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