src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  64 import jalview.io.AlignmentProperties;
  65 import jalview.io.AnnotationFile;
  66 import jalview.io.BioJsHTMLOutput;
  67 import jalview.io.DataSourceType;
  68 import jalview.io.FileFormat;
  69 import jalview.io.FileFormatI;
  70 import jalview.io.FileFormats;
  71 import jalview.io.FileLoader;
  72 import jalview.io.FormatAdapter;
  73 import jalview.io.HtmlSvgOutput;
  74 import jalview.io.IdentifyFile;
  75 import jalview.io.JPredFile;
  76 import jalview.io.JalviewFileChooser;
  77 import jalview.io.JalviewFileView;
  78 import jalview.io.JnetAnnotationMaker;
  79 import jalview.io.NewickFile;
  80 import jalview.io.TCoffeeScoreFile;
  81 import jalview.jbgui.GAlignFrame;
  82 import jalview.schemes.ColourSchemeI;
  83 import jalview.schemes.ColourSchemes;
  84 import jalview.schemes.ResidueColourScheme;
  85 import jalview.schemes.ResidueProperties;
  86 import jalview.schemes.TCoffeeColourScheme;
  87 import jalview.util.MessageManager;
  88 import jalview.viewmodel.AlignmentViewport;
  89 import jalview.ws.DBRefFetcher;
  90 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  91 import jalview.ws.jws1.Discoverer;
  92 import jalview.ws.jws2.Jws2Discoverer;
  93 import jalview.ws.jws2.jabaws2.Jws2Instance;
  94 import jalview.ws.seqfetcher.DbSourceProxy;
  95
  96 import java.awt.BorderLayout;
  97 import java.awt.Component;
  98 import java.awt.Rectangle;
  99 import java.awt.Toolkit;
 100 import java.awt.datatransfer.Clipboard;
 101 import java.awt.datatransfer.DataFlavor;
 102 import java.awt.datatransfer.StringSelection;
 103 import java.awt.datatransfer.Transferable;
 104 import java.awt.dnd.DnDConstants;
 105 import java.awt.dnd.DropTargetDragEvent;
 106 import java.awt.dnd.DropTargetDropEvent;
 107 import java.awt.dnd.DropTargetEvent;
 108 import java.awt.dnd.DropTargetListener;
 109 import java.awt.event.ActionEvent;
 110 import java.awt.event.ActionListener;
 111 import java.awt.event.FocusAdapter;
 112 import java.awt.event.FocusEvent;
 113 import java.awt.event.ItemEvent;
 114 import java.awt.event.ItemListener;
 115 import java.awt.event.KeyAdapter;
 116 import java.awt.event.KeyEvent;
 117 import java.awt.event.MouseEvent;
 118 import java.awt.print.PageFormat;
 119 import java.awt.print.PrinterJob;
 120 import java.beans.PropertyChangeEvent;
 121 import java.io.File;
 122 import java.io.FileWriter;
 123 import java.io.PrintWriter;
 124 import java.net.URL;
 125 import java.util.ArrayList;
 126 import java.util.Arrays;
 127 import java.util.Deque;
 128 import java.util.Enumeration;
 129 import java.util.Hashtable;
 130 import java.util.List;
 131 import java.util.Vector;
 132
 133 import javax.swing.JCheckBoxMenuItem;
 134 import javax.swing.JEditorPane;
 135 import javax.swing.JInternalFrame;
 136 import javax.swing.JLayeredPane;
 137 import javax.swing.JMenu;
 138 import javax.swing.JMenuItem;
 139 import javax.swing.JScrollPane;
 140 import javax.swing.SwingUtilities;
 141
 142 /**
 143  * DOCUMENT ME!
 144  *
 145  * @author $author$
 146  * @version $Revision$
 147  */
 148 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 149         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 150 {
 151
 152   public static final int DEFAULT_WIDTH = 700;
 153
 154   public static final int DEFAULT_HEIGHT = 500;
 155
 156   /*
 157    * The currently displayed panel (selected tabbed view if more than one)
 158    */
 159   public AlignmentPanel alignPanel;
 160
 161   AlignViewport viewport;
 162
 163   public AlignViewControllerI avc;
 164
 165   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 166
 167   /**
 168    * Last format used to load or save alignments in this window
 169    */
 170   FileFormatI currentFileFormat = null;
 171
 172   /**
 173    * Current filename for this alignment
 174    */
 175   String fileName = null;
 176
 177   /**
 178    * Creates a new AlignFrame object with specific width and height.
 179    *
 180    * @param al
 181    * @param width
 182    * @param height
 183    */
 184   public AlignFrame(AlignmentI al, int width, int height)
 185   {
 186     this(al, null, width, height);
 187   }
 188
 189   /**
 190    * Creates a new AlignFrame object with specific width, height and
 191    * sequenceSetId
 192    *
 193    * @param al
 194    * @param width
 195    * @param height
 196    * @param sequenceSetId
 197    */
 198   public AlignFrame(AlignmentI al, int width, int height,
 199           String sequenceSetId)
 200   {
 201     this(al, null, width, height, sequenceSetId);
 202   }
 203
 204   /**
 205    * Creates a new AlignFrame object with specific width, height and
 206    * sequenceSetId
 207    *
 208    * @param al
 209    * @param width
 210    * @param height
 211    * @param sequenceSetId
 212    * @param viewId
 213    */
 214   public AlignFrame(AlignmentI al, int width, int height,
 215           String sequenceSetId, String viewId)
 216   {
 217     this(al, null, width, height, sequenceSetId, viewId);
 218   }
 219
 220   /**
 221    * new alignment window with hidden columns
 222    *
 223    * @param al
 224    *          AlignmentI
 225    * @param hiddenColumns
 226    *          ColumnSelection or null
 227    * @param width
 228    *          Width of alignment frame
 229    * @param height
 230    *          height of frame.
 231    */
 232   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 233           int width, int height)
 234   {
 235     this(al, hiddenColumns, width, height, null);
 236   }
 237
 238   /**
 239    * Create alignment frame for al with hiddenColumns, a specific width and
 240    * height, and specific sequenceId
 241    *
 242    * @param al
 243    * @param hiddenColumns
 244    * @param width
 245    * @param height
 246    * @param sequenceSetId
 247    *          (may be null)
 248    */
 249   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 250           int width, int height, String sequenceSetId)
 251   {
 252     this(al, hiddenColumns, width, height, sequenceSetId, null);
 253   }
 254
 255   /**
 256    * Create alignment frame for al with hiddenColumns, a specific width and
 257    * height, and specific sequenceId
 258    *
 259    * @param al
 260    * @param hiddenColumns
 261    * @param width
 262    * @param height
 263    * @param sequenceSetId
 264    *          (may be null)
 265    * @param viewId
 266    *          (may be null)
 267    */
 268   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 269           int width, int height, String sequenceSetId, String viewId)
 270   {
 271     setSize(width, height);
 272
 273     if (al.getDataset() == null)
 274     {
 275       al.setDataset(null);
 276     }
 277
 278     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 279
 280     alignPanel = new AlignmentPanel(this, viewport);
 281
 282     addAlignmentPanel(alignPanel, true);
 283     init();
 284   }
 285
 286   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 287           ColumnSelection hiddenColumns, int width, int height)
 288   {
 289     setSize(width, height);
 290
 291     if (al.getDataset() == null)
 292     {
 293       al.setDataset(null);
 294     }
 295
 296     viewport = new AlignViewport(al, hiddenColumns);
 297
 298     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 299     {
 300       viewport.hideSequence(hiddenSeqs);
 301     }
 302     alignPanel = new AlignmentPanel(this, viewport);
 303     addAlignmentPanel(alignPanel, true);
 304     init();
 305   }
 306
 307   /**
 308    * Make a new AlignFrame from existing alignmentPanels
 309    *
 310    * @param ap
 311    *          AlignmentPanel
 312    * @param av
 313    *          AlignViewport
 314    */
 315   public AlignFrame(AlignmentPanel ap)
 316   {
 317     viewport = ap.av;
 318     alignPanel = ap;
 319     addAlignmentPanel(ap, false);
 320     init();
 321   }
 322
 323   /**
 324    * initalise the alignframe from the underlying viewport data and the
 325    * configurations
 326    */
 327   void init()
 328   {
 329     if (!Jalview.isHeadlessMode())
 330     {
 331       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 332     }
 333
 334     avc = new jalview.controller.AlignViewController(this, viewport,
 335             alignPanel);
 336     if (viewport.getAlignmentConservationAnnotation() == null)
 337     {
 338       // BLOSUM62Colour.setEnabled(false);
 339       conservationMenuItem.setEnabled(false);
 340       modifyConservation.setEnabled(false);
 341       // PIDColour.setEnabled(false);
 342       // abovePIDThreshold.setEnabled(false);
 343       // modifyPID.setEnabled(false);
 344     }
 345
 346     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 347             "No sort");
 348
 349     if (sortby.equals("Id"))
 350     {
 351       sortIDMenuItem_actionPerformed(null);
 352     }
 353     else if (sortby.equals("Pairwise Identity"))
 354     {
 355       sortPairwiseMenuItem_actionPerformed(null);
 356     }
 357
 358     this.alignPanel.av
 359             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 360
 361     setMenusFromViewport(viewport);
 362     buildSortByAnnotationScoresMenu();
 363     buildTreeMenu();
 364     buildColourMenu();
 365
 366     if (Desktop.desktop != null)
 367     {
 368       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 369       addServiceListeners();
 370       setGUINucleotide();
 371     }
 372
 373     if (viewport.getWrapAlignment())
 374     {
 375       wrapMenuItem_actionPerformed(null);
 376     }
 377
 378     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 379     {
 380       this.overviewMenuItem_actionPerformed(null);
 381     }
 382
 383     addKeyListener();
 384
 385     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 386     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 387     final String menuLabel = MessageManager
 388             .getString("label.copy_format_from");
 389     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 390             new ViewSetProvider()
 391             {
 392
 393               @Override
 394               public AlignmentPanel[] getAllAlignmentPanels()
 395               {
 396                 origview.clear();
 397                 origview.add(alignPanel);
 398                 // make an array of all alignment panels except for this one
 399                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 400                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 401                 aps.remove(AlignFrame.this.alignPanel);
 402                 return aps.toArray(new AlignmentPanel[aps.size()]);
 403               }
 404             }, selviews, new ItemListener()
 405             {
 406
 407               @Override
 408               public void itemStateChanged(ItemEvent e)
 409               {
 410                 if (origview.size() > 0)
 411                 {
 412                   final AlignmentPanel ap = origview.get(0);
 413
 414                   /*
 415                    * Copy the ViewStyle of the selected panel to 'this one'.
 416                    * Don't change value of 'scaleProteinAsCdna' unless copying
 417                    * from a SplitFrame.
 418                    */
 419                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 420                           .getViewStyle();
 421                   boolean fromSplitFrame = selviews.get(0)
 422                           .getAlignViewport().getCodingComplement() != null;
 423                   if (!fromSplitFrame)
 424                   {
 425                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 426                             .getViewStyle().isScaleProteinAsCdna());
 427                   }
 428                   ap.getAlignViewport().setViewStyle(vs);
 429
 430                   /*
 431                    * Also rescale ViewStyle of SplitFrame complement if there is
 432                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 433                    * the whole ViewStyle (allow cDNA protein to have different
 434                    * fonts)
 435                    */
 436                   AlignViewportI complement = ap.getAlignViewport()
 437                           .getCodingComplement();
 438                   if (complement != null && vs.isScaleProteinAsCdna())
 439                   {
 440                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 441                     ((SplitFrame) af.getSplitViewContainer())
 442                             .adjustLayout();
 443                     af.setMenusForViewport();
 444                   }
 445
 446                   ap.updateLayout();
 447                   ap.setSelected(true);
 448                   ap.alignFrame.setMenusForViewport();
 449
 450                 }
 451               }
 452             });
 453     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 454             .indexOf("devel") > -1
 455             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 456                     .indexOf("test") > -1)
 457     {
 458       formatMenu.add(vsel);
 459     }
 460     addFocusListener(new FocusAdapter()
 461     {
 462       @Override
 463       public void focusGained(FocusEvent e)
 464       {
 465         Jalview.setCurrentAlignFrame(AlignFrame.this);
 466       }
 467     });
 468
 469   }
 470
 471   /**
 472    * Change the filename and format for the alignment, and enable the 'reload'
 473    * button functionality.
 474    *
 475    * @param file
 476    *          valid filename
 477    * @param format
 478    *          format of file
 479    */
 480   public void setFileName(String file, FileFormatI format)
 481   {
 482     fileName = file;
 483     setFileFormat(format);
 484     reload.setEnabled(true);
 485   }
 486
 487   /**
 488    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 489    * events
 490    */
 491   void addKeyListener()
 492   {
 493     addKeyListener(new KeyAdapter()
 494     {
 495       @Override
 496       public void keyPressed(KeyEvent evt)
 497       {
 498         if (viewport.cursorMode
 499                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 500                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 501                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 502                 && Character.isDigit(evt.getKeyChar()))
 503         {
 504           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 505         }
 506
 507         switch (evt.getKeyCode())
 508         {
 509
 510         case 27: // escape key
 511           deselectAllSequenceMenuItem_actionPerformed(null);
 512
 513           break;
 514
 515         case KeyEvent.VK_DOWN:
 516           if (evt.isAltDown() || !viewport.cursorMode)
 517           {
 518             moveSelectedSequences(false);
 519           }
 520           if (viewport.cursorMode)
 521           {
 522             alignPanel.getSeqPanel().moveCursor(0, 1);
 523           }
 524           break;
 525
 526         case KeyEvent.VK_UP:
 527           if (evt.isAltDown() || !viewport.cursorMode)
 528           {
 529             moveSelectedSequences(true);
 530           }
 531           if (viewport.cursorMode)
 532           {
 533             alignPanel.getSeqPanel().moveCursor(0, -1);
 534           }
 535
 536           break;
 537
 538         case KeyEvent.VK_LEFT:
 539           if (evt.isAltDown() || !viewport.cursorMode)
 540           {
 541             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 542           }
 543           else
 544           {
 545             alignPanel.getSeqPanel().moveCursor(-1, 0);
 546           }
 547
 548           break;
 549
 550         case KeyEvent.VK_RIGHT:
 551           if (evt.isAltDown() || !viewport.cursorMode)
 552           {
 553             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 554           }
 555           else
 556           {
 557             alignPanel.getSeqPanel().moveCursor(1, 0);
 558           }
 559           break;
 560
 561         case KeyEvent.VK_SPACE:
 562           if (viewport.cursorMode)
 563           {
 564             alignPanel.getSeqPanel().insertGapAtCursor(
 565                     evt.isControlDown() || evt.isShiftDown()
 566                             || evt.isAltDown());
 567           }
 568           break;
 569
 570         // case KeyEvent.VK_A:
 571         // if (viewport.cursorMode)
 572         // {
 573         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 574         // //System.out.println("A");
 575         // }
 576         // break;
 577         /*
 578          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 579          * System.out.println("closing bracket"); } break;
 580          */
 581         case KeyEvent.VK_DELETE:
 582         case KeyEvent.VK_BACK_SPACE:
 583           if (!viewport.cursorMode)
 584           {
 585             cut_actionPerformed(null);
 586           }
 587           else
 588           {
 589             alignPanel.getSeqPanel().deleteGapAtCursor(
 590                     evt.isControlDown() || evt.isShiftDown()
 591                             || evt.isAltDown());
 592           }
 593
 594           break;
 595
 596         case KeyEvent.VK_S:
 597           if (viewport.cursorMode)
 598           {
 599             alignPanel.getSeqPanel().setCursorRow();
 600           }
 601           break;
 602         case KeyEvent.VK_C:
 603           if (viewport.cursorMode && !evt.isControlDown())
 604           {
 605             alignPanel.getSeqPanel().setCursorColumn();
 606           }
 607           break;
 608         case KeyEvent.VK_P:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().setCursorPosition();
 612           }
 613           break;
 614
 615         case KeyEvent.VK_ENTER:
 616         case KeyEvent.VK_COMMA:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorRowAndColumn();
 620           }
 621           break;
 622
 623         case KeyEvent.VK_Q:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 627           }
 628           break;
 629         case KeyEvent.VK_M:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 633           }
 634           break;
 635
 636         case KeyEvent.VK_F2:
 637           viewport.cursorMode = !viewport.cursorMode;
 638           statusBar.setText(MessageManager.formatMessage(
 639                   "label.keyboard_editing_mode",
 640                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 644             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 645           }
 646           alignPanel.getSeqPanel().seqCanvas.repaint();
 647           break;
 648
 649         case KeyEvent.VK_F1:
 650           try
 651           {
 652             Help.showHelpWindow();
 653           } catch (Exception ex)
 654           {
 655             ex.printStackTrace();
 656           }
 657           break;
 658         case KeyEvent.VK_H:
 659         {
 660           boolean toggleSeqs = !evt.isControlDown();
 661           boolean toggleCols = !evt.isShiftDown();
 662           toggleHiddenRegions(toggleSeqs, toggleCols);
 663           break;
 664         }
 665         case KeyEvent.VK_B:
 666         {
 667           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 668           boolean modifyExisting = true; // always modify, don't clear
 669                                          // evt.isShiftDown();
 670           boolean invertHighlighted = evt.isAltDown();
 671           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 672                   toggleSel);
 673           break;
 674         }
 675         case KeyEvent.VK_PAGE_UP:
 676           if (viewport.getWrapAlignment())
 677           {
 678             alignPanel.scrollUp(true);
 679           }
 680           else
 681           {
 682             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 683                     - viewport.endSeq + viewport.startSeq);
 684           }
 685           break;
 686         case KeyEvent.VK_PAGE_DOWN:
 687           if (viewport.getWrapAlignment())
 688           {
 689             alignPanel.scrollUp(false);
 690           }
 691           else
 692           {
 693             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 694                     + viewport.endSeq - viewport.startSeq);
 695           }
 696           break;
 697         }
 698       }
 699
 700       @Override
 701       public void keyReleased(KeyEvent evt)
 702       {
 703         switch (evt.getKeyCode())
 704         {
 705         case KeyEvent.VK_LEFT:
 706           if (evt.isAltDown() || !viewport.cursorMode)
 707           {
 708             viewport.firePropertyChange("alignment", null, viewport
 709                     .getAlignment().getSequences());
 710           }
 711           break;
 712
 713         case KeyEvent.VK_RIGHT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null, viewport
 717                     .getAlignment().getSequences());
 718           }
 719           break;
 720         }
 721       }
 722     });
 723   }
 724
 725   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 726   {
 727     ap.alignFrame = this;
 728     avc = new jalview.controller.AlignViewController(this, viewport,
 729             alignPanel);
 730
 731     alignPanels.add(ap);
 732
 733     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 734
 735     int aSize = alignPanels.size();
 736
 737     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 738
 739     if (aSize == 1 && ap.av.viewName == null)
 740     {
 741       this.getContentPane().add(ap, BorderLayout.CENTER);
 742     }
 743     else
 744     {
 745       if (aSize == 2)
 746       {
 747         setInitialTabVisible();
 748       }
 749
 750       expandViews.setEnabled(true);
 751       gatherViews.setEnabled(true);
 752       tabbedPane.addTab(ap.av.viewName, ap);
 753
 754       ap.setVisible(false);
 755     }
 756
 757     if (newPanel)
 758     {
 759       if (ap.av.isPadGaps())
 760       {
 761         ap.av.getAlignment().padGaps();
 762       }
 763       ap.av.updateConservation(ap);
 764       ap.av.updateConsensus(ap);
 765       ap.av.updateStrucConsensus(ap);
 766     }
 767   }
 768
 769   public void setInitialTabVisible()
 770   {
 771     expandViews.setEnabled(true);
 772     gatherViews.setEnabled(true);
 773     tabbedPane.setVisible(true);
 774     AlignmentPanel first = alignPanels.get(0);
 775     tabbedPane.addTab(first.av.viewName, first);
 776     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 777   }
 778
 779   public AlignViewport getViewport()
 780   {
 781     return viewport;
 782   }
 783
 784   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 785   private void addServiceListeners()
 786   {
 787     final java.beans.PropertyChangeListener thisListener;
 788     Desktop.instance.addJalviewPropertyChangeListener("services",
 789             thisListener = new java.beans.PropertyChangeListener()
 790             {
 791               @Override
 792               public void propertyChange(PropertyChangeEvent evt)
 793               {
 794                 // // System.out.println("Discoverer property change.");
 795                 // if (evt.getPropertyName().equals("services"))
 796                 {
 797                   SwingUtilities.invokeLater(new Runnable()
 798                   {
 799
 800                     @Override
 801                     public void run()
 802                     {
 803                       System.err
 804                               .println("Rebuild WS Menu for service change");
 805                       BuildWebServiceMenu();
 806                     }
 807
 808                   });
 809                 }
 810               }
 811             });
 812     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 813     {
 814       @Override
 815       public void internalFrameClosed(
 816               javax.swing.event.InternalFrameEvent evt)
 817       {
 818         // System.out.println("deregistering discoverer listener");
 819         Desktop.instance.removeJalviewPropertyChangeListener("services",
 820                 thisListener);
 821         closeMenuItem_actionPerformed(true);
 822       };
 823     });
 824     // Finally, build the menu once to get current service state
 825     new Thread(new Runnable()
 826     {
 827       @Override
 828       public void run()
 829       {
 830         BuildWebServiceMenu();
 831       }
 832     }).start();
 833   }
 834
 835   /**
 836    * Configure menu items that vary according to whether the alignment is
 837    * nucleotide or protein
 838    */
 839   public void setGUINucleotide()
 840   {
 841     AlignmentI al = getViewport().getAlignment();
 842     boolean nucleotide = al.isNucleotide();
 843
 844     showTranslation.setVisible(nucleotide);
 845     showReverse.setVisible(nucleotide);
 846     showReverseComplement.setVisible(nucleotide);
 847     conservationMenuItem.setEnabled(!nucleotide);
 848     modifyConservation.setEnabled(!nucleotide
 849             && conservationMenuItem.isSelected());
 850     showGroupConservation.setEnabled(!nucleotide);
 851
 852     showComplementMenuItem.setText(nucleotide ? MessageManager
 853             .getString("label.protein") : MessageManager
 854             .getString("label.nucleotide"));
 855   }
 856
 857   /**
 858    * set up menus for the current viewport. This may be called after any
 859    * operation that affects the data in the current view (selection changed,
 860    * etc) to update the menus to reflect the new state.
 861    */
 862   @Override
 863   public void setMenusForViewport()
 864   {
 865     setMenusFromViewport(viewport);
 866   }
 867
 868   /**
 869    * Need to call this method when tabs are selected for multiple views, or when
 870    * loading from Jalview2XML.java
 871    *
 872    * @param av
 873    *          AlignViewport
 874    */
 875   void setMenusFromViewport(AlignViewport av)
 876   {
 877     padGapsMenuitem.setSelected(av.isPadGaps());
 878     colourTextMenuItem.setSelected(av.isShowColourText());
 879     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 880     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 881     conservationMenuItem.setSelected(av.getConservationSelected());
 882     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 883     seqLimits.setSelected(av.getShowJVSuffix());
 884     idRightAlign.setSelected(av.isRightAlignIds());
 885     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 886     renderGapsMenuItem.setSelected(av.isRenderGaps());
 887     wrapMenuItem.setSelected(av.getWrapAlignment());
 888     scaleAbove.setVisible(av.getWrapAlignment());
 889     scaleLeft.setVisible(av.getWrapAlignment());
 890     scaleRight.setVisible(av.getWrapAlignment());
 891     annotationPanelMenuItem.setState(av.isShowAnnotation());
 892     /*
 893      * Show/hide annotations only enabled if annotation panel is shown
 894      */
 895     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 900     viewTextMenuItem.setSelected(av.getShowText());
 901     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 902     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 903     showGroupConservation.setSelected(av.isShowGroupConservation());
 904     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 905     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 906     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 907
 908     ColourMenuHelper.setColourSelected(colourMenu,
 909             av.getGlobalColourScheme());
 910
 911     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 912     hiddenMarkers.setState(av.getShowHiddenMarkers());
 913     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 914     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 915     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 916     autoCalculate.setSelected(av.autoCalculateConsensus);
 917     sortByTree.setSelected(av.sortByTree);
 918     listenToViewSelections.setSelected(av.followSelection);
 919
 920     showProducts.setEnabled(canShowProducts());
 921     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 922
 923     updateEditMenuBar();
 924   }
 925
 926   /**
 927    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 928    *
 929    * @param b
 930    */
 931   public void setGroovyEnabled(boolean b)
 932   {
 933     runGroovy.setEnabled(b);
 934   }
 935
 936   private IProgressIndicator progressBar;
 937
 938   /*
 939    * (non-Javadoc)
 940    *
 941    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 942    */
 943   @Override
 944   public void setProgressBar(String message, long id)
 945   {
 946     progressBar.setProgressBar(message, id);
 947   }
 948
 949   @Override
 950   public void registerHandler(final long id,
 951           final IProgressIndicatorHandler handler)
 952   {
 953     progressBar.registerHandler(id, handler);
 954   }
 955
 956   /**
 957    *
 958    * @return true if any progress bars are still active
 959    */
 960   @Override
 961   public boolean operationInProgress()
 962   {
 963     return progressBar.operationInProgress();
 964   }
 965
 966   @Override
 967   public void setStatus(String text)
 968   {
 969     statusBar.setText(text);
 970   }
 971
 972   /*
 973    * Added so Castor Mapping file can obtain Jalview Version
 974    */
 975   public String getVersion()
 976   {
 977     return jalview.bin.Cache.getProperty("VERSION");
 978   }
 979
 980   public FeatureRenderer getFeatureRenderer()
 981   {
 982     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 983   }
 984
 985   @Override
 986   public void fetchSequence_actionPerformed(ActionEvent e)
 987   {
 988     new jalview.gui.SequenceFetcher(this);
 989   }
 990
 991   @Override
 992   public void addFromFile_actionPerformed(ActionEvent e)
 993   {
 994     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 995   }
 996
 997   @Override
 998   public void reload_actionPerformed(ActionEvent e)
 999   {
1000     if (fileName != null)
1001     {
1002       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003       // originating file's format
1004       // TODO: work out how to recover feature settings for correct view(s) when
1005       // file is reloaded.
1006       if (FileFormat.Jalview.equals(currentFileFormat))
1007       {
1008         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009         for (int i = 0; i < frames.length; i++)
1010         {
1011           if (frames[i] instanceof AlignFrame && frames[i] != this
1012                   && ((AlignFrame) frames[i]).fileName != null
1013                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1014           {
1015             try
1016             {
1017               frames[i].setSelected(true);
1018               Desktop.instance.closeAssociatedWindows();
1019             } catch (java.beans.PropertyVetoException ex)
1020             {
1021             }
1022           }
1023
1024         }
1025         Desktop.instance.closeAssociatedWindows();
1026
1027         FileLoader loader = new FileLoader();
1028         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1029                 : DataSourceType.FILE;
1030         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1031       }
1032       else
1033       {
1034         Rectangle bounds = this.getBounds();
1035
1036         FileLoader loader = new FileLoader();
1037         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1040                 protocol, currentFileFormat);
1041
1042         newframe.setBounds(bounds);
1043         if (featureSettings != null && featureSettings.isShowing())
1044         {
1045           final Rectangle fspos = featureSettings.frame.getBounds();
1046           // TODO: need a 'show feature settings' function that takes bounds -
1047           // need to refactor Desktop.addFrame
1048           newframe.featureSettings_actionPerformed(null);
1049           final FeatureSettings nfs = newframe.featureSettings;
1050           SwingUtilities.invokeLater(new Runnable()
1051           {
1052             @Override
1053             public void run()
1054             {
1055               nfs.frame.setBounds(fspos);
1056             }
1057           });
1058           this.featureSettings.close();
1059           this.featureSettings = null;
1060         }
1061         this.closeMenuItem_actionPerformed(true);
1062       }
1063     }
1064   }
1065
1066   @Override
1067   public void addFromText_actionPerformed(ActionEvent e)
1068   {
1069     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1070             .getAlignPanel());
1071   }
1072
1073   @Override
1074   public void addFromURL_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1077   }
1078
1079   @Override
1080   public void save_actionPerformed(ActionEvent e)
1081   {
1082     if (fileName == null || (currentFileFormat == null)
1083             || fileName.startsWith("http"))
1084     {
1085       saveAs_actionPerformed(null);
1086     }
1087     else
1088     {
1089       saveAlignment(fileName, currentFileFormat);
1090     }
1091   }
1092
1093   /**
1094    * DOCUMENT ME!
1095    *
1096    * @param e
1097    *          DOCUMENT ME!
1098    */
1099   @Override
1100   public void saveAs_actionPerformed(ActionEvent e)
1101   {
1102     String format = currentFileFormat == null ? null : currentFileFormat
1103             .getName();
1104     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1105             Cache.getProperty("LAST_DIRECTORY"), format);
1106
1107     chooser.setFileView(new JalviewFileView());
1108     chooser.setDialogTitle(MessageManager
1109             .getString("label.save_alignment_to_file"));
1110     chooser.setToolTipText(MessageManager.getString("action.save"));
1111
1112     int value = chooser.showSaveDialog(this);
1113
1114     if (value == JalviewFileChooser.APPROVE_OPTION)
1115     {
1116       currentFileFormat = chooser.getSelectedFormat();
1117       while (currentFileFormat == null)
1118       {
1119         JvOptionPane
1120                 .showInternalMessageDialog(
1121                         Desktop.desktop,
1122                         MessageManager
1123                                 .getString("label.select_file_format_before_saving"),
1124                         MessageManager
1125                                 .getString("label.file_format_not_specified"),
1126                         JvOptionPane.WARNING_MESSAGE);
1127         currentFileFormat = chooser.getSelectedFormat();
1128         value = chooser.showSaveDialog(this);
1129         if (value != JalviewFileChooser.APPROVE_OPTION)
1130         {
1131           return;
1132         }
1133       }
1134
1135       fileName = chooser.getSelectedFile().getPath();
1136
1137       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1138
1139       Cache.setProperty("LAST_DIRECTORY", fileName);
1140       saveAlignment(fileName, currentFileFormat);
1141     }
1142   }
1143
1144   public boolean saveAlignment(String file, FileFormatI format)
1145   {
1146     boolean success = true;
1147
1148     if (FileFormat.Jalview.equals(format))
1149     {
1150       String shortName = title;
1151
1152       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1153       {
1154         shortName = shortName.substring(shortName
1155                 .lastIndexOf(java.io.File.separatorChar) + 1);
1156       }
1157
1158       success = new Jalview2XML().saveAlignment(this, file, shortName);
1159
1160       statusBar.setText(MessageManager.formatMessage(
1161               "label.successfully_saved_to_file_in_format", new Object[] {
1162                   fileName, format }));
1163
1164     }
1165     else
1166     {
1167       AlignmentExportData exportData = getAlignmentForExport(format,
1168               viewport, null);
1169       if (exportData.getSettings().isCancelled())
1170       {
1171         return false;
1172       }
1173       FormatAdapter f = new FormatAdapter(alignPanel,
1174               exportData.getSettings());
1175       String output = f.formatSequences(
1176               format,
1177               exportData.getAlignment(), // class cast exceptions will
1178               // occur in the distant future
1179               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180               f.getCacheSuffixDefault(format),
1181               viewport.getColumnSelection());
1182
1183       if (output == null)
1184       {
1185         success = false;
1186       }
1187       else
1188       {
1189         try
1190         {
1191           PrintWriter out = new PrintWriter(new FileWriter(file));
1192
1193           out.print(output);
1194           out.close();
1195           this.setTitle(file);
1196           statusBar.setText(MessageManager.formatMessage(
1197                   "label.successfully_saved_to_file_in_format",
1198                   new Object[] { fileName, format.getName() }));
1199         } catch (Exception ex)
1200         {
1201           success = false;
1202           ex.printStackTrace();
1203         }
1204       }
1205     }
1206
1207     if (!success)
1208     {
1209       JvOptionPane.showInternalMessageDialog(this, MessageManager
1210               .formatMessage("label.couldnt_save_file",
1211                       new Object[] { fileName }), MessageManager
1212               .getString("label.error_saving_file"),
1213               JvOptionPane.WARNING_MESSAGE);
1214     }
1215
1216     return success;
1217   }
1218
1219   private void warningMessage(String warning, String title)
1220   {
1221     if (new jalview.util.Platform().isHeadless())
1222     {
1223       System.err.println("Warning: " + title + "\nWarning: " + warning);
1224
1225     }
1226     else
1227     {
1228       JvOptionPane.showInternalMessageDialog(this, warning, title,
1229               JvOptionPane.WARNING_MESSAGE);
1230     }
1231     return;
1232   }
1233
1234   /**
1235    * DOCUMENT ME!
1236    *
1237    * @param e
1238    *          DOCUMENT ME!
1239    */
1240   @Override
1241   protected void outputText_actionPerformed(ActionEvent e)
1242   {
1243     FileFormatI fileFormat = FileFormats.getInstance().forName(
1244             e.getActionCommand());
1245     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1246             viewport, null);
1247     if (exportData.getSettings().isCancelled())
1248     {
1249       return;
1250     }
1251     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252     cap.setForInput(null);
1253     try
1254     {
1255       FileFormatI format = fileFormat;
1256       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257               .formatSequences(format,
1258                       exportData.getAlignment(),
1259                       exportData.getOmitHidden(),
1260                       exportData.getStartEndPostions(),
1261                       viewport.getColumnSelection()));
1262       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1263               "label.alignment_output_command",
1264               new Object[] { e.getActionCommand() }), 600, 500);
1265     } catch (OutOfMemoryError oom)
1266     {
1267       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1268       cap.dispose();
1269     }
1270
1271   }
1272
1273   public static AlignmentExportData getAlignmentForExport(
1274           FileFormatI format, AlignViewportI viewport,
1275           AlignExportSettingI exportSettings)
1276   {
1277     AlignmentI alignmentToExport = null;
1278     AlignExportSettingI settings = exportSettings;
1279     String[] omitHidden = null;
1280
1281     HiddenSequences hiddenSeqs = viewport.getAlignment()
1282             .getHiddenSequences();
1283
1284     alignmentToExport = viewport.getAlignment();
1285
1286     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287     if (settings == null)
1288     {
1289       settings = new AlignExportSettings(hasHiddenSeqs,
1290               viewport.hasHiddenColumns(), format);
1291     }
1292     // settings.isExportAnnotations();
1293
1294     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1295     {
1296       omitHidden = viewport.getViewAsString(false,
1297               settings.isExportHiddenSequences());
1298     }
1299
1300     int[] alignmentStartEnd = new int[2];
1301     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1302     {
1303       alignmentToExport = hiddenSeqs.getFullAlignment();
1304     }
1305     else
1306     {
1307       alignmentToExport = viewport.getAlignment();
1308     }
1309     alignmentStartEnd = alignmentToExport
1310             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1311                     .getHiddenColumns());
1312     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1313             omitHidden, alignmentStartEnd, settings);
1314     return ed;
1315   }
1316
1317   /**
1318    * DOCUMENT ME!
1319    *
1320    * @param e
1321    *          DOCUMENT ME!
1322    */
1323   @Override
1324   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1325   {
1326     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1327     htmlSVG.exportHTML(null);
1328   }
1329
1330   @Override
1331   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1332   {
1333     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1334     bjs.exportHTML(null);
1335   }
1336
1337   public void createImageMap(File file, String image)
1338   {
1339     alignPanel.makePNGImageMap(file, image);
1340   }
1341
1342   /**
1343    * DOCUMENT ME!
1344    *
1345    * @param e
1346    *          DOCUMENT ME!
1347    */
1348   @Override
1349   public void createPNG(File f)
1350   {
1351     alignPanel.makePNG(f);
1352   }
1353
1354   /**
1355    * DOCUMENT ME!
1356    *
1357    * @param e
1358    *          DOCUMENT ME!
1359    */
1360   @Override
1361   public void createEPS(File f)
1362   {
1363     alignPanel.makeEPS(f);
1364   }
1365
1366   @Override
1367   public void createSVG(File f)
1368   {
1369     alignPanel.makeSVG(f);
1370   }
1371
1372   @Override
1373   public void pageSetup_actionPerformed(ActionEvent e)
1374   {
1375     PrinterJob printJob = PrinterJob.getPrinterJob();
1376     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1377   }
1378
1379   /**
1380    * DOCUMENT ME!
1381    *
1382    * @param e
1383    *          DOCUMENT ME!
1384    */
1385   @Override
1386   public void printMenuItem_actionPerformed(ActionEvent e)
1387   {
1388     // Putting in a thread avoids Swing painting problems
1389     PrintThread thread = new PrintThread(alignPanel);
1390     thread.start();
1391   }
1392
1393   @Override
1394   public void exportFeatures_actionPerformed(ActionEvent e)
1395   {
1396     new AnnotationExporter().exportFeatures(alignPanel);
1397   }
1398
1399   @Override
1400   public void exportAnnotations_actionPerformed(ActionEvent e)
1401   {
1402     new AnnotationExporter().exportAnnotations(alignPanel);
1403   }
1404
1405   @Override
1406   public void associatedData_actionPerformed(ActionEvent e)
1407   {
1408     // Pick the tree file
1409     JalviewFileChooser chooser = new JalviewFileChooser(
1410             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1411     chooser.setFileView(new JalviewFileView());
1412     chooser.setDialogTitle(MessageManager
1413             .getString("label.load_jalview_annotations"));
1414     chooser.setToolTipText(MessageManager
1415             .getString("label.load_jalview_annotations"));
1416
1417     int value = chooser.showOpenDialog(null);
1418
1419     if (value == JalviewFileChooser.APPROVE_OPTION)
1420     {
1421       String choice = chooser.getSelectedFile().getPath();
1422       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1423       loadJalviewDataFile(choice, null, null, null);
1424     }
1425
1426   }
1427
1428   /**
1429    * Close the current view or all views in the alignment frame. If the frame
1430    * only contains one view then the alignment will be removed from memory.
1431    *
1432    * @param closeAllTabs
1433    */
1434   @Override
1435   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1436   {
1437     if (alignPanels != null && alignPanels.size() < 2)
1438     {
1439       closeAllTabs = true;
1440     }
1441
1442     try
1443     {
1444       if (alignPanels != null)
1445       {
1446         if (closeAllTabs)
1447         {
1448           if (this.isClosed())
1449           {
1450             // really close all the windows - otherwise wait till
1451             // setClosed(true) is called
1452             for (int i = 0; i < alignPanels.size(); i++)
1453             {
1454               AlignmentPanel ap = alignPanels.get(i);
1455               ap.closePanel();
1456             }
1457           }
1458         }
1459         else
1460         {
1461           closeView(alignPanel);
1462         }
1463       }
1464
1465       if (closeAllTabs)
1466       {
1467         /*
1468          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1469          * be called recursively, with the frame now in 'closed' state
1470          */
1471         this.setClosed(true);
1472       }
1473     } catch (Exception ex)
1474     {
1475       ex.printStackTrace();
1476     }
1477   }
1478
1479   /**
1480    * Close the specified panel and close up tabs appropriately.
1481    *
1482    * @param panelToClose
1483    */
1484   public void closeView(AlignmentPanel panelToClose)
1485   {
1486     int index = tabbedPane.getSelectedIndex();
1487     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1488     alignPanels.remove(panelToClose);
1489     panelToClose.closePanel();
1490     panelToClose = null;
1491
1492     tabbedPane.removeTabAt(closedindex);
1493     tabbedPane.validate();
1494
1495     if (index > closedindex || index == tabbedPane.getTabCount())
1496     {
1497       // modify currently selected tab index if necessary.
1498       index--;
1499     }
1500
1501     this.tabSelectionChanged(index);
1502   }
1503
1504   /**
1505    * DOCUMENT ME!
1506    */
1507   void updateEditMenuBar()
1508   {
1509
1510     if (viewport.getHistoryList().size() > 0)
1511     {
1512       undoMenuItem.setEnabled(true);
1513       CommandI command = viewport.getHistoryList().peek();
1514       undoMenuItem.setText(MessageManager.formatMessage(
1515               "label.undo_command",
1516               new Object[] { command.getDescription() }));
1517     }
1518     else
1519     {
1520       undoMenuItem.setEnabled(false);
1521       undoMenuItem.setText(MessageManager.getString("action.undo"));
1522     }
1523
1524     if (viewport.getRedoList().size() > 0)
1525     {
1526       redoMenuItem.setEnabled(true);
1527
1528       CommandI command = viewport.getRedoList().peek();
1529       redoMenuItem.setText(MessageManager.formatMessage(
1530               "label.redo_command",
1531               new Object[] { command.getDescription() }));
1532     }
1533     else
1534     {
1535       redoMenuItem.setEnabled(false);
1536       redoMenuItem.setText(MessageManager.getString("action.redo"));
1537     }
1538   }
1539
1540   @Override
1541   public void addHistoryItem(CommandI command)
1542   {
1543     if (command.getSize() > 0)
1544     {
1545       viewport.addToHistoryList(command);
1546       viewport.clearRedoList();
1547       updateEditMenuBar();
1548       viewport.updateHiddenColumns();
1549       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1550       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1551       // viewport.getColumnSelection()
1552       // .getHiddenColumns().size() > 0);
1553     }
1554   }
1555
1556   /**
1557    *
1558    * @return alignment objects for all views
1559    */
1560   AlignmentI[] getViewAlignments()
1561   {
1562     if (alignPanels != null)
1563     {
1564       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1565       int i = 0;
1566       for (AlignmentPanel ap : alignPanels)
1567       {
1568         als[i++] = ap.av.getAlignment();
1569       }
1570       return als;
1571     }
1572     if (viewport != null)
1573     {
1574       return new AlignmentI[] { viewport.getAlignment() };
1575     }
1576     return null;
1577   }
1578
1579   /**
1580    * DOCUMENT ME!
1581    *
1582    * @param e
1583    *          DOCUMENT ME!
1584    */
1585   @Override
1586   protected void undoMenuItem_actionPerformed(ActionEvent e)
1587   {
1588     if (viewport.getHistoryList().isEmpty())
1589     {
1590       return;
1591     }
1592     CommandI command = viewport.getHistoryList().pop();
1593     viewport.addToRedoList(command);
1594     command.undoCommand(getViewAlignments());
1595
1596     AlignmentViewport originalSource = getOriginatingSource(command);
1597     updateEditMenuBar();
1598
1599     if (originalSource != null)
1600     {
1601       if (originalSource != viewport)
1602       {
1603         Cache.log
1604                 .warn("Implementation worry: mismatch of viewport origin for undo");
1605       }
1606       originalSource.updateHiddenColumns();
1607       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1608       // null
1609       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1610       // viewport.getColumnSelection()
1611       // .getHiddenColumns().size() > 0);
1612       originalSource.firePropertyChange("alignment", null, originalSource
1613               .getAlignment().getSequences());
1614     }
1615   }
1616
1617   /**
1618    * DOCUMENT ME!
1619    *
1620    * @param e
1621    *          DOCUMENT ME!
1622    */
1623   @Override
1624   protected void redoMenuItem_actionPerformed(ActionEvent e)
1625   {
1626     if (viewport.getRedoList().size() < 1)
1627     {
1628       return;
1629     }
1630
1631     CommandI command = viewport.getRedoList().pop();
1632     viewport.addToHistoryList(command);
1633     command.doCommand(getViewAlignments());
1634
1635     AlignmentViewport originalSource = getOriginatingSource(command);
1636     updateEditMenuBar();
1637
1638     if (originalSource != null)
1639     {
1640
1641       if (originalSource != viewport)
1642       {
1643         Cache.log
1644                 .warn("Implementation worry: mismatch of viewport origin for redo");
1645       }
1646       originalSource.updateHiddenColumns();
1647       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648       // null
1649       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1650       // viewport.getColumnSelection()
1651       // .getHiddenColumns().size() > 0);
1652       originalSource.firePropertyChange("alignment", null, originalSource
1653               .getAlignment().getSequences());
1654     }
1655   }
1656
1657   AlignmentViewport getOriginatingSource(CommandI command)
1658   {
1659     AlignmentViewport originalSource = null;
1660     // For sequence removal and addition, we need to fire
1661     // the property change event FROM the viewport where the
1662     // original alignment was altered
1663     AlignmentI al = null;
1664     if (command instanceof EditCommand)
1665     {
1666       EditCommand editCommand = (EditCommand) command;
1667       al = editCommand.getAlignment();
1668       List<Component> comps = PaintRefresher.components.get(viewport
1669               .getSequenceSetId());
1670
1671       for (Component comp : comps)
1672       {
1673         if (comp instanceof AlignmentPanel)
1674         {
1675           if (al == ((AlignmentPanel) comp).av.getAlignment())
1676           {
1677             originalSource = ((AlignmentPanel) comp).av;
1678             break;
1679           }
1680         }
1681       }
1682     }
1683
1684     if (originalSource == null)
1685     {
1686       // The original view is closed, we must validate
1687       // the current view against the closed view first
1688       if (al != null)
1689       {
1690         PaintRefresher.validateSequences(al, viewport.getAlignment());
1691       }
1692
1693       originalSource = viewport;
1694     }
1695
1696     return originalSource;
1697   }
1698
1699   /**
1700    * DOCUMENT ME!
1701    *
1702    * @param up
1703    *          DOCUMENT ME!
1704    */
1705   public void moveSelectedSequences(boolean up)
1706   {
1707     SequenceGroup sg = viewport.getSelectionGroup();
1708
1709     if (sg == null)
1710     {
1711       return;
1712     }
1713     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1714             viewport.getHiddenRepSequences(), up);
1715     alignPanel.paintAlignment(true);
1716   }
1717
1718   synchronized void slideSequences(boolean right, int size)
1719   {
1720     List<SequenceI> sg = new ArrayList<SequenceI>();
1721     if (viewport.cursorMode)
1722     {
1723       sg.add(viewport.getAlignment().getSequenceAt(
1724               alignPanel.getSeqPanel().seqCanvas.cursorY));
1725     }
1726     else if (viewport.getSelectionGroup() != null
1727             && viewport.getSelectionGroup().getSize() != viewport
1728                     .getAlignment().getHeight())
1729     {
1730       sg = viewport.getSelectionGroup().getSequences(
1731               viewport.getHiddenRepSequences());
1732     }
1733
1734     if (sg.size() < 1)
1735     {
1736       return;
1737     }
1738
1739     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1740
1741     for (SequenceI seq : viewport.getAlignment().getSequences())
1742     {
1743       if (!sg.contains(seq))
1744       {
1745         invertGroup.add(seq);
1746       }
1747     }
1748
1749     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1750
1751     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1752     for (int i = 0; i < invertGroup.size(); i++)
1753     {
1754       seqs2[i] = invertGroup.get(i);
1755     }
1756
1757     SlideSequencesCommand ssc;
1758     if (right)
1759     {
1760       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1761               size, viewport.getGapCharacter());
1762     }
1763     else
1764     {
1765       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1766               size, viewport.getGapCharacter());
1767     }
1768
1769     int groupAdjustment = 0;
1770     if (ssc.getGapsInsertedBegin() && right)
1771     {
1772       if (viewport.cursorMode)
1773       {
1774         alignPanel.getSeqPanel().moveCursor(size, 0);
1775       }
1776       else
1777       {
1778         groupAdjustment = size;
1779       }
1780     }
1781     else if (!ssc.getGapsInsertedBegin() && !right)
1782     {
1783       if (viewport.cursorMode)
1784       {
1785         alignPanel.getSeqPanel().moveCursor(-size, 0);
1786       }
1787       else
1788       {
1789         groupAdjustment = -size;
1790       }
1791     }
1792
1793     if (groupAdjustment != 0)
1794     {
1795       viewport.getSelectionGroup().setStartRes(
1796               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1797       viewport.getSelectionGroup().setEndRes(
1798               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1799     }
1800
1801     /*
1802      * just extend the last slide command if compatible; but not if in
1803      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1804      */
1805     boolean appendHistoryItem = false;
1806     Deque<CommandI> historyList = viewport.getHistoryList();
1807     boolean inSplitFrame = getSplitViewContainer() != null;
1808     if (!inSplitFrame && historyList != null && historyList.size() > 0
1809             && historyList.peek() instanceof SlideSequencesCommand)
1810     {
1811       appendHistoryItem = ssc
1812               .appendSlideCommand((SlideSequencesCommand) historyList
1813                       .peek());
1814     }
1815
1816     if (!appendHistoryItem)
1817     {
1818       addHistoryItem(ssc);
1819     }
1820
1821     repaint();
1822   }
1823
1824   /**
1825    * DOCUMENT ME!
1826    *
1827    * @param e
1828    *          DOCUMENT ME!
1829    */
1830   @Override
1831   protected void copy_actionPerformed(ActionEvent e)
1832   {
1833     System.gc();
1834     if (viewport.getSelectionGroup() == null)
1835     {
1836       return;
1837     }
1838     // TODO: preserve the ordering of displayed alignment annotation in any
1839     // internal paste (particularly sequence associated annotation)
1840     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1841     String[] omitHidden = null;
1842
1843     if (viewport.hasHiddenColumns())
1844     {
1845       omitHidden = viewport.getViewAsString(true);
1846     }
1847
1848     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1849             seqs,
1850             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.startRes);
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.startRes);
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    */
3304   @Override
3305   protected void applyToAllGroups_actionPerformed()
3306   {
3307     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3308   }
3309
3310   /**
3311    * Action on user selecting a colour from the colour menu
3312    *
3313    * @param name
3314    *          the name (not the menu item label!) of the colour scheme
3315    */
3316   @Override
3317   public void changeColour_actionPerformed(String name)
3318   {
3319     /*
3320      * 'User Defined' opens a panel to configure or load a
3321      * user-defined colour scheme
3322      */
3323     if (ResidueColourScheme.USER_DEFINED.equals(name))
3324     {
3325       new UserDefinedColours(alignPanel, null);
3326       return;
3327     }
3328
3329     /*
3330      * otherwise set the chosen colour scheme (or null for 'None')
3331      */
3332     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3333             viewport.getAlignment(), viewport.getHiddenRepSequences());
3334     changeColour(cs);
3335   }
3336
3337   /**
3338    * Actions on setting or changing the alignment colour scheme
3339    *
3340    * @param cs
3341    */
3342   @Override
3343   public void changeColour(ColourSchemeI cs)
3344   {
3345     // TODO: pull up to controller method
3346     if (cs != null)
3347     {
3348       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3349       // Make sure viewport is up to date w.r.t. any sliders
3350       if (viewport.getAbovePIDThreshold())
3351       {
3352         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3353                 "Background");
3354         viewport.setThreshold(threshold);
3355       }
3356
3357       if (viewport.getConservationSelected())
3358       {
3359         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3360                 cs, "Background"));
3361       }
3362     }
3363
3364     viewport.setGlobalColourScheme(cs);
3365
3366     alignPanel.paintAlignment(true);
3367   }
3368
3369   /**
3370    * DOCUMENT ME!
3371    *
3372    * @param e
3373    *          DOCUMENT ME!
3374    */
3375   @Override
3376   protected void modifyPID_actionPerformed()
3377   {
3378     if (viewport.getAbovePIDThreshold()
3379             && viewport.getGlobalColourScheme() != null)
3380     {
3381       SliderPanel.setPIDSliderSource(alignPanel,
3382               viewport.getGlobalColourScheme(), "Background");
3383       SliderPanel.showPIDSlider();
3384     }
3385   }
3386
3387   /**
3388    * DOCUMENT ME!
3389    *
3390    * @param e
3391    *          DOCUMENT ME!
3392    */
3393   @Override
3394   protected void modifyConservation_actionPerformed()
3395   {
3396     if (viewport.getConservationSelected()
3397             && viewport.getGlobalColourScheme() != null)
3398     {
3399       SliderPanel.setConservationSlider(alignPanel,
3400               viewport.getGlobalColourScheme(), "Background");
3401       SliderPanel.showConservationSlider();
3402     }
3403   }
3404
3405   /**
3406    * Action on selecting or deselecting (Colour) By Conservation
3407    */
3408   @Override
3409   protected void conservationMenuItem_actionPerformed()
3410   {
3411     boolean selected = conservationMenuItem.isSelected();
3412     modifyConservation.setEnabled(selected);
3413     viewport.setConservationSelected(selected);
3414
3415     changeColour(viewport.getGlobalColourScheme());
3416     if (selected)
3417     {
3418       modifyConservation_actionPerformed();
3419     }
3420     else
3421     {
3422       SliderPanel.hideConservationSlider();
3423     }
3424   }
3425
3426   /**
3427    * Action on selecting or deselecting (Colour) Above PID Threshold
3428    */
3429   @Override
3430   public void abovePIDThreshold_actionPerformed()
3431   {
3432     boolean selected = abovePIDThreshold.isSelected();
3433     modifyPID.setEnabled(selected);
3434     viewport.setAbovePIDThreshold(selected);
3435
3436     changeColour(viewport.getGlobalColourScheme());
3437     if (selected)
3438     {
3439       modifyPID_actionPerformed();
3440     }
3441     else
3442     {
3443       SliderPanel.hidePIDSlider();
3444     }
3445   }
3446
3447   /**
3448    * DOCUMENT ME!
3449    *
3450    * @param e
3451    *          DOCUMENT ME!
3452    */
3453   @Override
3454   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3455   {
3456     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3457     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3458             .getAlignment().getSequenceAt(0), null);
3459     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3460             viewport.getAlignment()));
3461     alignPanel.paintAlignment(true);
3462   }
3463
3464   /**
3465    * DOCUMENT ME!
3466    *
3467    * @param e
3468    *          DOCUMENT ME!
3469    */
3470   @Override
3471   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3472   {
3473     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3474     AlignmentSorter.sortByID(viewport.getAlignment());
3475     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3476             viewport.getAlignment()));
3477     alignPanel.paintAlignment(true);
3478   }
3479
3480   /**
3481    * DOCUMENT ME!
3482    *
3483    * @param e
3484    *          DOCUMENT ME!
3485    */
3486   @Override
3487   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3488   {
3489     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3490     AlignmentSorter.sortByLength(viewport.getAlignment());
3491     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3492             viewport.getAlignment()));
3493     alignPanel.paintAlignment(true);
3494   }
3495
3496   /**
3497    * DOCUMENT ME!
3498    *
3499    * @param e
3500    *          DOCUMENT ME!
3501    */
3502   @Override
3503   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3504   {
3505     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3506     AlignmentSorter.sortByGroup(viewport.getAlignment());
3507     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3508             viewport.getAlignment()));
3509
3510     alignPanel.paintAlignment(true);
3511   }
3512
3513   /**
3514    * DOCUMENT ME!
3515    *
3516    * @param e
3517    *          DOCUMENT ME!
3518    */
3519   @Override
3520   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3521   {
3522     new RedundancyPanel(alignPanel, this);
3523   }
3524
3525   /**
3526    * DOCUMENT ME!
3527    *
3528    * @param e
3529    *          DOCUMENT ME!
3530    */
3531   @Override
3532   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3533   {
3534     if ((viewport.getSelectionGroup() == null)
3535             || (viewport.getSelectionGroup().getSize() < 2))
3536     {
3537       JvOptionPane.showInternalMessageDialog(this, MessageManager
3538               .getString("label.you_must_select_least_two_sequences"),
3539               MessageManager.getString("label.invalid_selection"),
3540               JvOptionPane.WARNING_MESSAGE);
3541     }
3542     else
3543     {
3544       JInternalFrame frame = new JInternalFrame();
3545       frame.setContentPane(new PairwiseAlignPanel(viewport));
3546       Desktop.addInternalFrame(frame,
3547               MessageManager.getString("action.pairwise_alignment"), 600,
3548               500);
3549     }
3550   }
3551
3552   /**
3553    * DOCUMENT ME!
3554    *
3555    * @param e
3556    *          DOCUMENT ME!
3557    */
3558   @Override
3559   public void PCAMenuItem_actionPerformed(ActionEvent e)
3560   {
3561     if (((viewport.getSelectionGroup() != null)
3562             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3563             .getSelectionGroup().getSize() > 0))
3564             || (viewport.getAlignment().getHeight() < 4))
3565     {
3566       JvOptionPane
3567               .showInternalMessageDialog(
3568                       this,
3569                       MessageManager
3570                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3571                       MessageManager
3572                               .getString("label.sequence_selection_insufficient"),
3573                       JvOptionPane.WARNING_MESSAGE);
3574
3575       return;
3576     }
3577
3578     new PCAPanel(alignPanel);
3579   }
3580
3581   @Override
3582   public void autoCalculate_actionPerformed(ActionEvent e)
3583   {
3584     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3585     if (viewport.autoCalculateConsensus)
3586     {
3587       viewport.firePropertyChange("alignment", null, viewport
3588               .getAlignment().getSequences());
3589     }
3590   }
3591
3592   @Override
3593   public void sortByTreeOption_actionPerformed(ActionEvent e)
3594   {
3595     viewport.sortByTree = sortByTree.isSelected();
3596   }
3597
3598   @Override
3599   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3600   {
3601     viewport.followSelection = listenToViewSelections.isSelected();
3602   }
3603
3604   /**
3605    * DOCUMENT ME!
3606    *
3607    * @param e
3608    *          DOCUMENT ME!
3609    */
3610   @Override
3611   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3612   {
3613     newTreePanel("AV", "PID", "Average distance tree using PID");
3614   }
3615
3616   /**
3617    * DOCUMENT ME!
3618    *
3619    * @param e
3620    *          DOCUMENT ME!
3621    */
3622   @Override
3623   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3624   {
3625     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3626   }
3627
3628   /**
3629    * DOCUMENT ME!
3630    *
3631    * @param e
3632    *          DOCUMENT ME!
3633    */
3634   @Override
3635   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3636   {
3637     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3638   }
3639
3640   /**
3641    * DOCUMENT ME!
3642    *
3643    * @param e
3644    *          DOCUMENT ME!
3645    */
3646   @Override
3647   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3648   {
3649     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3650   }
3651
3652   /**
3653    * DOCUMENT ME!
3654    *
3655    * @param type
3656    *          DOCUMENT ME!
3657    * @param pwType
3658    *          DOCUMENT ME!
3659    * @param title
3660    *          DOCUMENT ME!
3661    */
3662   void newTreePanel(String type, String pwType, String title)
3663   {
3664     TreePanel tp;
3665
3666     if (viewport.getSelectionGroup() != null
3667             && viewport.getSelectionGroup().getSize() > 0)
3668     {
3669       if (viewport.getSelectionGroup().getSize() < 3)
3670       {
3671         JvOptionPane
3672                 .showMessageDialog(
3673                         Desktop.desktop,
3674                         MessageManager
3675                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3676                         MessageManager
3677                                 .getString("label.not_enough_sequences"),
3678                         JvOptionPane.WARNING_MESSAGE);
3679         return;
3680       }
3681
3682       SequenceGroup sg = viewport.getSelectionGroup();
3683
3684       /* Decide if the selection is a column region */
3685       for (SequenceI _s : sg.getSequences())
3686       {
3687         if (_s.getLength() < sg.getEndRes())
3688         {
3689           JvOptionPane
3690                   .showMessageDialog(
3691                           Desktop.desktop,
3692                           MessageManager
3693                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3694                           MessageManager
3695                                   .getString("label.sequences_selection_not_aligned"),
3696                           JvOptionPane.WARNING_MESSAGE);
3697
3698           return;
3699         }
3700       }
3701
3702       title = title + " on region";
3703       tp = new TreePanel(alignPanel, type, pwType);
3704     }
3705     else
3706     {
3707       // are the visible sequences aligned?
3708       if (!viewport.getAlignment().isAligned(false))
3709       {
3710         JvOptionPane
3711                 .showMessageDialog(
3712                         Desktop.desktop,
3713                         MessageManager
3714                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3715                         MessageManager
3716                                 .getString("label.sequences_not_aligned"),
3717                         JvOptionPane.WARNING_MESSAGE);
3718
3719         return;
3720       }
3721
3722       if (viewport.getAlignment().getHeight() < 2)
3723       {
3724         return;
3725       }
3726
3727       tp = new TreePanel(alignPanel, type, pwType);
3728     }
3729
3730     title += " from ";
3731
3732     if (viewport.viewName != null)
3733     {
3734       title += viewport.viewName + " of ";
3735     }
3736
3737     title += this.title;
3738
3739     Desktop.addInternalFrame(tp, title, 600, 500);
3740   }
3741
3742   /**
3743    * DOCUMENT ME!
3744    *
3745    * @param title
3746    *          DOCUMENT ME!
3747    * @param order
3748    *          DOCUMENT ME!
3749    */
3750   public void addSortByOrderMenuItem(String title,
3751           final AlignmentOrder order)
3752   {
3753     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3754             "action.by_title_param", new Object[] { title }));
3755     sort.add(item);
3756     item.addActionListener(new java.awt.event.ActionListener()
3757     {
3758       @Override
3759       public void actionPerformed(ActionEvent e)
3760       {
3761         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3762
3763         // TODO: JBPNote - have to map order entries to curent SequenceI
3764         // pointers
3765         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3766
3767         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3768                 .getAlignment()));
3769
3770         alignPanel.paintAlignment(true);
3771       }
3772     });
3773   }
3774
3775   /**
3776    * Add a new sort by annotation score menu item
3777    *
3778    * @param sort
3779    *          the menu to add the option to
3780    * @param scoreLabel
3781    *          the label used to retrieve scores for each sequence on the
3782    *          alignment
3783    */
3784   public void addSortByAnnotScoreMenuItem(JMenu sort,
3785           final String scoreLabel)
3786   {
3787     final JMenuItem item = new JMenuItem(scoreLabel);
3788     sort.add(item);
3789     item.addActionListener(new java.awt.event.ActionListener()
3790     {
3791       @Override
3792       public void actionPerformed(ActionEvent e)
3793       {
3794         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3795         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3796                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3797         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3798                 viewport.getAlignment()));
3799         alignPanel.paintAlignment(true);
3800       }
3801     });
3802   }
3803
3804   /**
3805    * last hash for alignment's annotation array - used to minimise cost of
3806    * rebuild.
3807    */
3808   protected int _annotationScoreVectorHash;
3809
3810   /**
3811    * search the alignment and rebuild the sort by annotation score submenu the
3812    * last alignment annotation vector hash is stored to minimize cost of
3813    * rebuilding in subsequence calls.
3814    *
3815    */
3816   @Override
3817   public void buildSortByAnnotationScoresMenu()
3818   {
3819     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3820     {
3821       return;
3822     }
3823
3824     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3825     {
3826       sortByAnnotScore.removeAll();
3827       // almost certainly a quicker way to do this - but we keep it simple
3828       Hashtable scoreSorts = new Hashtable();
3829       AlignmentAnnotation aann[];
3830       for (SequenceI sqa : viewport.getAlignment().getSequences())
3831       {
3832         aann = sqa.getAnnotation();
3833         for (int i = 0; aann != null && i < aann.length; i++)
3834         {
3835           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3836           {
3837             scoreSorts.put(aann[i].label, aann[i].label);
3838           }
3839         }
3840       }
3841       Enumeration labels = scoreSorts.keys();
3842       while (labels.hasMoreElements())
3843       {
3844         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3845                 (String) labels.nextElement());
3846       }
3847       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3848       scoreSorts.clear();
3849
3850       _annotationScoreVectorHash = viewport.getAlignment()
3851               .getAlignmentAnnotation().hashCode();
3852     }
3853   }
3854
3855   /**
3856    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3857    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3858    * call. Listeners are added to remove the menu item when the treePanel is
3859    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3860    * modified.
3861    *
3862    * @param treePanel
3863    *          Displayed tree window.
3864    * @param title
3865    *          SortBy menu item title.
3866    */
3867   @Override
3868   public void buildTreeMenu()
3869   {
3870     calculateTree.removeAll();
3871     // build the calculate menu
3872
3873     for (final String type : new String[] { "NJ", "AV" })
3874     {
3875       String treecalcnm = MessageManager.getString("label.tree_calc_"
3876               + type.toLowerCase());
3877       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3878       {
3879         JMenuItem tm = new JMenuItem();
3880         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3881         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3882                 || sm.isProtein() == !viewport.getAlignment()
3883                         .isNucleotide())
3884         {
3885           String smn = MessageManager.getStringOrReturn(
3886                   "label.score_model_", sm.getName());
3887           final String title = MessageManager.formatMessage(
3888                   "label.treecalc_title", treecalcnm, smn);
3889           tm.setText(title);//
3890           tm.addActionListener(new java.awt.event.ActionListener()
3891           {
3892             @Override
3893             public void actionPerformed(ActionEvent e)
3894             {
3895               newTreePanel(type, pwtype, title);
3896             }
3897           });
3898           calculateTree.add(tm);
3899         }
3900
3901       }
3902     }
3903     sortByTreeMenu.removeAll();
3904
3905     List<Component> comps = PaintRefresher.components.get(viewport
3906             .getSequenceSetId());
3907     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3908     for (Component comp : comps)
3909     {
3910       if (comp instanceof TreePanel)
3911       {
3912         treePanels.add((TreePanel) comp);
3913       }
3914     }
3915
3916     if (treePanels.size() < 1)
3917     {
3918       sortByTreeMenu.setVisible(false);
3919       return;
3920     }
3921
3922     sortByTreeMenu.setVisible(true);
3923
3924     for (final TreePanel tp : treePanels)
3925     {
3926       final JMenuItem item = new JMenuItem(tp.getTitle());
3927       item.addActionListener(new java.awt.event.ActionListener()
3928       {
3929         @Override
3930         public void actionPerformed(ActionEvent e)
3931         {
3932           tp.sortByTree_actionPerformed();
3933           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3934
3935         }
3936       });
3937
3938       sortByTreeMenu.add(item);
3939     }
3940   }
3941
3942   public boolean sortBy(AlignmentOrder alorder, String undoname)
3943   {
3944     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3945     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3946     if (undoname != null)
3947     {
3948       addHistoryItem(new OrderCommand(undoname, oldOrder,
3949               viewport.getAlignment()));
3950     }
3951     alignPanel.paintAlignment(true);
3952     return true;
3953   }
3954
3955   /**
3956    * Work out whether the whole set of sequences or just the selected set will
3957    * be submitted for multiple alignment.
3958    *
3959    */
3960   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3961   {
3962     // Now, check we have enough sequences
3963     AlignmentView msa = null;
3964
3965     if ((viewport.getSelectionGroup() != null)
3966             && (viewport.getSelectionGroup().getSize() > 1))
3967     {
3968       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3969       // some common interface!
3970       /*
3971        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3972        * SequenceI[sz = seqs.getSize(false)];
3973        *
3974        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3975        * seqs.getSequenceAt(i); }
3976        */
3977       msa = viewport.getAlignmentView(true);
3978     }
3979     else if (viewport.getSelectionGroup() != null
3980             && viewport.getSelectionGroup().getSize() == 1)
3981     {
3982       int option = JvOptionPane.showConfirmDialog(this,
3983               MessageManager.getString("warn.oneseq_msainput_selection"),
3984               MessageManager.getString("label.invalid_selection"),
3985               JvOptionPane.OK_CANCEL_OPTION);
3986       if (option == JvOptionPane.OK_OPTION)
3987       {
3988         msa = viewport.getAlignmentView(false);
3989       }
3990     }
3991     else
3992     {
3993       msa = viewport.getAlignmentView(false);
3994     }
3995     return msa;
3996   }
3997
3998   /**
3999    * Decides what is submitted to a secondary structure prediction service: the
4000    * first sequence in the alignment, or in the current selection, or, if the
4001    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4002    * region or the whole alignment. (where the first sequence in the set is the
4003    * one that the prediction will be for).
4004    */
4005   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4006   {
4007     AlignmentView seqs = null;
4008
4009     if ((viewport.getSelectionGroup() != null)
4010             && (viewport.getSelectionGroup().getSize() > 0))
4011     {
4012       seqs = viewport.getAlignmentView(true);
4013     }
4014     else
4015     {
4016       seqs = viewport.getAlignmentView(false);
4017     }
4018     // limit sequences - JBPNote in future - could spawn multiple prediction
4019     // jobs
4020     // TODO: viewport.getAlignment().isAligned is a global state - the local
4021     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4022     if (!viewport.getAlignment().isAligned(false))
4023     {
4024       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4025       // TODO: if seqs.getSequences().length>1 then should really have warned
4026       // user!
4027
4028     }
4029     return seqs;
4030   }
4031
4032   /**
4033    * DOCUMENT ME!
4034    *
4035    * @param e
4036    *          DOCUMENT ME!
4037    */
4038   @Override
4039   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4040   {
4041     // Pick the tree file
4042     JalviewFileChooser chooser = new JalviewFileChooser(
4043             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4044     chooser.setFileView(new JalviewFileView());
4045     chooser.setDialogTitle(MessageManager
4046             .getString("label.select_newick_like_tree_file"));
4047     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4048
4049     int value = chooser.showOpenDialog(null);
4050
4051     if (value == JalviewFileChooser.APPROVE_OPTION)
4052     {
4053       String choice = chooser.getSelectedFile().getPath();
4054       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4055       jalview.io.NewickFile fin = null;
4056       try
4057       {
4058         fin = new NewickFile(choice, DataSourceType.FILE);
4059         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4060       } catch (Exception ex)
4061       {
4062         JvOptionPane
4063                 .showMessageDialog(
4064                         Desktop.desktop,
4065                         ex.getMessage(),
4066                         MessageManager
4067                                 .getString("label.problem_reading_tree_file"),
4068                         JvOptionPane.WARNING_MESSAGE);
4069         ex.printStackTrace();
4070       }
4071       if (fin != null && fin.hasWarningMessage())
4072       {
4073         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4074                 .getWarningMessage(), MessageManager
4075                 .getString("label.possible_problem_with_tree_file"),
4076                 JvOptionPane.WARNING_MESSAGE);
4077       }
4078     }
4079   }
4080
4081   public TreePanel ShowNewickTree(NewickFile nf, String title)
4082   {
4083     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4084   }
4085
4086   public TreePanel ShowNewickTree(NewickFile nf, String title,
4087           AlignmentView input)
4088   {
4089     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4090   }
4091
4092   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4093           int h, int x, int y)
4094   {
4095     return ShowNewickTree(nf, title, null, w, h, x, y);
4096   }
4097
4098   /**
4099    * Add a treeviewer for the tree extracted from a newick file object to the
4100    * current alignment view
4101    *
4102    * @param nf
4103    *          the tree
4104    * @param title
4105    *          tree viewer title
4106    * @param input
4107    *          Associated alignment input data (or null)
4108    * @param w
4109    *          width
4110    * @param h
4111    *          height
4112    * @param x
4113    *          position
4114    * @param y
4115    *          position
4116    * @return TreePanel handle
4117    */
4118   public TreePanel ShowNewickTree(NewickFile nf, String title,
4119           AlignmentView input, int w, int h, int x, int y)
4120   {
4121     TreePanel tp = null;
4122
4123     try
4124     {
4125       nf.parse();
4126
4127       if (nf.getTree() != null)
4128       {
4129         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4130
4131         tp.setSize(w, h);
4132
4133         if (x > 0 && y > 0)
4134         {
4135           tp.setLocation(x, y);
4136         }
4137
4138         Desktop.addInternalFrame(tp, title, w, h);
4139       }
4140     } catch (Exception ex)
4141     {
4142       ex.printStackTrace();
4143     }
4144
4145     return tp;
4146   }
4147
4148   private boolean buildingMenu = false;
4149
4150   /**
4151    * Generates menu items and listener event actions for web service clients
4152    *
4153    */
4154   public void BuildWebServiceMenu()
4155   {
4156     while (buildingMenu)
4157     {
4158       try
4159       {
4160         System.err.println("Waiting for building menu to finish.");
4161         Thread.sleep(10);
4162       } catch (Exception e)
4163       {
4164       }
4165     }
4166     final AlignFrame me = this;
4167     buildingMenu = true;
4168     new Thread(new Runnable()
4169     {
4170       @Override
4171       public void run()
4172       {
4173         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4174         try
4175         {
4176           // System.err.println("Building ws menu again "
4177           // + Thread.currentThread());
4178           // TODO: add support for context dependent disabling of services based
4179           // on
4180           // alignment and current selection
4181           // TODO: add additional serviceHandle parameter to specify abstract
4182           // handler
4183           // class independently of AbstractName
4184           // TODO: add in rediscovery GUI function to restart discoverer
4185           // TODO: group services by location as well as function and/or
4186           // introduce
4187           // object broker mechanism.
4188           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4189           final IProgressIndicator af = me;
4190
4191           /*
4192            * do not i18n these strings - they are hard-coded in class
4193            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4194            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4195            */
4196           final JMenu msawsmenu = new JMenu("Alignment");
4197           final JMenu secstrmenu = new JMenu(
4198                   "Secondary Structure Prediction");
4199           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4200           final JMenu analymenu = new JMenu("Analysis");
4201           final JMenu dismenu = new JMenu("Protein Disorder");
4202           // JAL-940 - only show secondary structure prediction services from
4203           // the legacy server
4204           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4205               // &&
4206           Discoverer.services != null && (Discoverer.services.size() > 0))
4207           {
4208             // TODO: refactor to allow list of AbstractName/Handler bindings to
4209             // be
4210             // stored or retrieved from elsewhere
4211             // No MSAWS used any more:
4212             // Vector msaws = null; // (Vector)
4213             // Discoverer.services.get("MsaWS");
4214             Vector secstrpr = (Vector) Discoverer.services
4215                     .get("SecStrPred");
4216             if (secstrpr != null)
4217             {
4218               // Add any secondary structure prediction services
4219               for (int i = 0, j = secstrpr.size(); i < j; i++)
4220               {
4221                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4222                         .get(i);
4223                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4224                         .getServiceClient(sh);
4225                 int p = secstrmenu.getItemCount();
4226                 impl.attachWSMenuEntry(secstrmenu, me);
4227                 int q = secstrmenu.getItemCount();
4228                 for (int litm = p; litm < q; litm++)
4229                 {
4230                   legacyItems.add(secstrmenu.getItem(litm));
4231                 }
4232               }
4233             }
4234           }
4235
4236           // Add all submenus in the order they should appear on the web
4237           // services menu
4238           wsmenu.add(msawsmenu);
4239           wsmenu.add(secstrmenu);
4240           wsmenu.add(dismenu);
4241           wsmenu.add(analymenu);
4242           // No search services yet
4243           // wsmenu.add(seqsrchmenu);
4244
4245           javax.swing.SwingUtilities.invokeLater(new Runnable()
4246           {
4247             @Override
4248             public void run()
4249             {
4250               try
4251               {
4252                 webService.removeAll();
4253                 // first, add discovered services onto the webservices menu
4254                 if (wsmenu.size() > 0)
4255                 {
4256                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4257                   {
4258                     webService.add(wsmenu.get(i));
4259                   }
4260                 }
4261                 else
4262                 {
4263                   webService.add(me.webServiceNoServices);
4264                 }
4265                 // TODO: move into separate menu builder class.
4266                 boolean new_sspred = false;
4267                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4268                 {
4269                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4270                   if (jws2servs != null)
4271                   {
4272                     if (jws2servs.hasServices())
4273                     {
4274                       jws2servs.attachWSMenuEntry(webService, me);
4275                       for (Jws2Instance sv : jws2servs.getServices())
4276                       {
4277                         if (sv.description.toLowerCase().contains("jpred"))
4278                         {
4279                           for (JMenuItem jmi : legacyItems)
4280                           {
4281                             jmi.setVisible(false);
4282                           }
4283                         }
4284                       }
4285
4286                     }
4287                     if (jws2servs.isRunning())
4288                     {
4289                       JMenuItem tm = new JMenuItem(
4290                               "Still discovering JABA Services");
4291                       tm.setEnabled(false);
4292                       webService.add(tm);
4293                     }
4294                   }
4295                 }
4296                 build_urlServiceMenu(me.webService);
4297                 build_fetchdbmenu(webService);
4298                 for (JMenu item : wsmenu)
4299                 {
4300                   if (item.getItemCount() == 0)
4301                   {
4302                     item.setEnabled(false);
4303                   }
4304                   else
4305                   {
4306                     item.setEnabled(true);
4307                   }
4308                 }
4309               } catch (Exception e)
4310               {
4311                 Cache.log
4312                         .debug("Exception during web service menu building process.",
4313                                 e);
4314               }
4315             }
4316           });
4317         } catch (Exception e)
4318         {
4319         }
4320         buildingMenu = false;
4321       }
4322     }).start();
4323
4324   }
4325
4326   /**
4327    * construct any groupURL type service menu entries.
4328    *
4329    * @param webService
4330    */
4331   private void build_urlServiceMenu(JMenu webService)
4332   {
4333     // TODO: remove this code when 2.7 is released
4334     // DEBUG - alignmentView
4335     /*
4336      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4337      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4338      *
4339      * @Override public void actionPerformed(ActionEvent e) {
4340      * jalview.datamodel.AlignmentView
4341      * .testSelectionViews(af.viewport.getAlignment(),
4342      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4343      *
4344      * }); webService.add(testAlView);
4345      */
4346     // TODO: refactor to RestClient discoverer and merge menu entries for
4347     // rest-style services with other types of analysis/calculation service
4348     // SHmmr test client - still being implemented.
4349     // DEBUG - alignmentView
4350
4351     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4352             .getRestClients())
4353     {
4354       client.attachWSMenuEntry(
4355               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4356               this);
4357     }
4358   }
4359
4360   /**
4361    * Searches the alignment sequences for xRefs and builds the Show
4362    * Cross-References menu (formerly called Show Products), with database
4363    * sources for which cross-references are found (protein sources for a
4364    * nucleotide alignment and vice versa)
4365    *
4366    * @return true if Show Cross-references menu should be enabled
4367    */
4368   public boolean canShowProducts()
4369   {
4370     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4371     AlignmentI dataset = viewport.getAlignment().getDataset();
4372
4373     showProducts.removeAll();
4374     final boolean dna = viewport.getAlignment().isNucleotide();
4375
4376     if (seqs == null || seqs.length == 0)
4377     {
4378       // nothing to see here.
4379       return false;
4380     }
4381
4382     boolean showp = false;
4383     try
4384     {
4385       List<String> ptypes = new CrossRef(seqs, dataset)
4386               .findXrefSourcesForSequences(dna);
4387
4388       for (final String source : ptypes)
4389       {
4390         showp = true;
4391         final AlignFrame af = this;
4392         JMenuItem xtype = new JMenuItem(source);
4393         xtype.addActionListener(new ActionListener()
4394         {
4395           @Override
4396           public void actionPerformed(ActionEvent e)
4397           {
4398             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4399           }
4400         });
4401         showProducts.add(xtype);
4402       }
4403       showProducts.setVisible(showp);
4404       showProducts.setEnabled(showp);
4405     } catch (Exception e)
4406     {
4407       Cache.log
4408               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4409                       e);
4410       return false;
4411     }
4412     return showp;
4413   }
4414
4415   /**
4416    * Finds and displays cross-references for the selected sequences (protein
4417    * products for nucleotide sequences, dna coding sequences for peptides).
4418    *
4419    * @param sel
4420    *          the sequences to show cross-references for
4421    * @param dna
4422    *          true if from a nucleotide alignment (so showing proteins)
4423    * @param source
4424    *          the database to show cross-references for
4425    */
4426   protected void showProductsFor(final SequenceI[] sel,
4427           final boolean _odna, final String source)
4428   {
4429     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4430             .start();
4431   }
4432
4433   /**
4434    * Construct and display a new frame containing the translation of this
4435    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4436    */
4437   @Override
4438   public void showTranslation_actionPerformed(ActionEvent e)
4439   {
4440     AlignmentI al = null;
4441     try
4442     {
4443       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4444
4445       al = dna.translateCdna();
4446     } catch (Exception ex)
4447     {
4448       jalview.bin.Cache.log.error(
4449               "Exception during translation. Please report this !", ex);
4450       final String msg = MessageManager
4451               .getString("label.error_when_translating_sequences_submit_bug_report");
4452       final String errorTitle = MessageManager
4453               .getString("label.implementation_error")
4454               + MessageManager.getString("label.translation_failed");
4455       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4456               JvOptionPane.ERROR_MESSAGE);
4457       return;
4458     }
4459     if (al == null || al.getHeight() == 0)
4460     {
4461       final String msg = MessageManager
4462               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4463       final String errorTitle = MessageManager
4464               .getString("label.translation_failed");
4465       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4466               JvOptionPane.WARNING_MESSAGE);
4467     }
4468     else
4469     {
4470       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4471       af.setFileFormat(this.currentFileFormat);
4472       final String newTitle = MessageManager.formatMessage(
4473               "label.translation_of_params",
4474               new Object[] { this.getTitle() });
4475       af.setTitle(newTitle);
4476       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4477       {
4478         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4479         viewport.openSplitFrame(af, new Alignment(seqs));
4480       }
4481       else
4482       {
4483         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4484                 DEFAULT_HEIGHT);
4485       }
4486     }
4487   }
4488
4489   /**
4490    * Set the file format
4491    *
4492    * @param format
4493    */
4494   public void setFileFormat(FileFormatI format)
4495   {
4496     this.currentFileFormat = format;
4497   }
4498
4499   /**
4500    * Try to load a features file onto the alignment.
4501    *
4502    * @param file
4503    *          contents or path to retrieve file
4504    * @param sourceType
4505    *          access mode of file (see jalview.io.AlignFile)
4506    * @return true if features file was parsed correctly.
4507    */
4508   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4509   {
4510     return avc.parseFeaturesFile(file, sourceType,
4511             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4512
4513   }
4514
4515   @Override
4516   public void refreshFeatureUI(boolean enableIfNecessary)
4517   {
4518     // note - currently this is only still here rather than in the controller
4519     // because of the featureSettings hard reference that is yet to be
4520     // abstracted
4521     if (enableIfNecessary)
4522     {
4523       viewport.setShowSequenceFeatures(true);
4524       showSeqFeatures.setSelected(true);
4525     }
4526
4527   }
4528
4529   @Override
4530   public void dragEnter(DropTargetDragEvent evt)
4531   {
4532   }
4533
4534   @Override
4535   public void dragExit(DropTargetEvent evt)
4536   {
4537   }
4538
4539   @Override
4540   public void dragOver(DropTargetDragEvent evt)
4541   {
4542   }
4543
4544   @Override
4545   public void dropActionChanged(DropTargetDragEvent evt)
4546   {
4547   }
4548
4549   @Override
4550   public void drop(DropTargetDropEvent evt)
4551   {
4552     // JAL-1552 - acceptDrop required before getTransferable call for
4553     // Java's Transferable for native dnd
4554     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4555     Transferable t = evt.getTransferable();
4556     List<String> files = new ArrayList<String>();
4557     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4558
4559     try
4560     {
4561       Desktop.transferFromDropTarget(files, protocols, evt, t);
4562     } catch (Exception e)
4563     {
4564       e.printStackTrace();
4565     }
4566     if (files != null)
4567     {
4568       try
4569       {
4570         // check to see if any of these files have names matching sequences in
4571         // the alignment
4572         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4573                 .getAlignment().getSequencesArray());
4574         /**
4575          * Object[] { String,SequenceI}
4576          */
4577         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4578         ArrayList<String> filesnotmatched = new ArrayList<String>();
4579         for (int i = 0; i < files.size(); i++)
4580         {
4581           String file = files.get(i).toString();
4582           String pdbfn = "";
4583           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4584           if (protocol == DataSourceType.FILE)
4585           {
4586             File fl = new File(file);
4587             pdbfn = fl.getName();
4588           }
4589           else if (protocol == DataSourceType.URL)
4590           {
4591             URL url = new URL(file);
4592             pdbfn = url.getFile();
4593           }
4594           if (pdbfn.length() > 0)
4595           {
4596             // attempt to find a match in the alignment
4597             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4598             int l = 0, c = pdbfn.indexOf(".");
4599             while (mtch == null && c != -1)
4600             {
4601               do
4602               {
4603                 l = c;
4604               } while ((c = pdbfn.indexOf(".", l)) > l);
4605               if (l > -1)
4606               {
4607                 pdbfn = pdbfn.substring(0, l);
4608               }
4609               mtch = idm.findAllIdMatches(pdbfn);
4610             }
4611             if (mtch != null)
4612             {
4613               FileFormatI type = null;
4614               try
4615               {
4616                 type = new IdentifyFile().identify(file, protocol);
4617               } catch (Exception ex)
4618               {
4619                 type = null;
4620               }
4621               if (type != null && type.isStructureFile())
4622               {
4623                 filesmatched.add(new Object[] { file, protocol, mtch });
4624                 continue;
4625               }
4626             }
4627             // File wasn't named like one of the sequences or wasn't a PDB file.
4628             filesnotmatched.add(file);
4629           }
4630         }
4631         int assocfiles = 0;
4632         if (filesmatched.size() > 0)
4633         {
4634           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4635                   || JvOptionPane
4636                           .showConfirmDialog(
4637                                   this,
4638                                   MessageManager
4639                                           .formatMessage(
4640                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4641                                                   new Object[] { Integer
4642                                                           .valueOf(
4643                                                                   filesmatched
4644                                                                           .size())
4645                                                           .toString() }),
4646                                   MessageManager
4647                                           .getString("label.automatically_associate_structure_files_by_name"),
4648                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4649
4650           {
4651             for (Object[] fm : filesmatched)
4652             {
4653               // try and associate
4654               // TODO: may want to set a standard ID naming formalism for
4655               // associating PDB files which have no IDs.
4656               for (SequenceI toassoc : (SequenceI[]) fm[2])
4657               {
4658                 PDBEntry pe = new AssociatePdbFileWithSeq()
4659                         .associatePdbWithSeq((String) fm[0],
4660                                 (DataSourceType) fm[1], toassoc, false,
4661                                 Desktop.instance);
4662                 if (pe != null)
4663                 {
4664                   System.err.println("Associated file : "
4665                           + ((String) fm[0]) + " with "
4666                           + toassoc.getDisplayId(true));
4667                   assocfiles++;
4668                 }
4669               }
4670               alignPanel.paintAlignment(true);
4671             }
4672           }
4673         }
4674         if (filesnotmatched.size() > 0)
4675         {
4676           if (assocfiles > 0
4677                   && (Cache.getDefault(
4678                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4679                           .showConfirmDialog(
4680                                   this,
4681                                   "<html>"
4682                                           + MessageManager
4683                                                   .formatMessage(
4684                                                           "label.ignore_unmatched_dropped_files_info",
4685                                                           new Object[] { Integer
4686                                                                   .valueOf(
4687                                                                           filesnotmatched
4688                                                                                   .size())
4689                                                                   .toString() })
4690                                           + "</html>",
4691                                   MessageManager
4692                                           .getString("label.ignore_unmatched_dropped_files"),
4693                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4694           {
4695             return;
4696           }
4697           for (String fn : filesnotmatched)
4698           {
4699             loadJalviewDataFile(fn, null, null, null);
4700           }
4701
4702         }
4703       } catch (Exception ex)
4704       {
4705         ex.printStackTrace();
4706       }
4707     }
4708   }
4709
4710   /**
4711    * Attempt to load a "dropped" file or URL string: First by testing whether
4712    * it's an Annotation file, then a JNet file, and finally a features file. If
4713    * all are false then the user may have dropped an alignment file onto this
4714    * AlignFrame.
4715    *
4716    * @param file
4717    *          either a filename or a URL string.
4718    */
4719   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4720           FileFormatI format, SequenceI assocSeq)
4721   {
4722     try
4723     {
4724       if (sourceType == null)
4725       {
4726         sourceType = FormatAdapter.checkProtocol(file);
4727       }
4728       // if the file isn't identified, or not positively identified as some
4729       // other filetype (PFAM is default unidentified alignment file type) then
4730       // try to parse as annotation.
4731       boolean isAnnotation = (format == null || FileFormat.Pfam
4732               .equals(format)) ? new AnnotationFile()
4733               .annotateAlignmentView(viewport, file, sourceType) : false;
4734
4735       if (!isAnnotation)
4736       {
4737         // first see if its a T-COFFEE score file
4738         TCoffeeScoreFile tcf = null;
4739         try
4740         {
4741           tcf = new TCoffeeScoreFile(file, sourceType);
4742           if (tcf.isValid())
4743           {
4744             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4745             {
4746               buildColourMenu();
4747               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4748               isAnnotation = true;
4749               statusBar
4750                       .setText(MessageManager
4751                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4752             }
4753             else
4754             {
4755               // some problem - if no warning its probable that the ID matching
4756               // process didn't work
4757               JvOptionPane
4758                       .showMessageDialog(
4759                               Desktop.desktop,
4760                               tcf.getWarningMessage() == null ? MessageManager
4761                                       .getString("label.check_file_matches_sequence_ids_alignment")
4762                                       : tcf.getWarningMessage(),
4763                               MessageManager
4764                                       .getString("label.problem_reading_tcoffee_score_file"),
4765                               JvOptionPane.WARNING_MESSAGE);
4766             }
4767           }
4768           else
4769           {
4770             tcf = null;
4771           }
4772         } catch (Exception x)
4773         {
4774           Cache.log
4775                   .debug("Exception when processing data source as T-COFFEE score file",
4776                           x);
4777           tcf = null;
4778         }
4779         if (tcf == null)
4780         {
4781           // try to see if its a JNet 'concise' style annotation file *before*
4782           // we
4783           // try to parse it as a features file
4784           if (format == null)
4785           {
4786             format = new IdentifyFile().identify(file, sourceType);
4787           }
4788           if (FileFormat.Jnet.equals(format))
4789           {
4790             JPredFile predictions = new JPredFile(
4791                     file, sourceType);
4792             new JnetAnnotationMaker();
4793             JnetAnnotationMaker.add_annotation(predictions,
4794                     viewport.getAlignment(), 0, false);
4795             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4796             viewport.getAlignment().setSeqrep(repseq);
4797             ColumnSelection cs = new ColumnSelection();
4798             cs.hideInsertionsFor(repseq);
4799             viewport.setColumnSelection(cs);
4800             isAnnotation = true;
4801           }
4802           // else if (IdentifyFile.FeaturesFile.equals(format))
4803           else if (FileFormat.Features.equals(format))
4804           {
4805             if (parseFeaturesFile(file, sourceType))
4806             {
4807               alignPanel.paintAlignment(true);
4808             }
4809           }
4810           else
4811           {
4812             new FileLoader().LoadFile(viewport, file, sourceType, format);
4813           }
4814         }
4815       }
4816       if (isAnnotation)
4817       {
4818
4819         alignPanel.adjustAnnotationHeight();
4820         viewport.updateSequenceIdColours();
4821         buildSortByAnnotationScoresMenu();
4822         alignPanel.paintAlignment(true);
4823       }
4824     } catch (Exception ex)
4825     {
4826       ex.printStackTrace();
4827     } catch (OutOfMemoryError oom)
4828     {
4829       try
4830       {
4831         System.gc();
4832       } catch (Exception x)
4833       {
4834       }
4835       new OOMWarning(
4836               "loading data "
4837                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4838                               : "using " + sourceType + " from " + file)
4839                               : ".")
4840                       + (format != null ? "(parsing as '" + format
4841                               + "' file)" : ""), oom, Desktop.desktop);
4842     }
4843   }
4844
4845   /**
4846    * Method invoked by the ChangeListener on the tabbed pane, in other words
4847    * when a different tabbed pane is selected by the user or programmatically.
4848    */
4849   @Override
4850   public void tabSelectionChanged(int index)
4851   {
4852     if (index > -1)
4853     {
4854       alignPanel = alignPanels.get(index);
4855       viewport = alignPanel.av;
4856       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4857       setMenusFromViewport(viewport);
4858     }
4859
4860     /*
4861      * If there is a frame linked to this one in a SplitPane, switch it to the
4862      * same view tab index. No infinite recursion of calls should happen, since
4863      * tabSelectionChanged() should not get invoked on setting the selected
4864      * index to an unchanged value. Guard against setting an invalid index
4865      * before the new view peer tab has been created.
4866      */
4867     final AlignViewportI peer = viewport.getCodingComplement();
4868     if (peer != null)
4869     {
4870       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4871       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4872       {
4873         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4874       }
4875     }
4876   }
4877
4878   /**
4879    * On right mouse click on view tab, prompt for and set new view name.
4880    */
4881   @Override
4882   public void tabbedPane_mousePressed(MouseEvent e)
4883   {
4884     if (e.isPopupTrigger())
4885     {
4886       String msg = MessageManager.getString("label.enter_view_name");
4887       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4888               JvOptionPane.QUESTION_MESSAGE);
4889
4890       if (reply != null)
4891       {
4892         viewport.viewName = reply;
4893         // TODO warn if reply is in getExistingViewNames()?
4894         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4895       }
4896     }
4897   }
4898
4899   public AlignViewport getCurrentView()
4900   {
4901     return viewport;
4902   }
4903
4904   /**
4905    * Open the dialog for regex description parsing.
4906    */
4907   @Override
4908   protected void extractScores_actionPerformed(ActionEvent e)
4909   {
4910     ParseProperties pp = new jalview.analysis.ParseProperties(
4911             viewport.getAlignment());
4912     // TODO: verify regex and introduce GUI dialog for version 2.5
4913     // if (pp.getScoresFromDescription("col", "score column ",
4914     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4915     // true)>0)
4916     if (pp.getScoresFromDescription("description column",
4917             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4918     {
4919       buildSortByAnnotationScoresMenu();
4920     }
4921   }
4922
4923   /*
4924    * (non-Javadoc)
4925    *
4926    * @see
4927    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4928    * )
4929    */
4930   @Override
4931   protected void showDbRefs_actionPerformed(ActionEvent e)
4932   {
4933     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4934   }
4935
4936   /*
4937    * (non-Javadoc)
4938    *
4939    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4940    * ActionEvent)
4941    */
4942   @Override
4943   protected void showNpFeats_actionPerformed(ActionEvent e)
4944   {
4945     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4946   }
4947
4948   /**
4949    * find the viewport amongst the tabs in this alignment frame and close that
4950    * tab
4951    *
4952    * @param av
4953    */
4954   public boolean closeView(AlignViewportI av)
4955   {
4956     if (viewport == av)
4957     {
4958       this.closeMenuItem_actionPerformed(false);
4959       return true;
4960     }
4961     Component[] comp = tabbedPane.getComponents();
4962     for (int i = 0; comp != null && i < comp.length; i++)
4963     {
4964       if (comp[i] instanceof AlignmentPanel)
4965       {
4966         if (((AlignmentPanel) comp[i]).av == av)
4967         {
4968           // close the view.
4969           closeView((AlignmentPanel) comp[i]);
4970           return true;
4971         }
4972       }
4973     }
4974     return false;
4975   }
4976
4977   protected void build_fetchdbmenu(JMenu webService)
4978   {
4979     // Temporary hack - DBRef Fetcher always top level ws entry.
4980     // TODO We probably want to store a sequence database checklist in
4981     // preferences and have checkboxes.. rather than individual sources selected
4982     // here
4983     final JMenu rfetch = new JMenu(
4984             MessageManager.getString("action.fetch_db_references"));
4985     rfetch.setToolTipText(MessageManager
4986             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4987     webService.add(rfetch);
4988
4989     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4990             MessageManager.getString("option.trim_retrieved_seqs"));
4991     trimrs.setToolTipText(MessageManager
4992             .getString("label.trim_retrieved_sequences"));
4993     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4994     trimrs.addActionListener(new ActionListener()
4995     {
4996       @Override
4997       public void actionPerformed(ActionEvent e)
4998       {
4999         trimrs.setSelected(trimrs.isSelected());
5000         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5001                 Boolean.valueOf(trimrs.isSelected()).toString());
5002       };
5003     });
5004     rfetch.add(trimrs);
5005     JMenuItem fetchr = new JMenuItem(
5006             MessageManager.getString("label.standard_databases"));
5007     fetchr.setToolTipText(MessageManager
5008             .getString("label.fetch_embl_uniprot"));
5009     fetchr.addActionListener(new ActionListener()
5010     {
5011
5012       @Override
5013       public void actionPerformed(ActionEvent e)
5014       {
5015         new Thread(new Runnable()
5016         {
5017           @Override
5018           public void run()
5019           {
5020             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5021                     .getAlignment().isNucleotide();
5022             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5023                     .getSequenceSelection(), alignPanel.alignFrame, null,
5024                     alignPanel.alignFrame.featureSettings, isNucleotide);
5025             dbRefFetcher.addListener(new FetchFinishedListenerI()
5026             {
5027               @Override
5028               public void finished()
5029               {
5030                 AlignFrame.this.setMenusForViewport();
5031               }
5032             });
5033             dbRefFetcher.fetchDBRefs(false);
5034           }
5035         }).start();
5036
5037       }
5038
5039     });
5040     rfetch.add(fetchr);
5041     final AlignFrame me = this;
5042     new Thread(new Runnable()
5043     {
5044       @Override
5045       public void run()
5046       {
5047         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5048                 .getSequenceFetcherSingleton(me);
5049         javax.swing.SwingUtilities.invokeLater(new Runnable()
5050         {
5051           @Override
5052           public void run()
5053           {
5054             String[] dbclasses = sf.getOrderedSupportedSources();
5055             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5056             // jalview.util.QuickSort.sort(otherdb, otherdb);
5057             List<DbSourceProxy> otherdb;
5058             JMenu dfetch = new JMenu();
5059             JMenu ifetch = new JMenu();
5060             JMenuItem fetchr = null;
5061             int comp = 0, icomp = 0, mcomp = 15;
5062             String mname = null;
5063             int dbi = 0;
5064             for (String dbclass : dbclasses)
5065             {
5066               otherdb = sf.getSourceProxy(dbclass);
5067               // add a single entry for this class, or submenu allowing 'fetch
5068               // all' or pick one
5069               if (otherdb == null || otherdb.size() < 1)
5070               {
5071                 continue;
5072               }
5073               // List<DbSourceProxy> dbs=otherdb;
5074               // otherdb=new ArrayList<DbSourceProxy>();
5075               // for (DbSourceProxy db:dbs)
5076               // {
5077               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5078               // }
5079               if (mname == null)
5080               {
5081                 mname = "From " + dbclass;
5082               }
5083               if (otherdb.size() == 1)
5084               {
5085                 final DbSourceProxy[] dassource = otherdb
5086                         .toArray(new DbSourceProxy[0]);
5087                 DbSourceProxy src = otherdb.get(0);
5088                 fetchr = new JMenuItem(src.getDbSource());
5089                 fetchr.addActionListener(new ActionListener()
5090                 {
5091
5092                   @Override
5093                   public void actionPerformed(ActionEvent e)
5094                   {
5095                     new Thread(new Runnable()
5096                     {
5097
5098                       @Override
5099                       public void run()
5100                       {
5101                         boolean isNucleotide = alignPanel.alignFrame
5102                                 .getViewport().getAlignment()
5103                                 .isNucleotide();
5104                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5105                                 alignPanel.av.getSequenceSelection(),
5106                                 alignPanel.alignFrame, dassource,
5107                                 alignPanel.alignFrame.featureSettings,
5108                                 isNucleotide);
5109                         dbRefFetcher
5110                                 .addListener(new FetchFinishedListenerI()
5111                                 {
5112                                   @Override
5113                                   public void finished()
5114                                   {
5115                                     AlignFrame.this.setMenusForViewport();
5116                                   }
5117                                 });
5118                         dbRefFetcher.fetchDBRefs(false);
5119                       }
5120                     }).start();
5121                   }
5122
5123                 });
5124                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5125                         MessageManager.formatMessage(
5126                                 "label.fetch_retrieve_from",
5127                                 new Object[] { src.getDbName() })));
5128                 dfetch.add(fetchr);
5129                 comp++;
5130               }
5131               else
5132               {
5133                 final DbSourceProxy[] dassource = otherdb
5134                         .toArray(new DbSourceProxy[0]);
5135                 // fetch all entry
5136                 DbSourceProxy src = otherdb.get(0);
5137                 fetchr = new JMenuItem(MessageManager.formatMessage(
5138                         "label.fetch_all_param",
5139                         new Object[] { src.getDbSource() }));
5140                 fetchr.addActionListener(new ActionListener()
5141                 {
5142                   @Override
5143                   public void actionPerformed(ActionEvent e)
5144                   {
5145                     new Thread(new Runnable()
5146                     {
5147
5148                       @Override
5149                       public void run()
5150                       {
5151                         boolean isNucleotide = alignPanel.alignFrame
5152                                 .getViewport().getAlignment()
5153                                 .isNucleotide();
5154                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5155                                 alignPanel.av.getSequenceSelection(),
5156                                 alignPanel.alignFrame, dassource,
5157                                 alignPanel.alignFrame.featureSettings,
5158                                 isNucleotide);
5159                         dbRefFetcher
5160                                 .addListener(new FetchFinishedListenerI()
5161                                 {
5162                                   @Override
5163                                   public void finished()
5164                                   {
5165                                     AlignFrame.this.setMenusForViewport();
5166                                   }
5167                                 });
5168                         dbRefFetcher.fetchDBRefs(false);
5169                       }
5170                     }).start();
5171                   }
5172                 });
5173
5174                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5175                         MessageManager.formatMessage(
5176                                 "label.fetch_retrieve_from_all_sources",
5177                                 new Object[] {
5178                                     Integer.valueOf(otherdb.size())
5179                                             .toString(), src.getDbSource(),
5180                                     src.getDbName() })));
5181                 dfetch.add(fetchr);
5182                 comp++;
5183                 // and then build the rest of the individual menus
5184                 ifetch = new JMenu(MessageManager.formatMessage(
5185                         "label.source_from_db_source",
5186                         new Object[] { src.getDbSource() }));
5187                 icomp = 0;
5188                 String imname = null;
5189                 int i = 0;
5190                 for (DbSourceProxy sproxy : otherdb)
5191                 {
5192                   String dbname = sproxy.getDbName();
5193                   String sname = dbname.length() > 5 ? dbname.substring(0,
5194                           5) + "..." : dbname;
5195                   String msname = dbname.length() > 10 ? dbname.substring(
5196                           0, 10) + "..." : dbname;
5197                   if (imname == null)
5198                   {
5199                     imname = MessageManager.formatMessage(
5200                             "label.from_msname", new Object[] { sname });
5201                   }
5202                   fetchr = new JMenuItem(msname);
5203                   final DbSourceProxy[] dassrc = { sproxy };
5204                   fetchr.addActionListener(new ActionListener()
5205                   {
5206
5207                     @Override
5208                     public void actionPerformed(ActionEvent e)
5209                     {
5210                       new Thread(new Runnable()
5211                       {
5212
5213                         @Override
5214                         public void run()
5215                         {
5216                           boolean isNucleotide = alignPanel.alignFrame
5217                                   .getViewport().getAlignment()
5218                                   .isNucleotide();
5219                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5220                                   alignPanel.av.getSequenceSelection(),
5221                                   alignPanel.alignFrame, dassrc,
5222                                   alignPanel.alignFrame.featureSettings,
5223                                   isNucleotide);
5224                           dbRefFetcher
5225                                   .addListener(new FetchFinishedListenerI()
5226                                   {
5227                                     @Override
5228                                     public void finished()
5229                                     {
5230                                       AlignFrame.this.setMenusForViewport();
5231                                     }
5232                                   });
5233                           dbRefFetcher.fetchDBRefs(false);
5234                         }
5235                       }).start();
5236                     }
5237
5238                   });
5239                   fetchr.setToolTipText("<html>"
5240                           + MessageManager.formatMessage(
5241                                   "label.fetch_retrieve_from", new Object[]
5242                                   { dbname }));
5243                   ifetch.add(fetchr);
5244                   ++i;
5245                   if (++icomp >= mcomp || i == (otherdb.size()))
5246                   {
5247                     ifetch.setText(MessageManager.formatMessage(
5248                             "label.source_to_target", imname, sname));
5249                     dfetch.add(ifetch);
5250                     ifetch = new JMenu();
5251                     imname = null;
5252                     icomp = 0;
5253                     comp++;
5254                   }
5255                 }
5256               }
5257               ++dbi;
5258               if (comp >= mcomp || dbi >= (dbclasses.length))
5259               {
5260                 dfetch.setText(MessageManager.formatMessage(
5261                         "label.source_to_target", mname, dbclass));
5262                 rfetch.add(dfetch);
5263                 dfetch = new JMenu();
5264                 mname = null;
5265                 comp = 0;
5266               }
5267             }
5268           }
5269         });
5270       }
5271     }).start();
5272
5273   }
5274
5275   /**
5276    * Left justify the whole alignment.
5277    */
5278   @Override
5279   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5280   {
5281     AlignmentI al = viewport.getAlignment();
5282     al.justify(false);
5283     viewport.firePropertyChange("alignment", null, al);
5284   }
5285
5286   /**
5287    * Right justify the whole alignment.
5288    */
5289   @Override
5290   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5291   {
5292     AlignmentI al = viewport.getAlignment();
5293     al.justify(true);
5294     viewport.firePropertyChange("alignment", null, al);
5295   }
5296
5297   @Override
5298   public void setShowSeqFeatures(boolean b)
5299   {
5300     showSeqFeatures.setSelected(b);
5301     viewport.setShowSequenceFeatures(b);
5302   }
5303
5304   /*
5305    * (non-Javadoc)
5306    *
5307    * @see
5308    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5309    * awt.event.ActionEvent)
5310    */
5311   @Override
5312   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5313   {
5314     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5315     alignPanel.paintAlignment(true);
5316   }
5317
5318   /*
5319    * (non-Javadoc)
5320    *
5321    * @see
5322    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5323    * .ActionEvent)
5324    */
5325   @Override
5326   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5327   {
5328     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5329     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5330
5331   }
5332
5333   /*
5334    * (non-Javadoc)
5335    *
5336    * @see
5337    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5338    * .event.ActionEvent)
5339    */
5340   @Override
5341   protected void showGroupConservation_actionPerformed(ActionEvent e)
5342   {
5343     viewport.setShowGroupConservation(showGroupConservation.getState());
5344     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5345   }
5346
5347   /*
5348    * (non-Javadoc)
5349    *
5350    * @see
5351    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5352    * .event.ActionEvent)
5353    */
5354   @Override
5355   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5356   {
5357     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5358     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5359   }
5360
5361   /*
5362    * (non-Javadoc)
5363    *
5364    * @see
5365    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5366    * .event.ActionEvent)
5367    */
5368   @Override
5369   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5370   {
5371     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5372     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5373   }
5374
5375   @Override
5376   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5377   {
5378     showSequenceLogo.setState(true);
5379     viewport.setShowSequenceLogo(true);
5380     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5381     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5382   }
5383
5384   @Override
5385   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5386   {
5387     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5388   }
5389
5390   /*
5391    * (non-Javadoc)
5392    *
5393    * @see
5394    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5395    * .event.ActionEvent)
5396    */
5397   @Override
5398   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5399   {
5400     if (avc.makeGroupsFromSelection())
5401     {
5402       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5403       alignPanel.updateAnnotation();
5404       alignPanel.paintAlignment(true);
5405     }
5406   }
5407
5408   public void clearAlignmentSeqRep()
5409   {
5410     // TODO refactor alignmentseqrep to controller
5411     if (viewport.getAlignment().hasSeqrep())
5412     {
5413       viewport.getAlignment().setSeqrep(null);
5414       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5415       alignPanel.updateAnnotation();
5416       alignPanel.paintAlignment(true);
5417     }
5418   }
5419
5420   @Override
5421   protected void createGroup_actionPerformed(ActionEvent e)
5422   {
5423     if (avc.createGroup())
5424     {
5425       alignPanel.alignmentChanged();
5426     }
5427   }
5428
5429   @Override
5430   protected void unGroup_actionPerformed(ActionEvent e)
5431   {
5432     if (avc.unGroup())
5433     {
5434       alignPanel.alignmentChanged();
5435     }
5436   }
5437
5438   /**
5439    * make the given alignmentPanel the currently selected tab
5440    *
5441    * @param alignmentPanel
5442    */
5443   public void setDisplayedView(AlignmentPanel alignmentPanel)
5444   {
5445     if (!viewport.getSequenceSetId().equals(
5446             alignmentPanel.av.getSequenceSetId()))
5447     {
5448       throw new Error(
5449               MessageManager
5450                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5451     }
5452     if (tabbedPane != null
5453             && tabbedPane.getTabCount() > 0
5454             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5455                     .getSelectedIndex())
5456     {
5457       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5458     }
5459   }
5460
5461   /**
5462    * Action on selection of menu options to Show or Hide annotations.
5463    *
5464    * @param visible
5465    * @param forSequences
5466    *          update sequence-related annotations
5467    * @param forAlignment
5468    *          update non-sequence-related annotations
5469    */
5470   @Override
5471   protected void setAnnotationsVisibility(boolean visible,
5472           boolean forSequences, boolean forAlignment)
5473   {
5474     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5475             .getAlignmentAnnotation();
5476     if (anns == null)
5477     {
5478       return;
5479     }
5480     for (AlignmentAnnotation aa : anns)
5481     {
5482       /*
5483        * don't display non-positional annotations on an alignment
5484        */
5485       if (aa.annotations == null)
5486       {
5487         continue;
5488       }
5489       boolean apply = (aa.sequenceRef == null && forAlignment)
5490               || (aa.sequenceRef != null && forSequences);
5491       if (apply)
5492       {
5493         aa.visible = visible;
5494       }
5495     }
5496     alignPanel.validateAnnotationDimensions(true);
5497     alignPanel.alignmentChanged();
5498   }
5499
5500   /**
5501    * Store selected annotation sort order for the view and repaint.
5502    */
5503   @Override
5504   protected void sortAnnotations_actionPerformed()
5505   {
5506     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5507     this.alignPanel.av
5508             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5509     alignPanel.paintAlignment(true);
5510   }
5511
5512   /**
5513    *
5514    * @return alignment panels in this alignment frame
5515    */
5516   public List<? extends AlignmentViewPanel> getAlignPanels()
5517   {
5518     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5519   }
5520
5521   /**
5522    * Open a new alignment window, with the cDNA associated with this (protein)
5523    * alignment, aligned as is the protein.
5524    */
5525   protected void viewAsCdna_actionPerformed()
5526   {
5527     // TODO no longer a menu action - refactor as required
5528     final AlignmentI alignment = getViewport().getAlignment();
5529     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5530     if (mappings == null)
5531     {
5532       return;
5533     }
5534     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5535     for (SequenceI aaSeq : alignment.getSequences())
5536     {
5537       for (AlignedCodonFrame acf : mappings)
5538       {
5539         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5540         if (dnaSeq != null)
5541         {
5542           /*
5543            * There is a cDNA mapping for this protein sequence - add to new
5544            * alignment. It will share the same dataset sequence as other mapped
5545            * cDNA (no new mappings need to be created).
5546            */
5547           final Sequence newSeq = new Sequence(dnaSeq);
5548           newSeq.setDatasetSequence(dnaSeq);
5549           cdnaSeqs.add(newSeq);
5550         }
5551       }
5552     }
5553     if (cdnaSeqs.size() == 0)
5554     {
5555       // show a warning dialog no mapped cDNA
5556       return;
5557     }
5558     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5559             .size()]));
5560     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5561             AlignFrame.DEFAULT_HEIGHT);
5562     cdna.alignAs(alignment);
5563     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5564             + this.title;
5565     Desktop.addInternalFrame(alignFrame, newtitle,
5566             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5567   }
5568
5569   /**
5570    * Set visibility of dna/protein complement view (available when shown in a
5571    * split frame).
5572    *
5573    * @param show
5574    */
5575   @Override
5576   protected void showComplement_actionPerformed(boolean show)
5577   {
5578     SplitContainerI sf = getSplitViewContainer();
5579     if (sf != null)
5580     {
5581       sf.setComplementVisible(this, show);
5582     }
5583   }
5584
5585   /**
5586    * Generate the reverse (optionally complemented) of the selected sequences,
5587    * and add them to the alignment
5588    */
5589   @Override
5590   protected void showReverse_actionPerformed(boolean complement)
5591   {
5592     AlignmentI al = null;
5593     try
5594     {
5595       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5596       al = dna.reverseCdna(complement);
5597       viewport.addAlignment(al, "");
5598       addHistoryItem(new EditCommand(
5599               MessageManager.getString("label.add_sequences"),
5600               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5601               viewport.getAlignment()));
5602     } catch (Exception ex)
5603     {
5604       System.err.println(ex.getMessage());
5605       return;
5606     }
5607   }
5608
5609   /**
5610    * Try to run a script in the Groovy console, having first ensured that this
5611    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5612    * be targeted at this alignment.
5613    */
5614   @Override
5615   protected void runGroovy_actionPerformed()
5616   {
5617     Jalview.setCurrentAlignFrame(this);
5618     groovy.ui.Console console = Desktop.getGroovyConsole();
5619     if (console != null)
5620     {
5621       try
5622       {
5623         console.runScript();
5624       } catch (Exception ex)
5625       {
5626         System.err.println((ex.toString()));
5627         JvOptionPane
5628                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5629                         .getString("label.couldnt_run_groovy_script"),
5630                         MessageManager
5631                                 .getString("label.groovy_support_failed"),
5632                         JvOptionPane.ERROR_MESSAGE);
5633       }
5634     }
5635     else
5636     {
5637       System.err.println("Can't run Groovy script as console not found");
5638     }
5639   }
5640
5641   /**
5642    * Hides columns containing (or not containing) a specified feature, provided
5643    * that would not leave all columns hidden
5644    *
5645    * @param featureType
5646    * @param columnsContaining
5647    * @return
5648    */
5649   public boolean hideFeatureColumns(String featureType,
5650           boolean columnsContaining)
5651   {
5652     boolean notForHiding = avc.markColumnsContainingFeatures(
5653             columnsContaining, false, false, featureType);
5654     if (notForHiding)
5655     {
5656       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5657               false, featureType))
5658       {
5659         getViewport().hideSelectedColumns();
5660         return true;
5661       }
5662     }
5663     return false;
5664   }
5665
5666   @Override
5667   protected void selectHighlightedColumns_actionPerformed(
5668           ActionEvent actionEvent)
5669   {
5670     // include key modifier check in case user selects from menu
5671     avc.markHighlightedColumns(
5672             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5673             true,
5674             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5675   }
5676
5677   /**
5678    * Rebuilds the Colour menu, including any user-defined colours which have
5679    * been loaded either on startup or during the session
5680    */
5681   public void buildColourMenu()
5682   {
5683     colourMenu.removeAll();
5684
5685     colourMenu.add(applyToAllGroups);
5686     colourMenu.add(textColour);
5687     colourMenu.addSeparator();
5688
5689     ColourMenuHelper.addMenuItems(colourMenu, this,
5690             viewport.getAlignment(), false);
5691
5692     colourMenu.addSeparator();
5693     colourMenu.add(conservationMenuItem);
5694     colourMenu.add(modifyConservation);
5695     colourMenu.add(abovePIDThreshold);
5696     colourMenu.add(modifyPID);
5697     colourMenu.add(annotationColour);
5698
5699     /*
5700      * select the default colour for the alignment (this may be
5701      * overridden later)
5702      */
5703     boolean nucleotide = viewport.getAlignment().isNucleotide();
5704     String defaultColourScheme = Cache.getDefault(
5705             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
5706                     : Preferences.DEFAULT_COLOUR_PROT,
5707             ResidueColourScheme.NONE);
5708
5709     ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
5710   }
5711 }
5712
5713 class PrintThread extends Thread
5714 {
5715   AlignmentPanel ap;
5716
5717   public PrintThread(AlignmentPanel ap)
5718   {
5719     this.ap = ap;
5720   }
5721
5722   static PageFormat pf;
5723
5724   @Override
5725   public void run()
5726   {
5727     PrinterJob printJob = PrinterJob.getPrinterJob();
5728
5729     if (pf != null)
5730     {
5731       printJob.setPrintable(ap, pf);
5732     }
5733     else
5734     {
5735       printJob.setPrintable(ap);
5736     }
5737
5738     if (printJob.printDialog())
5739     {
5740       try
5741       {
5742         printJob.print();
5743       } catch (Exception PrintException)
5744       {
5745         PrintException.printStackTrace();
5746       }
5747     }
5748   }
5749 }