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