[] { src.getDbSource() }));
5180                 icomp = 0;
5181                 String imname = null;
5182                 int i = 0;
5183                 for (DbSourceProxy sproxy : otherdb)
5184                 {
5185                   String dbname = sproxy.getDbName();
5186                   String sname = dbname.length() > 5 ? dbname.substring(0,
5187                           5) + "..." : dbname;
5188                   String msname = dbname.length() > 10 ? dbname.substring(
5189                           0, 10) + "..." : dbname;
5190                   if (imname == null)
5191                   {
5192                     imname = MessageManager.formatMessage(
5193                             "label.from_msname", new Object[] { sname });
5194                   }
5195                   fetchr = new JMenuItem(msname);
5196                   final DbSourceProxy[] dassrc = { sproxy };
5197                   fetchr.addActionListener(new ActionListener()
5198                   {
5199
5200                     @Override
5201                     public void actionPerformed(ActionEvent e)
5202                     {
5203                       new Thread(new Runnable()
5204                       {
5205
5206                         @Override
5207                         public void run()
5208                         {
5209                           boolean isNucleotide = alignPanel.alignFrame
5210                                   .getViewport().getAlignment()
5211                                   .isNucleotide();
5212                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5213                                   alignPanel.av.getSequenceSelection(),
5214                                   alignPanel.alignFrame, dassrc,
5215                                   alignPanel.alignFrame.featureSettings,
5216                                   isNucleotide);
5217                           dbRefFetcher
5218                                   .addListener(new FetchFinishedListenerI()
5219                                   {
5220                                     @Override
5221                                     public void finished()
5222                                     {
5223                                       AlignFrame.this.setMenusForViewport();
5224                                     }
5225                                   });
5226                           dbRefFetcher.fetchDBRefs(false);
5227                         }
5228                       }).start();
5229                     }
5230
5231                   });
5232                   fetchr.setToolTipText("<html>"
5233                           + MessageManager.formatMessage(
5234                                   "label.fetch_retrieve_from", new Object[]
5235                                   { dbname }));
5236                   ifetch.add(fetchr);
5237                   ++i;
5238                   if (++icomp >= mcomp || i == (otherdb.size()))
5239                   {
5240                     ifetch.setText(MessageManager.formatMessage(
5241                             "label.source_to_target", imname, sname));
5242                     dfetch.add(ifetch);
5243                     ifetch = new JMenu();
5244                     imname = null;
5245                     icomp = 0;
5246                     comp++;
5247                   }
5248                 }
5249               }
5250               ++dbi;
5251               if (comp >= mcomp || dbi >= (dbclasses.length))
5252               {
5253                 dfetch.setText(MessageManager.formatMessage(
5254                         "label.source_to_target", mname, dbclass));
5255                 rfetch.add(dfetch);
5256                 dfetch = new JMenu();
5257                 mname = null;
5258                 comp = 0;
5259               }
5260             }
5261           }
5262         });
5263       }
5264     }).start();
5265
5266   }
5267
5268   /**
5269    * Left justify the whole alignment.
5270    */
5271   @Override
5272   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5273   {
5274     AlignmentI al = viewport.getAlignment();
5275     al.justify(false);
5276     viewport.firePropertyChange("alignment", null, al);
5277   }
5278
5279   /**
5280    * Right justify the whole alignment.
5281    */
5282   @Override
5283   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5284   {
5285     AlignmentI al = viewport.getAlignment();
5286     al.justify(true);
5287     viewport.firePropertyChange("alignment", null, al);
5288   }
5289
5290   @Override
5291   public void setShowSeqFeatures(boolean b)
5292   {
5293     showSeqFeatures.setSelected(b);
5294     viewport.setShowSequenceFeatures(b);
5295   }
5296
5297   /*
5298    * (non-Javadoc)
5299    *
5300    * @see
5301    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5302    * awt.event.ActionEvent)
5303    */
5304   @Override
5305   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5306   {
5307     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5308     alignPanel.paintAlignment(true);
5309   }
5310
5311   /*
5312    * (non-Javadoc)
5313    *
5314    * @see
5315    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5316    * .ActionEvent)
5317    */
5318   @Override
5319   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5320   {
5321     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5322     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5323
5324   }
5325
5326   /*
5327    * (non-Javadoc)
5328    *
5329    * @see
5330    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5331    * .event.ActionEvent)
5332    */
5333   @Override
5334   protected void showGroupConservation_actionPerformed(ActionEvent e)
5335   {
5336     viewport.setShowGroupConservation(showGroupConservation.getState());
5337     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5338   }
5339
5340   /*
5341    * (non-Javadoc)
5342    *
5343    * @see
5344    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5345    * .event.ActionEvent)
5346    */
5347   @Override
5348   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5349   {
5350     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5351     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5352   }
5353
5354   /*
5355    * (non-Javadoc)
5356    *
5357    * @see
5358    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5359    * .event.ActionEvent)
5360    */
5361   @Override
5362   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5363   {
5364     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5365     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5366   }
5367
5368   @Override
5369   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5370   {
5371     showSequenceLogo.setState(true);
5372     viewport.setShowSequenceLogo(true);
5373     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5374     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5375   }
5376
5377   @Override
5378   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5379   {
5380     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5381   }
5382
5383   /*
5384    * (non-Javadoc)
5385    *
5386    * @see
5387    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5388    * .event.ActionEvent)
5389    */
5390   @Override
5391   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5392   {
5393     if (avc.makeGroupsFromSelection())
5394     {
5395       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5396       alignPanel.updateAnnotation();
5397       alignPanel.paintAlignment(true);
5398     }
5399   }
5400
5401   public void clearAlignmentSeqRep()
5402   {
5403     // TODO refactor alignmentseqrep to controller
5404     if (viewport.getAlignment().hasSeqrep())
5405     {
5406       viewport.getAlignment().setSeqrep(null);
5407       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5408       alignPanel.updateAnnotation();
5409       alignPanel.paintAlignment(true);
5410     }
5411   }
5412
5413   @Override
5414   protected void createGroup_actionPerformed(ActionEvent e)
5415   {
5416     if (avc.createGroup())
5417     {
5418       alignPanel.alignmentChanged();
5419     }
5420   }
5421
5422   @Override
5423   protected void unGroup_actionPerformed(ActionEvent e)
5424   {
5425     if (avc.unGroup())
5426     {
5427       alignPanel.alignmentChanged();
5428     }
5429   }
5430
5431   /**
5432    * make the given alignmentPanel the currently selected tab
5433    *
5434    * @param alignmentPanel
5435    */
5436   public void setDisplayedView(AlignmentPanel alignmentPanel)
5437   {
5438     if (!viewport.getSequenceSetId().equals(
5439             alignmentPanel.av.getSequenceSetId()))
5440     {
5441       throw new Error(
5442               MessageManager
5443                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5444     }
5445     if (tabbedPane != null
5446             && tabbedPane.getTabCount() > 0
5447             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5448                     .getSelectedIndex())
5449     {
5450       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5451     }
5452   }
5453
5454   /**
5455    * Action on selection of menu options to Show or Hide annotations.
5456    *
5457    * @param visible
5458    * @param forSequences
5459    *          update sequence-related annotations
5460    * @param forAlignment
5461    *          update non-sequence-related annotations
5462    */
5463   @Override
5464   protected void setAnnotationsVisibility(boolean visible,
5465           boolean forSequences, boolean forAlignment)
5466   {
5467     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5468             .getAlignmentAnnotation();
5469     if (anns == null)
5470     {
5471       return;
5472     }
5473     for (AlignmentAnnotation aa : anns)
5474     {
5475       /*
5476        * don't display non-positional annotations on an alignment
5477        */
5478       if (aa.annotations == null)
5479       {
5480         continue;
5481       }
5482       boolean apply = (aa.sequenceRef == null && forAlignment)
5483               || (aa.sequenceRef != null && forSequences);
5484       if (apply)
5485       {
5486         aa.visible = visible;
5487       }
5488     }
5489     alignPanel.validateAnnotationDimensions(true);
5490     alignPanel.alignmentChanged();
5491   }
5492
5493   /**
5494    * Store selected annotation sort order for the view and repaint.
5495    */
5496   @Override
5497   protected void sortAnnotations_actionPerformed()
5498   {
5499     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5500     this.alignPanel.av
5501             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5502     alignPanel.paintAlignment(true);
5503   }
5504
5505   /**
5506    *
5507    * @return alignment panels in this alignment frame
5508    */
5509   public List<? extends AlignmentViewPanel> getAlignPanels()
5510   {
5511     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5512   }
5513
5514   /**
5515    * Open a new alignment window, with the cDNA associated with this (protein)
5516    * alignment, aligned as is the protein.
5517    */
5518   protected void viewAsCdna_actionPerformed()
5519   {
5520     // TODO no longer a menu action - refactor as required
5521     final AlignmentI alignment = getViewport().getAlignment();
5522     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5523     if (mappings == null)
5524     {
5525       return;
5526     }
5527     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5528     for (SequenceI aaSeq : alignment.getSequences())
5529     {
5530       for (AlignedCodonFrame acf : mappings)
5531       {
5532         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5533         if (dnaSeq != null)
5534         {
5535           /*
5536            * There is a cDNA mapping for this protein sequence - add to new
5537            * alignment. It will share the same dataset sequence as other mapped
5538            * cDNA (no new mappings need to be created).
5539            */
5540           final Sequence newSeq = new Sequence(dnaSeq);
5541           newSeq.setDatasetSequence(dnaSeq);
5542           cdnaSeqs.add(newSeq);
5543         }
5544       }
5545     }
5546     if (cdnaSeqs.size() == 0)
5547     {
5548       // show a warning dialog no mapped cDNA
5549       return;
5550     }
5551     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5552             .size()]));
5553     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5554             AlignFrame.DEFAULT_HEIGHT);
5555     cdna.alignAs(alignment);
5556     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5557             + this.title;
5558     Desktop.addInternalFrame(alignFrame, newtitle,
5559             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5560   }
5561
5562   /**
5563    * Set visibility of dna/protein complement view (available when shown in a
5564    * split frame).
5565    *
5566    * @param show
5567    */
5568   @Override
5569   protected void showComplement_actionPerformed(boolean show)
5570   {
5571     SplitContainerI sf = getSplitViewContainer();
5572     if (sf != null)
5573     {
5574       sf.setComplementVisible(this, show);
5575     }
5576   }
5577
5578   /**
5579    * Generate the reverse (optionally complemented) of the selected sequences,
5580    * and add them to the alignment
5581    */
5582   @Override
5583   protected void showReverse_actionPerformed(boolean complement)
5584   {
5585     AlignmentI al = null;
5586     try
5587     {
5588       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5589       al = dna.reverseCdna(complement);
5590       viewport.addAlignment(al, "");
5591       addHistoryItem(new EditCommand(
5592               MessageManager.getString("label.add_sequences"),
5593               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5594               viewport.getAlignment()));
5595     } catch (Exception ex)
5596     {
5597       System.err.println(ex.getMessage());
5598       return;
5599     }
5600   }
5601
5602   /**
5603    * Try to run a script in the Groovy console, having first ensured that this
5604    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5605    * be targeted at this alignment.
5606    */
5607   @Override
5608   protected void runGroovy_actionPerformed()
5609   {
5610     Jalview.setCurrentAlignFrame(this);
5611     groovy.ui.Console console = Desktop.getGroovyConsole();
5612     if (console != null)
5613     {
5614       try
5615       {
5616         console.runScript();
5617       } catch (Exception ex)
5618       {
5619         System.err.println((ex.toString()));
5620         JvOptionPane
5621                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5622                         .getString("label.couldnt_run_groovy_script"),
5623                         MessageManager
5624                                 .getString("label.groovy_support_failed"),
5625                         JvOptionPane.ERROR_MESSAGE);
5626       }
5627     }
5628     else
5629     {
5630       System.err.println("Can't run Groovy script as console not found");
5631     }
5632   }
5633
5634   /**
5635    * Hides columns containing (or not containing) a specified feature, provided
5636    * that would not leave all columns hidden
5637    *
5638    * @param featureType
5639    * @param columnsContaining
5640    * @return
5641    */
5642   public boolean hideFeatureColumns(String featureType,
5643           boolean columnsContaining)
5644   {
5645     boolean notForHiding = avc.markColumnsContainingFeatures(
5646             columnsContaining, false, false, featureType);
5647     if (notForHiding)
5648     {
5649       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5650               false, featureType))
5651       {
5652         getViewport().hideSelectedColumns();
5653         return true;
5654       }
5655     }
5656     return false;
5657   }
5658
5659   @Override
5660   protected void selectHighlightedColumns_actionPerformed(
5661           ActionEvent actionEvent)
5662   {
5663     // include key modifier check in case user selects from menu
5664     avc.markHighlightedColumns(
5665             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5666             true,
5667             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5668   }
5669
5670   /**
5671    * Rebuilds the Colour menu, including any user-defined colours which have
5672    * been loaded either on startup or during the session
5673    */
5674   public void buildColourMenu()
5675   {
5676     colourMenu.removeAll();
5677
5678     colourMenu.add(applyToAllGroups);
5679     colourMenu.add(textColour);
5680     colourMenu.addSeparator();
5681
5682     ColourMenuHelper.addMenuItems(colourMenu, this,
5683             viewport.getAlignment(), false);
5684
5685     colourMenu.addSeparator();
5686     colourMenu.add(conservationMenuItem);
5687     colourMenu.add(modifyConservation);
5688     colourMenu.add(abovePIDThreshold);
5689     colourMenu.add(modifyPID);
5690     colourMenu.add(annotationColour);
5691
5692     /*
5693      * select the default colour for the alignment (this may be
5694      * overridden later)
5695      */
5696     boolean nucleotide = viewport.getAlignment().isNucleotide();
5697     String defaultColourScheme = Cache.getDefault(
5698             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
5699                     : Preferences.DEFAULT_COLOUR_PROT,
5700             ResidueColourScheme.NONE);
5701
5702     ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
5703   }
5704 }
5705
5706 class PrintThread extends Thread
5707 {
5708   AlignmentPanel ap;
5709
5710   public PrintThread(AlignmentPanel ap)
5711   {
5712     this.ap = ap;
5713   }
5714
5715   static PageFormat pf;
5716
5717   @Override
5718   public void run()
5719   {
5720     PrinterJob printJob = PrinterJob.getPrinterJob();
5721
5722     if (pf != null)
5723     {
5724       printJob.setPrintable(ap, pf);
5725     }
5726     else
5727     {
5728       printJob.setPrintable(ap);
5729     }
5730
5731     if (printJob.printDialog())
5732     {
5733       try
5734       {
5735         printJob.print();
5736       } catch (Exception PrintException)
5737       {
5738         PrintException.printStackTrace();
5739       }
5740     }
5741   }
5742 }