src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.api.analysis.SimilarityParamsI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  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, ColumnSelection 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, ColumnSelection 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, ColumnSelection 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           ColumnSelection 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         new TreeChooser(AlignFrame.this);
 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),
1197               viewport.getColumnSelection());
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.getStartEndPostions(),
1276                       viewport.getColumnSelection()));
1277       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1278               "label.alignment_output_command",
1279               new Object[] { e.getActionCommand() }), 600, 500);
1280     } catch (OutOfMemoryError oom)
1281     {
1282       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1283       cap.dispose();
1284     }
1285
1286   }
1287
1288   public static AlignmentExportData getAlignmentForExport(
1289           FileFormatI format, AlignViewportI viewport,
1290           AlignExportSettingI exportSettings)
1291   {
1292     AlignmentI alignmentToExport = null;
1293     AlignExportSettingI settings = exportSettings;
1294     String[] omitHidden = null;
1295
1296     HiddenSequences hiddenSeqs = viewport.getAlignment()
1297             .getHiddenSequences();
1298
1299     alignmentToExport = viewport.getAlignment();
1300
1301     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1302     if (settings == null)
1303     {
1304       settings = new AlignExportSettings(hasHiddenSeqs,
1305               viewport.hasHiddenColumns(), format);
1306     }
1307     // settings.isExportAnnotations();
1308
1309     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1310     {
1311       omitHidden = viewport.getViewAsString(false,
1312               settings.isExportHiddenSequences());
1313     }
1314
1315     int[] alignmentStartEnd = new int[2];
1316     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1317     {
1318       alignmentToExport = hiddenSeqs.getFullAlignment();
1319     }
1320     else
1321     {
1322       alignmentToExport = viewport.getAlignment();
1323     }
1324     alignmentStartEnd = alignmentToExport
1325             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1326                     .getHiddenColumns());
1327     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1328             omitHidden, alignmentStartEnd, settings);
1329     return ed;
1330   }
1331
1332   /**
1333    * DOCUMENT ME!
1334    *
1335    * @param e
1336    *          DOCUMENT ME!
1337    */
1338   @Override
1339   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1340   {
1341     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1342     htmlSVG.exportHTML(null);
1343   }
1344
1345   @Override
1346   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1347   {
1348     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1349     bjs.exportHTML(null);
1350   }
1351
1352   public void createImageMap(File file, String image)
1353   {
1354     alignPanel.makePNGImageMap(file, image);
1355   }
1356
1357   /**
1358    * DOCUMENT ME!
1359    *
1360    * @param e
1361    *          DOCUMENT ME!
1362    */
1363   @Override
1364   public void createPNG(File f)
1365   {
1366     alignPanel.makePNG(f);
1367   }
1368
1369   /**
1370    * DOCUMENT ME!
1371    *
1372    * @param e
1373    *          DOCUMENT ME!
1374    */
1375   @Override
1376   public void createEPS(File f)
1377   {
1378     alignPanel.makeEPS(f);
1379   }
1380
1381   @Override
1382   public void createSVG(File f)
1383   {
1384     alignPanel.makeSVG(f);
1385   }
1386
1387   @Override
1388   public void pageSetup_actionPerformed(ActionEvent e)
1389   {
1390     PrinterJob printJob = PrinterJob.getPrinterJob();
1391     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1392   }
1393
1394   /**
1395    * DOCUMENT ME!
1396    *
1397    * @param e
1398    *          DOCUMENT ME!
1399    */
1400   @Override
1401   public void printMenuItem_actionPerformed(ActionEvent e)
1402   {
1403     // Putting in a thread avoids Swing painting problems
1404     PrintThread thread = new PrintThread(alignPanel);
1405     thread.start();
1406   }
1407
1408   @Override
1409   public void exportFeatures_actionPerformed(ActionEvent e)
1410   {
1411     new AnnotationExporter().exportFeatures(alignPanel);
1412   }
1413
1414   @Override
1415   public void exportAnnotations_actionPerformed(ActionEvent e)
1416   {
1417     new AnnotationExporter().exportAnnotations(alignPanel);
1418   }
1419
1420   @Override
1421   public void associatedData_actionPerformed(ActionEvent e)
1422   {
1423     // Pick the tree file
1424     JalviewFileChooser chooser = new JalviewFileChooser(
1425             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1426     chooser.setFileView(new JalviewFileView());
1427     chooser.setDialogTitle(MessageManager
1428             .getString("label.load_jalview_annotations"));
1429     chooser.setToolTipText(MessageManager
1430             .getString("label.load_jalview_annotations"));
1431
1432     int value = chooser.showOpenDialog(null);
1433
1434     if (value == JalviewFileChooser.APPROVE_OPTION)
1435     {
1436       String choice = chooser.getSelectedFile().getPath();
1437       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1438       loadJalviewDataFile(choice, null, null, null);
1439     }
1440
1441   }
1442
1443   /**
1444    * Close the current view or all views in the alignment frame. If the frame
1445    * only contains one view then the alignment will be removed from memory.
1446    *
1447    * @param closeAllTabs
1448    */
1449   @Override
1450   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1451   {
1452     if (alignPanels != null && alignPanels.size() < 2)
1453     {
1454       closeAllTabs = true;
1455     }
1456
1457     try
1458     {
1459       if (alignPanels != null)
1460       {
1461         if (closeAllTabs)
1462         {
1463           if (this.isClosed())
1464           {
1465             // really close all the windows - otherwise wait till
1466             // setClosed(true) is called
1467             for (int i = 0; i < alignPanels.size(); i++)
1468             {
1469               AlignmentPanel ap = alignPanels.get(i);
1470               ap.closePanel();
1471             }
1472           }
1473         }
1474         else
1475         {
1476           closeView(alignPanel);
1477         }
1478       }
1479
1480       if (closeAllTabs)
1481       {
1482         /*
1483          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1484          * be called recursively, with the frame now in 'closed' state
1485          */
1486         this.setClosed(true);
1487       }
1488     } catch (Exception ex)
1489     {
1490       ex.printStackTrace();
1491     }
1492   }
1493
1494   /**
1495    * Close the specified panel and close up tabs appropriately.
1496    *
1497    * @param panelToClose
1498    */
1499   public void closeView(AlignmentPanel panelToClose)
1500   {
1501     int index = tabbedPane.getSelectedIndex();
1502     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1503     alignPanels.remove(panelToClose);
1504     panelToClose.closePanel();
1505     panelToClose = null;
1506
1507     tabbedPane.removeTabAt(closedindex);
1508     tabbedPane.validate();
1509
1510     if (index > closedindex || index == tabbedPane.getTabCount())
1511     {
1512       // modify currently selected tab index if necessary.
1513       index--;
1514     }
1515
1516     this.tabSelectionChanged(index);
1517   }
1518
1519   /**
1520    * DOCUMENT ME!
1521    */
1522   void updateEditMenuBar()
1523   {
1524
1525     if (viewport.getHistoryList().size() > 0)
1526     {
1527       undoMenuItem.setEnabled(true);
1528       CommandI command = viewport.getHistoryList().peek();
1529       undoMenuItem.setText(MessageManager.formatMessage(
1530               "label.undo_command",
1531               new Object[] { command.getDescription() }));
1532     }
1533     else
1534     {
1535       undoMenuItem.setEnabled(false);
1536       undoMenuItem.setText(MessageManager.getString("action.undo"));
1537     }
1538
1539     if (viewport.getRedoList().size() > 0)
1540     {
1541       redoMenuItem.setEnabled(true);
1542
1543       CommandI command = viewport.getRedoList().peek();
1544       redoMenuItem.setText(MessageManager.formatMessage(
1545               "label.redo_command",
1546               new Object[] { command.getDescription() }));
1547     }
1548     else
1549     {
1550       redoMenuItem.setEnabled(false);
1551       redoMenuItem.setText(MessageManager.getString("action.redo"));
1552     }
1553   }
1554
1555   @Override
1556   public void addHistoryItem(CommandI command)
1557   {
1558     if (command.getSize() > 0)
1559     {
1560       viewport.addToHistoryList(command);
1561       viewport.clearRedoList();
1562       updateEditMenuBar();
1563       viewport.updateHiddenColumns();
1564       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1565       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1566       // viewport.getColumnSelection()
1567       // .getHiddenColumns().size() > 0);
1568     }
1569   }
1570
1571   /**
1572    *
1573    * @return alignment objects for all views
1574    */
1575   AlignmentI[] getViewAlignments()
1576   {
1577     if (alignPanels != null)
1578     {
1579       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1580       int i = 0;
1581       for (AlignmentPanel ap : alignPanels)
1582       {
1583         als[i++] = ap.av.getAlignment();
1584       }
1585       return als;
1586     }
1587     if (viewport != null)
1588     {
1589       return new AlignmentI[] { viewport.getAlignment() };
1590     }
1591     return null;
1592   }
1593
1594   /**
1595    * DOCUMENT ME!
1596    *
1597    * @param e
1598    *          DOCUMENT ME!
1599    */
1600   @Override
1601   protected void undoMenuItem_actionPerformed(ActionEvent e)
1602   {
1603     if (viewport.getHistoryList().isEmpty())
1604     {
1605       return;
1606     }
1607     CommandI command = viewport.getHistoryList().pop();
1608     viewport.addToRedoList(command);
1609     command.undoCommand(getViewAlignments());
1610
1611     AlignmentViewport originalSource = getOriginatingSource(command);
1612     updateEditMenuBar();
1613
1614     if (originalSource != null)
1615     {
1616       if (originalSource != viewport)
1617       {
1618         Cache.log
1619                 .warn("Implementation worry: mismatch of viewport origin for undo");
1620       }
1621       originalSource.updateHiddenColumns();
1622       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1623       // null
1624       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1625       // viewport.getColumnSelection()
1626       // .getHiddenColumns().size() > 0);
1627       originalSource.firePropertyChange("alignment", null, originalSource
1628               .getAlignment().getSequences());
1629     }
1630   }
1631
1632   /**
1633    * DOCUMENT ME!
1634    *
1635    * @param e
1636    *          DOCUMENT ME!
1637    */
1638   @Override
1639   protected void redoMenuItem_actionPerformed(ActionEvent e)
1640   {
1641     if (viewport.getRedoList().size() < 1)
1642     {
1643       return;
1644     }
1645
1646     CommandI command = viewport.getRedoList().pop();
1647     viewport.addToHistoryList(command);
1648     command.doCommand(getViewAlignments());
1649
1650     AlignmentViewport originalSource = getOriginatingSource(command);
1651     updateEditMenuBar();
1652
1653     if (originalSource != null)
1654     {
1655
1656       if (originalSource != viewport)
1657       {
1658         Cache.log
1659                 .warn("Implementation worry: mismatch of viewport origin for redo");
1660       }
1661       originalSource.updateHiddenColumns();
1662       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1663       // null
1664       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1665       // viewport.getColumnSelection()
1666       // .getHiddenColumns().size() > 0);
1667       originalSource.firePropertyChange("alignment", null, originalSource
1668               .getAlignment().getSequences());
1669     }
1670   }
1671
1672   AlignmentViewport getOriginatingSource(CommandI command)
1673   {
1674     AlignmentViewport originalSource = null;
1675     // For sequence removal and addition, we need to fire
1676     // the property change event FROM the viewport where the
1677     // original alignment was altered
1678     AlignmentI al = null;
1679     if (command instanceof EditCommand)
1680     {
1681       EditCommand editCommand = (EditCommand) command;
1682       al = editCommand.getAlignment();
1683       List<Component> comps = PaintRefresher.components.get(viewport
1684               .getSequenceSetId());
1685
1686       for (Component comp : comps)
1687       {
1688         if (comp instanceof AlignmentPanel)
1689         {
1690           if (al == ((AlignmentPanel) comp).av.getAlignment())
1691           {
1692             originalSource = ((AlignmentPanel) comp).av;
1693             break;
1694           }
1695         }
1696       }
1697     }
1698
1699     if (originalSource == null)
1700     {
1701       // The original view is closed, we must validate
1702       // the current view against the closed view first
1703       if (al != null)
1704       {
1705         PaintRefresher.validateSequences(al, viewport.getAlignment());
1706       }
1707
1708       originalSource = viewport;
1709     }
1710
1711     return originalSource;
1712   }
1713
1714   /**
1715    * DOCUMENT ME!
1716    *
1717    * @param up
1718    *          DOCUMENT ME!
1719    */
1720   public void moveSelectedSequences(boolean up)
1721   {
1722     SequenceGroup sg = viewport.getSelectionGroup();
1723
1724     if (sg == null)
1725     {
1726       return;
1727     }
1728     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1729             viewport.getHiddenRepSequences(), up);
1730     alignPanel.paintAlignment(true);
1731   }
1732
1733   synchronized void slideSequences(boolean right, int size)
1734   {
1735     List<SequenceI> sg = new ArrayList<SequenceI>();
1736     if (viewport.cursorMode)
1737     {
1738       sg.add(viewport.getAlignment().getSequenceAt(
1739               alignPanel.getSeqPanel().seqCanvas.cursorY));
1740     }
1741     else if (viewport.getSelectionGroup() != null
1742             && viewport.getSelectionGroup().getSize() != viewport
1743                     .getAlignment().getHeight())
1744     {
1745       sg = viewport.getSelectionGroup().getSequences(
1746               viewport.getHiddenRepSequences());
1747     }
1748
1749     if (sg.size() < 1)
1750     {
1751       return;
1752     }
1753
1754     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1755
1756     for (SequenceI seq : viewport.getAlignment().getSequences())
1757     {
1758       if (!sg.contains(seq))
1759       {
1760         invertGroup.add(seq);
1761       }
1762     }
1763
1764     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1765
1766     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1767     for (int i = 0; i < invertGroup.size(); i++)
1768     {
1769       seqs2[i] = invertGroup.get(i);
1770     }
1771
1772     SlideSequencesCommand ssc;
1773     if (right)
1774     {
1775       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1776               size, viewport.getGapCharacter());
1777     }
1778     else
1779     {
1780       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1781               size, viewport.getGapCharacter());
1782     }
1783
1784     int groupAdjustment = 0;
1785     if (ssc.getGapsInsertedBegin() && right)
1786     {
1787       if (viewport.cursorMode)
1788       {
1789         alignPanel.getSeqPanel().moveCursor(size, 0);
1790       }
1791       else
1792       {
1793         groupAdjustment = size;
1794       }
1795     }
1796     else if (!ssc.getGapsInsertedBegin() && !right)
1797     {
1798       if (viewport.cursorMode)
1799       {
1800         alignPanel.getSeqPanel().moveCursor(-size, 0);
1801       }
1802       else
1803       {
1804         groupAdjustment = -size;
1805       }
1806     }
1807
1808     if (groupAdjustment != 0)
1809     {
1810       viewport.getSelectionGroup().setStartRes(
1811               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1812       viewport.getSelectionGroup().setEndRes(
1813               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1814     }
1815
1816     /*
1817      * just extend the last slide command if compatible; but not if in
1818      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1819      */
1820     boolean appendHistoryItem = false;
1821     Deque<CommandI> historyList = viewport.getHistoryList();
1822     boolean inSplitFrame = getSplitViewContainer() != null;
1823     if (!inSplitFrame && historyList != null && historyList.size() > 0
1824             && historyList.peek() instanceof SlideSequencesCommand)
1825     {
1826       appendHistoryItem = ssc
1827               .appendSlideCommand((SlideSequencesCommand) historyList
1828                       .peek());
1829     }
1830
1831     if (!appendHistoryItem)
1832     {
1833       addHistoryItem(ssc);
1834     }
1835
1836     repaint();
1837   }
1838
1839   /**
1840    * DOCUMENT ME!
1841    *
1842    * @param e
1843    *          DOCUMENT ME!
1844    */
1845   @Override
1846   protected void copy_actionPerformed(ActionEvent e)
1847   {
1848     System.gc();
1849     if (viewport.getSelectionGroup() == null)
1850     {
1851       return;
1852     }
1853     // TODO: preserve the ordering of displayed alignment annotation in any
1854     // internal paste (particularly sequence associated annotation)
1855     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1856     String[] omitHidden = null;
1857
1858     if (viewport.hasHiddenColumns())
1859     {
1860       omitHidden = viewport.getViewAsString(true);
1861     }
1862
1863     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1864             seqs, omitHidden, null);
1865
1866     StringSelection ss = new StringSelection(output);
1867
1868     try
1869     {
1870       jalview.gui.Desktop.internalCopy = true;
1871       // Its really worth setting the clipboard contents
1872       // to empty before setting the large StringSelection!!
1873       Toolkit.getDefaultToolkit().getSystemClipboard()
1874               .setContents(new StringSelection(""), null);
1875
1876       Toolkit.getDefaultToolkit().getSystemClipboard()
1877               .setContents(ss, Desktop.instance);
1878     } catch (OutOfMemoryError er)
1879     {
1880       new OOMWarning("copying region", er);
1881       return;
1882     }
1883
1884     ArrayList<int[]> hiddenColumns = null;
1885     if (viewport.hasHiddenColumns())
1886     {
1887       hiddenColumns = new ArrayList<int[]>();
1888       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1889               .getSelectionGroup().getEndRes();
1890       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1891       {
1892         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1893         {
1894           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1895               region[1] - hiddenOffset });
1896         }
1897       }
1898     }
1899
1900     Desktop.jalviewClipboard = new Object[] { seqs,
1901         viewport.getAlignment().getDataset(), hiddenColumns };
1902     statusBar.setText(MessageManager.formatMessage(
1903             "label.copied_sequences_to_clipboard", new Object[] { Integer
1904                     .valueOf(seqs.length).toString() }));
1905   }
1906
1907   /**
1908    * DOCUMENT ME!
1909    *
1910    * @param e
1911    *          DOCUMENT ME!
1912    */
1913   @Override
1914   protected void pasteNew_actionPerformed(ActionEvent e)
1915   {
1916     paste(true);
1917   }
1918
1919   /**
1920    * DOCUMENT ME!
1921    *
1922    * @param e
1923    *          DOCUMENT ME!
1924    */
1925   @Override
1926   protected void pasteThis_actionPerformed(ActionEvent e)
1927   {
1928     paste(false);
1929   }
1930
1931   /**
1932    * Paste contents of Jalview clipboard
1933    *
1934    * @param newAlignment
1935    *          true to paste to a new alignment, otherwise add to this.
1936    */
1937   void paste(boolean newAlignment)
1938   {
1939     boolean externalPaste = true;
1940     try
1941     {
1942       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1943       Transferable contents = c.getContents(this);
1944
1945       if (contents == null)
1946       {
1947         return;
1948       }
1949
1950       String str;
1951       FileFormatI format;
1952       try
1953       {
1954         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1955         if (str.length() < 1)
1956         {
1957           return;
1958         }
1959
1960         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1961
1962       } catch (OutOfMemoryError er)
1963       {
1964         new OOMWarning("Out of memory pasting sequences!!", er);
1965         return;
1966       }
1967
1968       SequenceI[] sequences;
1969       boolean annotationAdded = false;
1970       AlignmentI alignment = null;
1971
1972       if (Desktop.jalviewClipboard != null)
1973       {
1974         // The clipboard was filled from within Jalview, we must use the
1975         // sequences
1976         // And dataset from the copied alignment
1977         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1978         // be doubly sure that we create *new* sequence objects.
1979         sequences = new SequenceI[newseq.length];
1980         for (int i = 0; i < newseq.length; i++)
1981         {
1982           sequences[i] = new Sequence(newseq[i]);
1983         }
1984         alignment = new Alignment(sequences);
1985         externalPaste = false;
1986       }
1987       else
1988       {
1989         // parse the clipboard as an alignment.
1990         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1991                 format);
1992         sequences = alignment.getSequencesArray();
1993       }
1994
1995       int alwidth = 0;
1996       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1997       int fgroup = -1;
1998
1999       if (newAlignment)
2000       {
2001
2002         if (Desktop.jalviewClipboard != null)
2003         {
2004           // dataset is inherited
2005           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2006         }
2007         else
2008         {
2009           // new dataset is constructed
2010           alignment.setDataset(null);
2011         }
2012         alwidth = alignment.getWidth() + 1;
2013       }
2014       else
2015       {
2016         AlignmentI pastedal = alignment; // preserve pasted alignment object
2017         // Add pasted sequences and dataset into existing alignment.
2018         alignment = viewport.getAlignment();
2019         alwidth = alignment.getWidth() + 1;
2020         // decide if we need to import sequences from an existing dataset
2021         boolean importDs = Desktop.jalviewClipboard != null
2022                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2023         // importDs==true instructs us to copy over new dataset sequences from
2024         // an existing alignment
2025         Vector newDs = (importDs) ? new Vector() : null; // used to create
2026         // minimum dataset set
2027
2028         for (int i = 0; i < sequences.length; i++)
2029         {
2030           if (importDs)
2031           {
2032             newDs.addElement(null);
2033           }
2034           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2035           // paste
2036           if (importDs && ds != null)
2037           {
2038             if (!newDs.contains(ds))
2039             {
2040               newDs.setElementAt(ds, i);
2041               ds = new Sequence(ds);
2042               // update with new dataset sequence
2043               sequences[i].setDatasetSequence(ds);
2044             }
2045             else
2046             {
2047               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2048             }
2049           }
2050           else
2051           {
2052             // copy and derive new dataset sequence
2053             sequences[i] = sequences[i].deriveSequence();
2054             alignment.getDataset().addSequence(
2055                     sequences[i].getDatasetSequence());
2056             // TODO: avoid creation of duplicate dataset sequences with a
2057             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2058           }
2059           alignment.addSequence(sequences[i]); // merges dataset
2060         }
2061         if (newDs != null)
2062         {
2063           newDs.clear(); // tidy up
2064         }
2065         if (alignment.getAlignmentAnnotation() != null)
2066         {
2067           for (AlignmentAnnotation alan : alignment
2068                   .getAlignmentAnnotation())
2069           {
2070             if (alan.graphGroup > fgroup)
2071             {
2072               fgroup = alan.graphGroup;
2073             }
2074           }
2075         }
2076         if (pastedal.getAlignmentAnnotation() != null)
2077         {
2078           // Add any annotation attached to alignment.
2079           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2080           for (int i = 0; i < alann.length; i++)
2081           {
2082             annotationAdded = true;
2083             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2084             {
2085               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2086               if (newann.graphGroup > -1)
2087               {
2088                 if (newGraphGroups.size() <= newann.graphGroup
2089                         || newGraphGroups.get(newann.graphGroup) == null)
2090                 {
2091                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2092                   {
2093                     newGraphGroups.add(q, null);
2094                   }
2095                   newGraphGroups.set(newann.graphGroup, new Integer(
2096                           ++fgroup));
2097                 }
2098                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2099                         .intValue();
2100               }
2101
2102               newann.padAnnotation(alwidth);
2103               alignment.addAnnotation(newann);
2104             }
2105           }
2106         }
2107       }
2108       if (!newAlignment)
2109       {
2110         // /////
2111         // ADD HISTORY ITEM
2112         //
2113         addHistoryItem(new EditCommand(
2114                 MessageManager.getString("label.add_sequences"),
2115                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2116       }
2117       // Add any annotations attached to sequences
2118       for (int i = 0; i < sequences.length; i++)
2119       {
2120         if (sequences[i].getAnnotation() != null)
2121         {
2122           AlignmentAnnotation newann;
2123           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2124           {
2125             annotationAdded = true;
2126             newann = sequences[i].getAnnotation()[a];
2127             newann.adjustForAlignment();
2128             newann.padAnnotation(alwidth);
2129             if (newann.graphGroup > -1)
2130             {
2131               if (newann.graphGroup > -1)
2132               {
2133                 if (newGraphGroups.size() <= newann.graphGroup
2134                         || newGraphGroups.get(newann.graphGroup) == null)
2135                 {
2136                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2137                   {
2138                     newGraphGroups.add(q, null);
2139                   }
2140                   newGraphGroups.set(newann.graphGroup, new Integer(
2141                           ++fgroup));
2142                 }
2143                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2144                         .intValue();
2145               }
2146             }
2147             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2148             // was
2149             // duplicated
2150             // earlier
2151             alignment
2152                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2153           }
2154         }
2155       }
2156       if (!newAlignment)
2157       {
2158
2159         // propagate alignment changed.
2160         vpRanges.setEndSeq(alignment.getHeight());
2161         if (annotationAdded)
2162         {
2163           // Duplicate sequence annotation in all views.
2164           AlignmentI[] alview = this.getViewAlignments();
2165           for (int i = 0; i < sequences.length; i++)
2166           {
2167             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2168             if (sann == null)
2169             {
2170               continue;
2171             }
2172             for (int avnum = 0; avnum < alview.length; avnum++)
2173             {
2174               if (alview[avnum] != alignment)
2175               {
2176                 // duplicate in a view other than the one with input focus
2177                 int avwidth = alview[avnum].getWidth() + 1;
2178                 // this relies on sann being preserved after we
2179                 // modify the sequence's annotation array for each duplication
2180                 for (int a = 0; a < sann.length; a++)
2181                 {
2182                   AlignmentAnnotation newann = new AlignmentAnnotation(
2183                           sann[a]);
2184                   sequences[i].addAlignmentAnnotation(newann);
2185                   newann.padAnnotation(avwidth);
2186                   alview[avnum].addAnnotation(newann); // annotation was
2187                   // duplicated earlier
2188                   // TODO JAL-1145 graphGroups are not updated for sequence
2189                   // annotation added to several views. This may cause
2190                   // strangeness
2191                   alview[avnum].setAnnotationIndex(newann, a);
2192                 }
2193               }
2194             }
2195           }
2196           buildSortByAnnotationScoresMenu();
2197         }
2198         viewport.firePropertyChange("alignment", null,
2199                 alignment.getSequences());
2200         if (alignPanels != null)
2201         {
2202           for (AlignmentPanel ap : alignPanels)
2203           {
2204             ap.validateAnnotationDimensions(false);
2205           }
2206         }
2207         else
2208         {
2209           alignPanel.validateAnnotationDimensions(false);
2210         }
2211
2212       }
2213       else
2214       {
2215         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2216                 DEFAULT_HEIGHT);
2217         String newtitle = new String("Copied sequences");
2218
2219         if (Desktop.jalviewClipboard != null
2220                 && Desktop.jalviewClipboard[2] != null)
2221         {
2222           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2223           for (int[] region : hc)
2224           {
2225             af.viewport.hideColumns(region[0], region[1]);
2226           }
2227         }
2228
2229         // >>>This is a fix for the moment, until a better solution is
2230         // found!!<<<
2231         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2232                 .transferSettings(
2233                         alignPanel.getSeqPanel().seqCanvas
2234                                 .getFeatureRenderer());
2235
2236         // TODO: maintain provenance of an alignment, rather than just make the
2237         // title a concatenation of operations.
2238         if (!externalPaste)
2239         {
2240           if (title.startsWith("Copied sequences"))
2241           {
2242             newtitle = title;
2243           }
2244           else
2245           {
2246             newtitle = newtitle.concat("- from " + title);
2247           }
2248         }
2249         else
2250         {
2251           newtitle = new String("Pasted sequences");
2252         }
2253
2254         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2255                 DEFAULT_HEIGHT);
2256
2257       }
2258
2259     } catch (Exception ex)
2260     {
2261       ex.printStackTrace();
2262       System.out.println("Exception whilst pasting: " + ex);
2263       // could be anything being pasted in here
2264     }
2265
2266   }
2267
2268   @Override
2269   protected void expand_newalign(ActionEvent e)
2270   {
2271     try
2272     {
2273       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2274               .getAlignment(), -1);
2275       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2276               DEFAULT_HEIGHT);
2277       String newtitle = new String("Flanking alignment");
2278
2279       if (Desktop.jalviewClipboard != null
2280               && Desktop.jalviewClipboard[2] != null)
2281       {
2282         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2283         for (int region[] : hc)
2284         {
2285           af.viewport.hideColumns(region[0], region[1]);
2286         }
2287       }
2288
2289       // >>>This is a fix for the moment, until a better solution is
2290       // found!!<<<
2291       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2292               .transferSettings(
2293                       alignPanel.getSeqPanel().seqCanvas
2294                               .getFeatureRenderer());
2295
2296       // TODO: maintain provenance of an alignment, rather than just make the
2297       // title a concatenation of operations.
2298       {
2299         if (title.startsWith("Copied sequences"))
2300         {
2301           newtitle = title;
2302         }
2303         else
2304         {
2305           newtitle = newtitle.concat("- from " + title);
2306         }
2307       }
2308
2309       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2310
2311     } catch (Exception ex)
2312     {
2313       ex.printStackTrace();
2314       System.out.println("Exception whilst pasting: " + ex);
2315       // could be anything being pasted in here
2316     } catch (OutOfMemoryError oom)
2317     {
2318       new OOMWarning("Viewing flanking region of alignment", oom);
2319     }
2320   }
2321
2322   /**
2323    * DOCUMENT ME!
2324    *
2325    * @param e
2326    *          DOCUMENT ME!
2327    */
2328   @Override
2329   protected void cut_actionPerformed(ActionEvent e)
2330   {
2331     copy_actionPerformed(null);
2332     delete_actionPerformed(null);
2333   }
2334
2335   /**
2336    * DOCUMENT ME!
2337    *
2338    * @param e
2339    *          DOCUMENT ME!
2340    */
2341   @Override
2342   protected void delete_actionPerformed(ActionEvent evt)
2343   {
2344
2345     SequenceGroup sg = viewport.getSelectionGroup();
2346     if (sg == null)
2347     {
2348       return;
2349     }
2350
2351     /*
2352      * If the cut affects all sequences, warn, remove highlighted columns
2353      */
2354     if (sg.getSize() == viewport.getAlignment().getHeight())
2355     {
2356       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2357               .getAlignment().getWidth()) ? true : false;
2358       if (isEntireAlignWidth)
2359       {
2360         int confirm = JvOptionPane.showConfirmDialog(this,
2361                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2362                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2363                 JvOptionPane.OK_CANCEL_OPTION);
2364
2365         if (confirm == JvOptionPane.CANCEL_OPTION
2366                 || confirm == JvOptionPane.CLOSED_OPTION)
2367         {
2368           return;
2369         }
2370       }
2371       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2372               sg.getEndRes() + 1);
2373     }
2374     SequenceI[] cut = sg.getSequences()
2375             .toArray(new SequenceI[sg.getSize()]);
2376
2377     addHistoryItem(new EditCommand(
2378             MessageManager.getString("label.cut_sequences"), Action.CUT,
2379             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2380             viewport.getAlignment()));
2381
2382     viewport.setSelectionGroup(null);
2383     viewport.sendSelection();
2384     viewport.getAlignment().deleteGroup(sg);
2385
2386     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2387             .getSequences());
2388     if (viewport.getAlignment().getHeight() < 1)
2389     {
2390       try
2391       {
2392         this.setClosed(true);
2393       } catch (Exception ex)
2394       {
2395       }
2396     }
2397   }
2398
2399   /**
2400    * DOCUMENT ME!
2401    *
2402    * @param e
2403    *          DOCUMENT ME!
2404    */
2405   @Override
2406   protected void deleteGroups_actionPerformed(ActionEvent e)
2407   {
2408     if (avc.deleteGroups())
2409     {
2410       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2411       alignPanel.updateAnnotation();
2412       alignPanel.paintAlignment(true);
2413     }
2414   }
2415
2416   /**
2417    * DOCUMENT ME!
2418    *
2419    * @param e
2420    *          DOCUMENT ME!
2421    */
2422   @Override
2423   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2424   {
2425     SequenceGroup sg = new SequenceGroup();
2426
2427     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2428     {
2429       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2430     }
2431
2432     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2433     viewport.setSelectionGroup(sg);
2434     viewport.sendSelection();
2435     // JAL-2034 - should delegate to
2436     // alignPanel to decide if overview needs
2437     // updating.
2438     alignPanel.paintAlignment(false);
2439     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2440   }
2441
2442   /**
2443    * DOCUMENT ME!
2444    *
2445    * @param e
2446    *          DOCUMENT ME!
2447    */
2448   @Override
2449   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2450   {
2451     if (viewport.cursorMode)
2452     {
2453       alignPanel.getSeqPanel().keyboardNo1 = null;
2454       alignPanel.getSeqPanel().keyboardNo2 = null;
2455     }
2456     viewport.setSelectionGroup(null);
2457     viewport.getColumnSelection().clear();
2458     viewport.setSelectionGroup(null);
2459     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2460     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2461     // JAL-2034 - should delegate to
2462     // alignPanel to decide if overview needs
2463     // updating.
2464     alignPanel.paintAlignment(false);
2465     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466     viewport.sendSelection();
2467   }
2468
2469   /**
2470    * DOCUMENT ME!
2471    *
2472    * @param e
2473    *          DOCUMENT ME!
2474    */
2475   @Override
2476   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2477   {
2478     SequenceGroup sg = viewport.getSelectionGroup();
2479
2480     if (sg == null)
2481     {
2482       selectAllSequenceMenuItem_actionPerformed(null);
2483
2484       return;
2485     }
2486
2487     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2488     {
2489       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2490     }
2491     // JAL-2034 - should delegate to
2492     // alignPanel to decide if overview needs
2493     // updating.
2494
2495     alignPanel.paintAlignment(true);
2496     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2497     viewport.sendSelection();
2498   }
2499
2500   @Override
2501   public void invertColSel_actionPerformed(ActionEvent e)
2502   {
2503     viewport.invertColumnSelection();
2504     alignPanel.paintAlignment(true);
2505     viewport.sendSelection();
2506   }
2507
2508   /**
2509    * DOCUMENT ME!
2510    *
2511    * @param e
2512    *          DOCUMENT ME!
2513    */
2514   @Override
2515   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2516   {
2517     trimAlignment(true);
2518   }
2519
2520   /**
2521    * DOCUMENT ME!
2522    *
2523    * @param e
2524    *          DOCUMENT ME!
2525    */
2526   @Override
2527   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2528   {
2529     trimAlignment(false);
2530   }
2531
2532   void trimAlignment(boolean trimLeft)
2533   {
2534     ColumnSelection colSel = viewport.getColumnSelection();
2535     int column;
2536
2537     if (!colSel.isEmpty())
2538     {
2539       if (trimLeft)
2540       {
2541         column = colSel.getMin();
2542       }
2543       else
2544       {
2545         column = colSel.getMax();
2546       }
2547
2548       SequenceI[] seqs;
2549       if (viewport.getSelectionGroup() != null)
2550       {
2551         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2552                 viewport.getHiddenRepSequences());
2553       }
2554       else
2555       {
2556         seqs = viewport.getAlignment().getSequencesArray();
2557       }
2558
2559       TrimRegionCommand trimRegion;
2560       if (trimLeft)
2561       {
2562         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2563                 column, viewport.getAlignment());
2564         vpRanges.setStartRes(0);
2565       }
2566       else
2567       {
2568         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2569                 column, viewport.getAlignment());
2570       }
2571
2572       statusBar.setText(MessageManager.formatMessage(
2573               "label.removed_columns",
2574               new String[] { Integer.valueOf(trimRegion.getSize())
2575                       .toString() }));
2576
2577       addHistoryItem(trimRegion);
2578
2579       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2580       {
2581         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2582                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2583         {
2584           viewport.getAlignment().deleteGroup(sg);
2585         }
2586       }
2587
2588       viewport.firePropertyChange("alignment", null, viewport
2589               .getAlignment().getSequences());
2590     }
2591   }
2592
2593   /**
2594    * DOCUMENT ME!
2595    *
2596    * @param e
2597    *          DOCUMENT ME!
2598    */
2599   @Override
2600   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2601   {
2602     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2603
2604     SequenceI[] seqs;
2605     if (viewport.getSelectionGroup() != null)
2606     {
2607       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2608               viewport.getHiddenRepSequences());
2609       start = viewport.getSelectionGroup().getStartRes();
2610       end = viewport.getSelectionGroup().getEndRes();
2611     }
2612     else
2613     {
2614       seqs = viewport.getAlignment().getSequencesArray();
2615     }
2616
2617     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2618             "Remove Gapped Columns", seqs, start, end,
2619             viewport.getAlignment());
2620
2621     addHistoryItem(removeGapCols);
2622
2623     statusBar.setText(MessageManager.formatMessage(
2624             "label.removed_empty_columns",
2625             new Object[] { Integer.valueOf(removeGapCols.getSize())
2626                     .toString() }));
2627
2628     // This is to maintain viewport position on first residue
2629     // of first sequence
2630     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2631     int startRes = seq.findPosition(vpRanges.getStartRes());
2632     // ShiftList shifts;
2633     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2634     // edit.alColumnChanges=shifts.getInverse();
2635     // if (viewport.hasHiddenColumns)
2636     // viewport.getColumnSelection().compensateForEdits(shifts);
2637     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2638     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2639             .getSequences());
2640
2641   }
2642
2643   /**
2644    * DOCUMENT ME!
2645    *
2646    * @param e
2647    *          DOCUMENT ME!
2648    */
2649   @Override
2650   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2651   {
2652     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2653
2654     SequenceI[] seqs;
2655     if (viewport.getSelectionGroup() != null)
2656     {
2657       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2658               viewport.getHiddenRepSequences());
2659       start = viewport.getSelectionGroup().getStartRes();
2660       end = viewport.getSelectionGroup().getEndRes();
2661     }
2662     else
2663     {
2664       seqs = viewport.getAlignment().getSequencesArray();
2665     }
2666
2667     // This is to maintain viewport position on first residue
2668     // of first sequence
2669     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2670     int startRes = seq.findPosition(vpRanges.getStartRes());
2671
2672     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2673             viewport.getAlignment()));
2674
2675     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2676
2677     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2678             .getSequences());
2679
2680   }
2681
2682   /**
2683    * DOCUMENT ME!
2684    *
2685    * @param e
2686    *          DOCUMENT ME!
2687    */
2688   @Override
2689   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2690   {
2691     viewport.setPadGaps(padGapsMenuitem.isSelected());
2692     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2693             .getSequences());
2694   }
2695
2696   /**
2697    * DOCUMENT ME!
2698    *
2699    * @param e
2700    *          DOCUMENT ME!
2701    */
2702   @Override
2703   public void findMenuItem_actionPerformed(ActionEvent e)
2704   {
2705     new Finder();
2706   }
2707
2708   /**
2709    * Create a new view of the current alignment.
2710    */
2711   @Override
2712   public void newView_actionPerformed(ActionEvent e)
2713   {
2714     newView(null, true);
2715   }
2716
2717   /**
2718    * Creates and shows a new view of the current alignment.
2719    *
2720    * @param viewTitle
2721    *          title of newly created view; if null, one will be generated
2722    * @param copyAnnotation
2723    *          if true then duplicate all annnotation, groups and settings
2724    * @return new alignment panel, already displayed.
2725    */
2726   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2727   {
2728     /*
2729      * Create a new AlignmentPanel (with its own, new Viewport)
2730      */
2731     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2732             true);
2733     if (!copyAnnotation)
2734     {
2735       /*
2736        * remove all groups and annotation except for the automatic stuff
2737        */
2738       newap.av.getAlignment().deleteAllGroups();
2739       newap.av.getAlignment().deleteAllAnnotations(false);
2740     }
2741
2742     newap.av.setGatherViewsHere(false);
2743
2744     if (viewport.viewName == null)
2745     {
2746       viewport.viewName = MessageManager
2747               .getString("label.view_name_original");
2748     }
2749
2750     /*
2751      * Views share the same edits undo and redo stacks
2752      */
2753     newap.av.setHistoryList(viewport.getHistoryList());
2754     newap.av.setRedoList(viewport.getRedoList());
2755
2756     /*
2757      * Views share the same mappings; need to deregister any new mappings
2758      * created by copyAlignPanel, and register the new reference to the shared
2759      * mappings
2760      */
2761     newap.av.replaceMappings(viewport.getAlignment());
2762
2763     newap.av.viewName = getNewViewName(viewTitle);
2764
2765     addAlignmentPanel(newap, true);
2766     newap.alignmentChanged();
2767
2768     if (alignPanels.size() == 2)
2769     {
2770       viewport.setGatherViewsHere(true);
2771     }
2772     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2773     return newap;
2774   }
2775
2776   /**
2777    * Make a new name for the view, ensuring it is unique within the current
2778    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2779    * these now use viewId. Unique view names are still desirable for usability.)
2780    *
2781    * @param viewTitle
2782    * @return
2783    */
2784   protected String getNewViewName(String viewTitle)
2785   {
2786     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2787     boolean addFirstIndex = false;
2788     if (viewTitle == null || viewTitle.trim().length() == 0)
2789     {
2790       viewTitle = MessageManager.getString("action.view");
2791       addFirstIndex = true;
2792     }
2793     else
2794     {
2795       index = 1;// we count from 1 if given a specific name
2796     }
2797     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2798
2799     List<Component> comps = PaintRefresher.components.get(viewport
2800             .getSequenceSetId());
2801
2802     List<String> existingNames = getExistingViewNames(comps);
2803
2804     while (existingNames.contains(newViewName))
2805     {
2806       newViewName = viewTitle + " " + (++index);
2807     }
2808     return newViewName;
2809   }
2810
2811   /**
2812    * Returns a list of distinct view names found in the given list of
2813    * components. View names are held on the viewport of an AlignmentPanel.
2814    *
2815    * @param comps
2816    * @return
2817    */
2818   protected List<String> getExistingViewNames(List<Component> comps)
2819   {
2820     List<String> existingNames = new ArrayList<String>();
2821     for (Component comp : comps)
2822     {
2823       if (comp instanceof AlignmentPanel)
2824       {
2825         AlignmentPanel ap = (AlignmentPanel) comp;
2826         if (!existingNames.contains(ap.av.viewName))
2827         {
2828           existingNames.add(ap.av.viewName);
2829         }
2830       }
2831     }
2832     return existingNames;
2833   }
2834
2835   /**
2836    * Explode tabbed views into separate windows.
2837    */
2838   @Override
2839   public void expandViews_actionPerformed(ActionEvent e)
2840   {
2841     Desktop.explodeViews(this);
2842   }
2843
2844   /**
2845    * Gather views in separate windows back into a tabbed presentation.
2846    */
2847   @Override
2848   public void gatherViews_actionPerformed(ActionEvent e)
2849   {
2850     Desktop.instance.gatherViews(this);
2851   }
2852
2853   /**
2854    * DOCUMENT ME!
2855    *
2856    * @param e
2857    *          DOCUMENT ME!
2858    */
2859   @Override
2860   public void font_actionPerformed(ActionEvent e)
2861   {
2862     new FontChooser(alignPanel);
2863   }
2864
2865   /**
2866    * DOCUMENT ME!
2867    *
2868    * @param e
2869    *          DOCUMENT ME!
2870    */
2871   @Override
2872   protected void seqLimit_actionPerformed(ActionEvent e)
2873   {
2874     viewport.setShowJVSuffix(seqLimits.isSelected());
2875
2876     alignPanel.getIdPanel().getIdCanvas()
2877             .setPreferredSize(alignPanel.calculateIdWidth());
2878     alignPanel.paintAlignment(true);
2879   }
2880
2881   @Override
2882   public void idRightAlign_actionPerformed(ActionEvent e)
2883   {
2884     viewport.setRightAlignIds(idRightAlign.isSelected());
2885     alignPanel.paintAlignment(true);
2886   }
2887
2888   @Override
2889   public void centreColumnLabels_actionPerformed(ActionEvent e)
2890   {
2891     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2892     alignPanel.paintAlignment(true);
2893   }
2894
2895   /*
2896    * (non-Javadoc)
2897    *
2898    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2899    */
2900   @Override
2901   protected void followHighlight_actionPerformed()
2902   {
2903     /*
2904      * Set the 'follow' flag on the Viewport (and scroll to position if now
2905      * true).
2906      */
2907     final boolean state = this.followHighlightMenuItem.getState();
2908     viewport.setFollowHighlight(state);
2909     if (state)
2910     {
2911       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2912     }
2913   }
2914
2915   /**
2916    * DOCUMENT ME!
2917    *
2918    * @param e
2919    *          DOCUMENT ME!
2920    */
2921   @Override
2922   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2923   {
2924     viewport.setColourText(colourTextMenuItem.isSelected());
2925     alignPanel.paintAlignment(true);
2926   }
2927
2928   /**
2929    * DOCUMENT ME!
2930    *
2931    * @param e
2932    *          DOCUMENT ME!
2933    */
2934   @Override
2935   public void wrapMenuItem_actionPerformed(ActionEvent e)
2936   {
2937     scaleAbove.setVisible(wrapMenuItem.isSelected());
2938     scaleLeft.setVisible(wrapMenuItem.isSelected());
2939     scaleRight.setVisible(wrapMenuItem.isSelected());
2940     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2941     alignPanel.updateLayout();
2942   }
2943
2944   @Override
2945   public void showAllSeqs_actionPerformed(ActionEvent e)
2946   {
2947     viewport.showAllHiddenSeqs();
2948   }
2949
2950   @Override
2951   public void showAllColumns_actionPerformed(ActionEvent e)
2952   {
2953     viewport.showAllHiddenColumns();
2954     repaint();
2955     viewport.sendSelection();
2956   }
2957
2958   @Override
2959   public void hideSelSequences_actionPerformed(ActionEvent e)
2960   {
2961     viewport.hideAllSelectedSeqs();
2962     // alignPanel.paintAlignment(true);
2963   }
2964
2965   /**
2966    * called by key handler and the hide all/show all menu items
2967    *
2968    * @param toggleSeqs
2969    * @param toggleCols
2970    */
2971   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2972   {
2973
2974     boolean hide = false;
2975     SequenceGroup sg = viewport.getSelectionGroup();
2976     if (!toggleSeqs && !toggleCols)
2977     {
2978       // Hide everything by the current selection - this is a hack - we do the
2979       // invert and then hide
2980       // first check that there will be visible columns after the invert.
2981       if (viewport.hasSelectedColumns()
2982               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2983                       .getEndRes()))
2984       {
2985         // now invert the sequence set, if required - empty selection implies
2986         // that no hiding is required.
2987         if (sg != null)
2988         {
2989           invertSequenceMenuItem_actionPerformed(null);
2990           sg = viewport.getSelectionGroup();
2991           toggleSeqs = true;
2992
2993         }
2994         viewport.expandColSelection(sg, true);
2995         // finally invert the column selection and get the new sequence
2996         // selection.
2997         invertColSel_actionPerformed(null);
2998         toggleCols = true;
2999       }
3000     }
3001
3002     if (toggleSeqs)
3003     {
3004       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3005       {
3006         hideSelSequences_actionPerformed(null);
3007         hide = true;
3008       }
3009       else if (!(toggleCols && viewport.hasSelectedColumns()))
3010       {
3011         showAllSeqs_actionPerformed(null);
3012       }
3013     }
3014
3015     if (toggleCols)
3016     {
3017       if (viewport.hasSelectedColumns())
3018       {
3019         hideSelColumns_actionPerformed(null);
3020         if (!toggleSeqs)
3021         {
3022           viewport.setSelectionGroup(sg);
3023         }
3024       }
3025       else if (!hide)
3026       {
3027         showAllColumns_actionPerformed(null);
3028       }
3029     }
3030   }
3031
3032   /*
3033    * (non-Javadoc)
3034    *
3035    * @see
3036    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3037    * event.ActionEvent)
3038    */
3039   @Override
3040   public void hideAllButSelection_actionPerformed(ActionEvent e)
3041   {
3042     toggleHiddenRegions(false, false);
3043     viewport.sendSelection();
3044   }
3045
3046   /*
3047    * (non-Javadoc)
3048    *
3049    * @see
3050    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3051    * .ActionEvent)
3052    */
3053   @Override
3054   public void hideAllSelection_actionPerformed(ActionEvent e)
3055   {
3056     SequenceGroup sg = viewport.getSelectionGroup();
3057     viewport.expandColSelection(sg, false);
3058     viewport.hideAllSelectedSeqs();
3059     viewport.hideSelectedColumns();
3060     alignPanel.paintAlignment(true);
3061     viewport.sendSelection();
3062   }
3063
3064   /*
3065    * (non-Javadoc)
3066    *
3067    * @see
3068    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3069    * ActionEvent)
3070    */
3071   @Override
3072   public void showAllhidden_actionPerformed(ActionEvent e)
3073   {
3074     viewport.showAllHiddenColumns();
3075     viewport.showAllHiddenSeqs();
3076     alignPanel.paintAlignment(true);
3077     viewport.sendSelection();
3078   }
3079
3080   @Override
3081   public void hideSelColumns_actionPerformed(ActionEvent e)
3082   {
3083     viewport.hideSelectedColumns();
3084     alignPanel.paintAlignment(true);
3085     viewport.sendSelection();
3086   }
3087
3088   @Override
3089   public void hiddenMarkers_actionPerformed(ActionEvent e)
3090   {
3091     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3092     repaint();
3093   }
3094
3095   /**
3096    * DOCUMENT ME!
3097    *
3098    * @param e
3099    *          DOCUMENT ME!
3100    */
3101   @Override
3102   protected void scaleAbove_actionPerformed(ActionEvent e)
3103   {
3104     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3105     alignPanel.paintAlignment(true);
3106   }
3107
3108   /**
3109    * DOCUMENT ME!
3110    *
3111    * @param e
3112    *          DOCUMENT ME!
3113    */
3114   @Override
3115   protected void scaleLeft_actionPerformed(ActionEvent e)
3116   {
3117     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3118     alignPanel.paintAlignment(true);
3119   }
3120
3121   /**
3122    * DOCUMENT ME!
3123    *
3124    * @param e
3125    *          DOCUMENT ME!
3126    */
3127   @Override
3128   protected void scaleRight_actionPerformed(ActionEvent e)
3129   {
3130     viewport.setScaleRightWrapped(scaleRight.isSelected());
3131     alignPanel.paintAlignment(true);
3132   }
3133
3134   /**
3135    * DOCUMENT ME!
3136    *
3137    * @param e
3138    *          DOCUMENT ME!
3139    */
3140   @Override
3141   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3142   {
3143     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3144     alignPanel.paintAlignment(true);
3145   }
3146
3147   /**
3148    * DOCUMENT ME!
3149    *
3150    * @param e
3151    *          DOCUMENT ME!
3152    */
3153   @Override
3154   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3155   {
3156     viewport.setShowText(viewTextMenuItem.isSelected());
3157     alignPanel.paintAlignment(true);
3158   }
3159
3160   /**
3161    * DOCUMENT ME!
3162    *
3163    * @param e
3164    *          DOCUMENT ME!
3165    */
3166   @Override
3167   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3168   {
3169     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3170     alignPanel.paintAlignment(true);
3171   }
3172
3173   public FeatureSettings featureSettings;
3174
3175   @Override
3176   public FeatureSettingsControllerI getFeatureSettingsUI()
3177   {
3178     return featureSettings;
3179   }
3180
3181   @Override
3182   public void featureSettings_actionPerformed(ActionEvent e)
3183   {
3184     if (featureSettings != null)
3185     {
3186       featureSettings.close();
3187       featureSettings = null;
3188     }
3189     if (!showSeqFeatures.isSelected())
3190     {
3191       // make sure features are actually displayed
3192       showSeqFeatures.setSelected(true);
3193       showSeqFeatures_actionPerformed(null);
3194     }
3195     featureSettings = new FeatureSettings(this);
3196   }
3197
3198   /**
3199    * Set or clear 'Show Sequence Features'
3200    *
3201    * @param evt
3202    *          DOCUMENT ME!
3203    */
3204   @Override
3205   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3206   {
3207     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3208     alignPanel.paintAlignment(true);
3209     if (alignPanel.getOverviewPanel() != null)
3210     {
3211       alignPanel.getOverviewPanel().updateOverviewImage();
3212     }
3213   }
3214
3215   /**
3216    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3217    * the annotations panel as a whole.
3218    *
3219    * The options to show/hide all annotations should be enabled when the panel
3220    * is shown, and disabled when the panel is hidden.
3221    *
3222    * @param e
3223    */
3224   @Override
3225   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3226   {
3227     final boolean setVisible = annotationPanelMenuItem.isSelected();
3228     viewport.setShowAnnotation(setVisible);
3229     this.showAllSeqAnnotations.setEnabled(setVisible);
3230     this.hideAllSeqAnnotations.setEnabled(setVisible);
3231     this.showAllAlAnnotations.setEnabled(setVisible);
3232     this.hideAllAlAnnotations.setEnabled(setVisible);
3233     alignPanel.updateLayout();
3234   }
3235
3236   @Override
3237   public void alignmentProperties()
3238   {
3239     JEditorPane editPane = new JEditorPane("text/html", "");
3240     editPane.setEditable(false);
3241     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3242             .formatAsHtml();
3243     editPane.setText(MessageManager.formatMessage("label.html_content",
3244             new Object[] { contents.toString() }));
3245     JInternalFrame frame = new JInternalFrame();
3246     frame.getContentPane().add(new JScrollPane(editPane));
3247
3248     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3249             "label.alignment_properties", new Object[] { getTitle() }),
3250             500, 400);
3251   }
3252
3253   /**
3254    * DOCUMENT ME!
3255    *
3256    * @param e
3257    *          DOCUMENT ME!
3258    */
3259   @Override
3260   public void overviewMenuItem_actionPerformed(ActionEvent e)
3261   {
3262     if (alignPanel.overviewPanel != null)
3263     {
3264       return;
3265     }
3266
3267     JInternalFrame frame = new JInternalFrame();
3268     OverviewPanel overview = new OverviewPanel(alignPanel);
3269     frame.setContentPane(overview);
3270     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3271             "label.overview_params", new Object[] { this.getTitle() }),
3272             frame.getWidth(), frame.getHeight());
3273     frame.pack();
3274     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3275     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3276     {
3277       @Override
3278       public void internalFrameClosed(
3279               javax.swing.event.InternalFrameEvent evt)
3280       {
3281         alignPanel.setOverviewPanel(null);
3282       };
3283     });
3284
3285     alignPanel.setOverviewPanel(overview);
3286   }
3287
3288   @Override
3289   public void textColour_actionPerformed()
3290   {
3291     new TextColourChooser().chooseColour(alignPanel, null);
3292   }
3293
3294   /*
3295    * public void covariationColour_actionPerformed() {
3296    * changeColour(new
3297    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3298    * ()[0])); }
3299    */
3300   @Override
3301   public void annotationColour_actionPerformed()
3302   {
3303     new AnnotationColourChooser(viewport, alignPanel);
3304   }
3305
3306   @Override
3307   public void annotationColumn_actionPerformed(ActionEvent e)
3308   {
3309     new AnnotationColumnChooser(viewport, alignPanel);
3310   }
3311
3312   /**
3313    * Action on the user checking or unchecking the option to apply the selected
3314    * colour scheme to all groups. If unchecked, groups may have their own
3315    * independent colour schemes.
3316    *
3317    * @param selected
3318    */
3319   @Override
3320   public void applyToAllGroups_actionPerformed(boolean selected)
3321   {
3322     viewport.setColourAppliesToAllGroups(selected);
3323   }
3324
3325   /**
3326    * Action on user selecting a colour from the colour menu
3327    *
3328    * @param name
3329    *          the name (not the menu item label!) of the colour scheme
3330    */
3331   @Override
3332   public void changeColour_actionPerformed(String name)
3333   {
3334     /*
3335      * 'User Defined' opens a panel to configure or load a
3336      * user-defined colour scheme
3337      */
3338     if (ResidueColourScheme.USER_DEFINED.equals(name))
3339     {
3340       new UserDefinedColours(alignPanel, null);
3341       return;
3342     }
3343
3344     /*
3345      * otherwise set the chosen colour scheme (or null for 'None')
3346      */
3347     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3348             viewport.getAlignment(), viewport.getHiddenRepSequences());
3349     changeColour(cs);
3350   }
3351
3352   /**
3353    * Actions on setting or changing the alignment colour scheme
3354    *
3355    * @param cs
3356    */
3357   @Override
3358   public void changeColour(ColourSchemeI cs)
3359   {
3360     // TODO: pull up to controller method
3361     if (cs != null)
3362     {
3363       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3364     }
3365
3366     viewport.setGlobalColourScheme(cs);
3367
3368     alignPanel.paintAlignment(true);
3369   }
3370
3371   /**
3372    * Show the PID threshold slider panel
3373    */
3374   @Override
3375   protected void modifyPID_actionPerformed()
3376   {
3377     SliderPanel.setPIDSliderSource(alignPanel,
3378             viewport.getResidueShading(), alignPanel.getViewName());
3379     SliderPanel.showPIDSlider();
3380   }
3381
3382   /**
3383    * Show the Conservation slider panel
3384    */
3385   @Override
3386   protected void modifyConservation_actionPerformed()
3387   {
3388     SliderPanel.setConservationSlider(alignPanel,
3389             viewport.getResidueShading(), alignPanel.getViewName());
3390     SliderPanel.showConservationSlider();
3391   }
3392
3393   /**
3394    * Action on selecting or deselecting (Colour) By Conservation
3395    */
3396   @Override
3397   public void conservationMenuItem_actionPerformed(boolean selected)
3398   {
3399     modifyConservation.setEnabled(selected);
3400     viewport.setConservationSelected(selected);
3401     viewport.getResidueShading().setConservationApplied(selected);
3402
3403     changeColour(viewport.getGlobalColourScheme());
3404     if (selected)
3405     {
3406       modifyConservation_actionPerformed();
3407     }
3408     else
3409     {
3410       SliderPanel.hideConservationSlider();
3411     }
3412   }
3413
3414   /**
3415    * Action on selecting or deselecting (Colour) Above PID Threshold
3416    */
3417   @Override
3418   public void abovePIDThreshold_actionPerformed(boolean selected)
3419   {
3420     modifyPID.setEnabled(selected);
3421     viewport.setAbovePIDThreshold(selected);
3422     if (!selected)
3423     {
3424       viewport.getResidueShading().setThreshold(0,
3425               viewport.isIgnoreGapsConsensus());
3426     }
3427
3428     changeColour(viewport.getGlobalColourScheme());
3429     if (selected)
3430     {
3431       modifyPID_actionPerformed();
3432     }
3433     else
3434     {
3435       SliderPanel.hidePIDSlider();
3436     }
3437   }
3438
3439   /**
3440    * DOCUMENT ME!
3441    *
3442    * @param e
3443    *          DOCUMENT ME!
3444    */
3445   @Override
3446   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3447   {
3448     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3449     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3450             .getAlignment().getSequenceAt(0), null);
3451     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3452             viewport.getAlignment()));
3453     alignPanel.paintAlignment(true);
3454   }
3455
3456   /**
3457    * DOCUMENT ME!
3458    *
3459    * @param e
3460    *          DOCUMENT ME!
3461    */
3462   @Override
3463   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3464   {
3465     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3466     AlignmentSorter.sortByID(viewport.getAlignment());
3467     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3468             viewport.getAlignment()));
3469     alignPanel.paintAlignment(true);
3470   }
3471
3472   /**
3473    * DOCUMENT ME!
3474    *
3475    * @param e
3476    *          DOCUMENT ME!
3477    */
3478   @Override
3479   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3480   {
3481     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3482     AlignmentSorter.sortByLength(viewport.getAlignment());
3483     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3484             viewport.getAlignment()));
3485     alignPanel.paintAlignment(true);
3486   }
3487
3488   /**
3489    * DOCUMENT ME!
3490    *
3491    * @param e
3492    *          DOCUMENT ME!
3493    */
3494   @Override
3495   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3496   {
3497     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3498     AlignmentSorter.sortByGroup(viewport.getAlignment());
3499     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3500             viewport.getAlignment()));
3501
3502     alignPanel.paintAlignment(true);
3503   }
3504
3505   /**
3506    * DOCUMENT ME!
3507    *
3508    * @param e
3509    *          DOCUMENT ME!
3510    */
3511   @Override
3512   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3513   {
3514     new RedundancyPanel(alignPanel, this);
3515   }
3516
3517   /**
3518    * DOCUMENT ME!
3519    *
3520    * @param e
3521    *          DOCUMENT ME!
3522    */
3523   @Override
3524   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3525   {
3526     if ((viewport.getSelectionGroup() == null)
3527             || (viewport.getSelectionGroup().getSize() < 2))
3528     {
3529       JvOptionPane.showInternalMessageDialog(this, MessageManager
3530               .getString("label.you_must_select_least_two_sequences"),
3531               MessageManager.getString("label.invalid_selection"),
3532               JvOptionPane.WARNING_MESSAGE);
3533     }
3534     else
3535     {
3536       JInternalFrame frame = new JInternalFrame();
3537       frame.setContentPane(new PairwiseAlignPanel(viewport));
3538       Desktop.addInternalFrame(frame,
3539               MessageManager.getString("action.pairwise_alignment"), 600,
3540               500);
3541     }
3542   }
3543
3544   /**
3545    * DOCUMENT ME!
3546    *
3547    * @param e
3548    *          DOCUMENT ME!
3549    */
3550   @Override
3551   public void PCAMenuItem_actionPerformed(ActionEvent e)
3552   {
3553     if (((viewport.getSelectionGroup() != null)
3554             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3555             .getSelectionGroup().getSize() > 0))
3556             || (viewport.getAlignment().getHeight() < 4))
3557     {
3558       JvOptionPane
3559               .showInternalMessageDialog(
3560                       this,
3561                       MessageManager
3562                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3563                       MessageManager
3564                               .getString("label.sequence_selection_insufficient"),
3565                       JvOptionPane.WARNING_MESSAGE);
3566
3567       return;
3568     }
3569
3570     new PCAPanel(alignPanel);
3571   }
3572
3573   @Override
3574   public void autoCalculate_actionPerformed(ActionEvent e)
3575   {
3576     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3577     if (viewport.autoCalculateConsensus)
3578     {
3579       viewport.firePropertyChange("alignment", null, viewport
3580               .getAlignment().getSequences());
3581     }
3582   }
3583
3584   @Override
3585   public void sortByTreeOption_actionPerformed(ActionEvent e)
3586   {
3587     viewport.sortByTree = sortByTree.isSelected();
3588   }
3589
3590   @Override
3591   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3592   {
3593     viewport.followSelection = listenToViewSelections.isSelected();
3594   }
3595
3596   /**
3597    * Constructs a tree panel and adds it to the desktop
3598    *
3599    * @param type
3600    *          tree type (NJ or AV)
3601    * @param sm
3602    *          distance or similarity score model used to compute the tree
3603    * @param options
3604    *          parameters for the distance or similarity calculation
3605    */
3606   void newTreePanel(String type, ScoreModelI sm, SimilarityParamsI options)
3607   {
3608     String frameTitle = "";
3609     TreePanel tp;
3610
3611     if (viewport.getSelectionGroup() != null
3612             && viewport.getSelectionGroup().getSize() > 0)
3613     {
3614       if (viewport.getSelectionGroup().getSize() < 3)
3615       {
3616         JvOptionPane
3617                 .showMessageDialog(
3618                         Desktop.desktop,
3619                         MessageManager
3620                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3621                         MessageManager
3622                                 .getString("label.not_enough_sequences"),
3623                         JvOptionPane.WARNING_MESSAGE);
3624         return;
3625       }
3626
3627       SequenceGroup sg = viewport.getSelectionGroup();
3628
3629       /* Decide if the selection is a column region */
3630       for (SequenceI _s : sg.getSequences())
3631       {
3632         if (_s.getLength() < sg.getEndRes())
3633         {
3634           JvOptionPane
3635                   .showMessageDialog(
3636                           Desktop.desktop,
3637                           MessageManager
3638                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3639                           MessageManager
3640                                   .getString("label.sequences_selection_not_aligned"),
3641                           JvOptionPane.WARNING_MESSAGE);
3642
3643           return;
3644         }
3645       }
3646
3647       tp = new TreePanel(alignPanel, type, sm, options);
3648       frameTitle = tp.getPanelTitle() + " on region";
3649     }
3650     else
3651     {
3652       // are the visible sequences aligned?
3653       if (!viewport.getAlignment().isAligned(false))
3654       {
3655         JvOptionPane
3656                 .showMessageDialog(
3657                         Desktop.desktop,
3658                         MessageManager
3659                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3660                         MessageManager
3661                                 .getString("label.sequences_not_aligned"),
3662                         JvOptionPane.WARNING_MESSAGE);
3663
3664         return;
3665       }
3666
3667       if (viewport.getAlignment().getHeight() < 2)
3668       {
3669         return;
3670       }
3671
3672       tp = new TreePanel(alignPanel, type, sm, options);
3673       frameTitle = tp.getPanelTitle();
3674     }
3675
3676     frameTitle += " from ";
3677
3678     if (viewport.viewName != null)
3679     {
3680       frameTitle += viewport.viewName + " of ";
3681     }
3682
3683     frameTitle += this.title;
3684
3685     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3686   }
3687
3688   /**
3689    * DOCUMENT ME!
3690    *
3691    * @param title
3692    *          DOCUMENT ME!
3693    * @param order
3694    *          DOCUMENT ME!
3695    */
3696   public void addSortByOrderMenuItem(String title,
3697           final AlignmentOrder order)
3698   {
3699     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3700             "action.by_title_param", new Object[] { title }));
3701     sort.add(item);
3702     item.addActionListener(new java.awt.event.ActionListener()
3703     {
3704       @Override
3705       public void actionPerformed(ActionEvent e)
3706       {
3707         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3708
3709         // TODO: JBPNote - have to map order entries to curent SequenceI
3710         // pointers
3711         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3712
3713         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3714                 .getAlignment()));
3715
3716         alignPanel.paintAlignment(true);
3717       }
3718     });
3719   }
3720
3721   /**
3722    * Add a new sort by annotation score menu item
3723    *
3724    * @param sort
3725    *          the menu to add the option to
3726    * @param scoreLabel
3727    *          the label used to retrieve scores for each sequence on the
3728    *          alignment
3729    */
3730   public void addSortByAnnotScoreMenuItem(JMenu sort,
3731           final String scoreLabel)
3732   {
3733     final JMenuItem item = new JMenuItem(scoreLabel);
3734     sort.add(item);
3735     item.addActionListener(new java.awt.event.ActionListener()
3736     {
3737       @Override
3738       public void actionPerformed(ActionEvent e)
3739       {
3740         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3741         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3742                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3743         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3744                 viewport.getAlignment()));
3745         alignPanel.paintAlignment(true);
3746       }
3747     });
3748   }
3749
3750   /**
3751    * last hash for alignment's annotation array - used to minimise cost of
3752    * rebuild.
3753    */
3754   protected int _annotationScoreVectorHash;
3755
3756   /**
3757    * search the alignment and rebuild the sort by annotation score submenu the
3758    * last alignment annotation vector hash is stored to minimize cost of
3759    * rebuilding in subsequence calls.
3760    *
3761    */
3762   @Override
3763   public void buildSortByAnnotationScoresMenu()
3764   {
3765     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3766     {
3767       return;
3768     }
3769
3770     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3771     {
3772       sortByAnnotScore.removeAll();
3773       // almost certainly a quicker way to do this - but we keep it simple
3774       Hashtable scoreSorts = new Hashtable();
3775       AlignmentAnnotation aann[];
3776       for (SequenceI sqa : viewport.getAlignment().getSequences())
3777       {
3778         aann = sqa.getAnnotation();
3779         for (int i = 0; aann != null && i < aann.length; i++)
3780         {
3781           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3782           {
3783             scoreSorts.put(aann[i].label, aann[i].label);
3784           }
3785         }
3786       }
3787       Enumeration labels = scoreSorts.keys();
3788       while (labels.hasMoreElements())
3789       {
3790         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3791                 (String) labels.nextElement());
3792       }
3793       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3794       scoreSorts.clear();
3795
3796       _annotationScoreVectorHash = viewport.getAlignment()
3797               .getAlignmentAnnotation().hashCode();
3798     }
3799   }
3800
3801   /**
3802    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3803    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3804    * call. Listeners are added to remove the menu item when the treePanel is
3805    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3806    * modified.
3807    */
3808   @Override
3809   public void buildTreeSortMenu()
3810   {
3811     sortByTreeMenu.removeAll();
3812
3813     List<Component> comps = PaintRefresher.components.get(viewport
3814             .getSequenceSetId());
3815     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3816     for (Component comp : comps)
3817     {
3818       if (comp instanceof TreePanel)
3819       {
3820         treePanels.add((TreePanel) comp);
3821       }
3822     }
3823
3824     if (treePanels.size() < 1)
3825     {
3826       sortByTreeMenu.setVisible(false);
3827       return;
3828     }
3829
3830     sortByTreeMenu.setVisible(true);
3831
3832     for (final TreePanel tp : treePanels)
3833     {
3834       final JMenuItem item = new JMenuItem(tp.getTitle());
3835       item.addActionListener(new java.awt.event.ActionListener()
3836       {
3837         @Override
3838         public void actionPerformed(ActionEvent e)
3839         {
3840           tp.sortByTree_actionPerformed();
3841           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3842
3843         }
3844       });
3845
3846       sortByTreeMenu.add(item);
3847     }
3848   }
3849
3850   public boolean sortBy(AlignmentOrder alorder, String undoname)
3851   {
3852     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3853     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3854     if (undoname != null)
3855     {
3856       addHistoryItem(new OrderCommand(undoname, oldOrder,
3857               viewport.getAlignment()));
3858     }
3859     alignPanel.paintAlignment(true);
3860     return true;
3861   }
3862
3863   /**
3864    * Work out whether the whole set of sequences or just the selected set will
3865    * be submitted for multiple alignment.
3866    *
3867    */
3868   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3869   {
3870     // Now, check we have enough sequences
3871     AlignmentView msa = null;
3872
3873     if ((viewport.getSelectionGroup() != null)
3874             && (viewport.getSelectionGroup().getSize() > 1))
3875     {
3876       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3877       // some common interface!
3878       /*
3879        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3880        * SequenceI[sz = seqs.getSize(false)];
3881        *
3882        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3883        * seqs.getSequenceAt(i); }
3884        */
3885       msa = viewport.getAlignmentView(true);
3886     }
3887     else if (viewport.getSelectionGroup() != null
3888             && viewport.getSelectionGroup().getSize() == 1)
3889     {
3890       int option = JvOptionPane.showConfirmDialog(this,
3891               MessageManager.getString("warn.oneseq_msainput_selection"),
3892               MessageManager.getString("label.invalid_selection"),
3893               JvOptionPane.OK_CANCEL_OPTION);
3894       if (option == JvOptionPane.OK_OPTION)
3895       {
3896         msa = viewport.getAlignmentView(false);
3897       }
3898     }
3899     else
3900     {
3901       msa = viewport.getAlignmentView(false);
3902     }
3903     return msa;
3904   }
3905
3906   /**
3907    * Decides what is submitted to a secondary structure prediction service: the
3908    * first sequence in the alignment, or in the current selection, or, if the
3909    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3910    * region or the whole alignment. (where the first sequence in the set is the
3911    * one that the prediction will be for).
3912    */
3913   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3914   {
3915     AlignmentView seqs = null;
3916
3917     if ((viewport.getSelectionGroup() != null)
3918             && (viewport.getSelectionGroup().getSize() > 0))
3919     {
3920       seqs = viewport.getAlignmentView(true);
3921     }
3922     else
3923     {
3924       seqs = viewport.getAlignmentView(false);
3925     }
3926     // limit sequences - JBPNote in future - could spawn multiple prediction
3927     // jobs
3928     // TODO: viewport.getAlignment().isAligned is a global state - the local
3929     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3930     if (!viewport.getAlignment().isAligned(false))
3931     {
3932       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3933       // TODO: if seqs.getSequences().length>1 then should really have warned
3934       // user!
3935
3936     }
3937     return seqs;
3938   }
3939
3940   /**
3941    * DOCUMENT ME!
3942    *
3943    * @param e
3944    *          DOCUMENT ME!
3945    */
3946   @Override
3947   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3948   {
3949     // Pick the tree file
3950     JalviewFileChooser chooser = new JalviewFileChooser(
3951             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3952     chooser.setFileView(new JalviewFileView());
3953     chooser.setDialogTitle(MessageManager
3954             .getString("label.select_newick_like_tree_file"));
3955     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3956
3957     int value = chooser.showOpenDialog(null);
3958
3959     if (value == JalviewFileChooser.APPROVE_OPTION)
3960     {
3961       String filePath = chooser.getSelectedFile().getPath();
3962       Cache.setProperty("LAST_DIRECTORY", filePath);
3963       NewickFile fin = null;
3964       try
3965       {
3966         fin = new NewickFile(filePath, DataSourceType.FILE);
3967         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3968       } catch (Exception ex)
3969       {
3970         JvOptionPane
3971                 .showMessageDialog(
3972                         Desktop.desktop,
3973                         ex.getMessage(),
3974                         MessageManager
3975                                 .getString("label.problem_reading_tree_file"),
3976                         JvOptionPane.WARNING_MESSAGE);
3977         ex.printStackTrace();
3978       }
3979       if (fin != null && fin.hasWarningMessage())
3980       {
3981         JvOptionPane.showMessageDialog(Desktop.desktop, fin
3982                 .getWarningMessage(), MessageManager
3983                 .getString("label.possible_problem_with_tree_file"),
3984                 JvOptionPane.WARNING_MESSAGE);
3985       }
3986     }
3987   }
3988
3989   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3990   {
3991     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3992   }
3993
3994   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3995           int h, int x, int y)
3996   {
3997     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3998   }
3999
4000   /**
4001    * Add a treeviewer for the tree extracted from a Newick file object to the
4002    * current alignment view
4003    *
4004    * @param nf
4005    *          the tree
4006    * @param title
4007    *          tree viewer title
4008    * @param input
4009    *          Associated alignment input data (or null)
4010    * @param w
4011    *          width
4012    * @param h
4013    *          height
4014    * @param x
4015    *          position
4016    * @param y
4017    *          position
4018    * @return TreePanel handle
4019    */
4020   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4021           AlignmentView input, int w, int h, int x, int y)
4022   {
4023     TreePanel tp = null;
4024
4025     try
4026     {
4027       nf.parse();
4028
4029       if (nf.getTree() != null)
4030       {
4031         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4032
4033         tp.setSize(w, h);
4034
4035         if (x > 0 && y > 0)
4036         {
4037           tp.setLocation(x, y);
4038         }
4039
4040         Desktop.addInternalFrame(tp, treeTitle, w, h);
4041       }
4042     } catch (Exception ex)
4043     {
4044       ex.printStackTrace();
4045     }
4046
4047     return tp;
4048   }
4049
4050   private boolean buildingMenu = false;
4051
4052   /**
4053    * Generates menu items and listener event actions for web service clients
4054    *
4055    */
4056   public void BuildWebServiceMenu()
4057   {
4058     while (buildingMenu)
4059     {
4060       try
4061       {
4062         System.err.println("Waiting for building menu to finish.");
4063         Thread.sleep(10);
4064       } catch (Exception e)
4065       {
4066       }
4067     }
4068     final AlignFrame me = this;
4069     buildingMenu = true;
4070     new Thread(new Runnable()
4071     {
4072       @Override
4073       public void run()
4074       {
4075         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4076         try
4077         {
4078           // System.err.println("Building ws menu again "
4079           // + Thread.currentThread());
4080           // TODO: add support for context dependent disabling of services based
4081           // on
4082           // alignment and current selection
4083           // TODO: add additional serviceHandle parameter to specify abstract
4084           // handler
4085           // class independently of AbstractName
4086           // TODO: add in rediscovery GUI function to restart discoverer
4087           // TODO: group services by location as well as function and/or
4088           // introduce
4089           // object broker mechanism.
4090           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4091           final IProgressIndicator af = me;
4092
4093           /*
4094            * do not i18n these strings - they are hard-coded in class
4095            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4096            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4097            */
4098           final JMenu msawsmenu = new JMenu("Alignment");
4099           final JMenu secstrmenu = new JMenu(
4100                   "Secondary Structure Prediction");
4101           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4102           final JMenu analymenu = new JMenu("Analysis");
4103           final JMenu dismenu = new JMenu("Protein Disorder");
4104           // JAL-940 - only show secondary structure prediction services from
4105           // the legacy server
4106           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4107               // &&
4108           Discoverer.services != null && (Discoverer.services.size() > 0))
4109           {
4110             // TODO: refactor to allow list of AbstractName/Handler bindings to
4111             // be
4112             // stored or retrieved from elsewhere
4113             // No MSAWS used any more:
4114             // Vector msaws = null; // (Vector)
4115             // Discoverer.services.get("MsaWS");
4116             Vector secstrpr = (Vector) Discoverer.services
4117                     .get("SecStrPred");
4118             if (secstrpr != null)
4119             {
4120               // Add any secondary structure prediction services
4121               for (int i = 0, j = secstrpr.size(); i < j; i++)
4122               {
4123                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4124                         .get(i);
4125                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4126                         .getServiceClient(sh);
4127                 int p = secstrmenu.getItemCount();
4128                 impl.attachWSMenuEntry(secstrmenu, me);
4129                 int q = secstrmenu.getItemCount();
4130                 for (int litm = p; litm < q; litm++)
4131                 {
4132                   legacyItems.add(secstrmenu.getItem(litm));
4133                 }
4134               }
4135             }
4136           }
4137
4138           // Add all submenus in the order they should appear on the web
4139           // services menu
4140           wsmenu.add(msawsmenu);
4141           wsmenu.add(secstrmenu);
4142           wsmenu.add(dismenu);
4143           wsmenu.add(analymenu);
4144           // No search services yet
4145           // wsmenu.add(seqsrchmenu);
4146
4147           javax.swing.SwingUtilities.invokeLater(new Runnable()
4148           {
4149             @Override
4150             public void run()
4151             {
4152               try
4153               {
4154                 webService.removeAll();
4155                 // first, add discovered services onto the webservices menu
4156                 if (wsmenu.size() > 0)
4157                 {
4158                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4159                   {
4160                     webService.add(wsmenu.get(i));
4161                   }
4162                 }
4163                 else
4164                 {
4165                   webService.add(me.webServiceNoServices);
4166                 }
4167                 // TODO: move into separate menu builder class.
4168                 boolean new_sspred = false;
4169                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4170                 {
4171                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4172                   if (jws2servs != null)
4173                   {
4174                     if (jws2servs.hasServices())
4175                     {
4176                       jws2servs.attachWSMenuEntry(webService, me);
4177                       for (Jws2Instance sv : jws2servs.getServices())
4178                       {
4179                         if (sv.description.toLowerCase().contains("jpred"))
4180                         {
4181                           for (JMenuItem jmi : legacyItems)
4182                           {
4183                             jmi.setVisible(false);
4184                           }
4185                         }
4186                       }
4187
4188                     }
4189                     if (jws2servs.isRunning())
4190                     {
4191                       JMenuItem tm = new JMenuItem(
4192                               "Still discovering JABA Services");
4193                       tm.setEnabled(false);
4194                       webService.add(tm);
4195                     }
4196                   }
4197                 }
4198                 build_urlServiceMenu(me.webService);
4199                 build_fetchdbmenu(webService);
4200                 for (JMenu item : wsmenu)
4201                 {
4202                   if (item.getItemCount() == 0)
4203                   {
4204                     item.setEnabled(false);
4205                   }
4206                   else
4207                   {
4208                     item.setEnabled(true);
4209                   }
4210                 }
4211               } catch (Exception e)
4212               {
4213                 Cache.log
4214                         .debug("Exception during web service menu building process.",
4215                                 e);
4216               }
4217             }
4218           });
4219         } catch (Exception e)
4220         {
4221         }
4222         buildingMenu = false;
4223       }
4224     }).start();
4225
4226   }
4227
4228   /**
4229    * construct any groupURL type service menu entries.
4230    *
4231    * @param webService
4232    */
4233   private void build_urlServiceMenu(JMenu webService)
4234   {
4235     // TODO: remove this code when 2.7 is released
4236     // DEBUG - alignmentView
4237     /*
4238      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4239      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4240      *
4241      * @Override public void actionPerformed(ActionEvent e) {
4242      * jalview.datamodel.AlignmentView
4243      * .testSelectionViews(af.viewport.getAlignment(),
4244      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4245      *
4246      * }); webService.add(testAlView);
4247      */
4248     // TODO: refactor to RestClient discoverer and merge menu entries for
4249     // rest-style services with other types of analysis/calculation service
4250     // SHmmr test client - still being implemented.
4251     // DEBUG - alignmentView
4252
4253     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4254             .getRestClients())
4255     {
4256       client.attachWSMenuEntry(
4257               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4258               this);
4259     }
4260   }
4261
4262   /**
4263    * Searches the alignment sequences for xRefs and builds the Show
4264    * Cross-References menu (formerly called Show Products), with database
4265    * sources for which cross-references are found (protein sources for a
4266    * nucleotide alignment and vice versa)
4267    *
4268    * @return true if Show Cross-references menu should be enabled
4269    */
4270   public boolean canShowProducts()
4271   {
4272     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4273     AlignmentI dataset = viewport.getAlignment().getDataset();
4274
4275     showProducts.removeAll();
4276     final boolean dna = viewport.getAlignment().isNucleotide();
4277
4278     if (seqs == null || seqs.length == 0)
4279     {
4280       // nothing to see here.
4281       return false;
4282     }
4283
4284     boolean showp = false;
4285     try
4286     {
4287       List<String> ptypes = new CrossRef(seqs, dataset)
4288               .findXrefSourcesForSequences(dna);
4289
4290       for (final String source : ptypes)
4291       {
4292         showp = true;
4293         final AlignFrame af = this;
4294         JMenuItem xtype = new JMenuItem(source);
4295         xtype.addActionListener(new ActionListener()
4296         {
4297           @Override
4298           public void actionPerformed(ActionEvent e)
4299           {
4300             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4301           }
4302         });
4303         showProducts.add(xtype);
4304       }
4305       showProducts.setVisible(showp);
4306       showProducts.setEnabled(showp);
4307     } catch (Exception e)
4308     {
4309       Cache.log
4310               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4311                       e);
4312       return false;
4313     }
4314     return showp;
4315   }
4316
4317   /**
4318    * Finds and displays cross-references for the selected sequences (protein
4319    * products for nucleotide sequences, dna coding sequences for peptides).
4320    *
4321    * @param sel
4322    *          the sequences to show cross-references for
4323    * @param dna
4324    *          true if from a nucleotide alignment (so showing proteins)
4325    * @param source
4326    *          the database to show cross-references for
4327    */
4328   protected void showProductsFor(final SequenceI[] sel,
4329           final boolean _odna, final String source)
4330   {
4331     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4332             .start();
4333   }
4334
4335   /**
4336    * Construct and display a new frame containing the translation of this
4337    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4338    */
4339   @Override
4340   public void showTranslation_actionPerformed(ActionEvent e)
4341   {
4342     AlignmentI al = null;
4343     try
4344     {
4345       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4346
4347       al = dna.translateCdna();
4348     } catch (Exception ex)
4349     {
4350       jalview.bin.Cache.log.error(
4351               "Exception during translation. Please report this !", ex);
4352       final String msg = MessageManager
4353               .getString("label.error_when_translating_sequences_submit_bug_report");
4354       final String errorTitle = MessageManager
4355               .getString("label.implementation_error")
4356               + MessageManager.getString("label.translation_failed");
4357       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4358               JvOptionPane.ERROR_MESSAGE);
4359       return;
4360     }
4361     if (al == null || al.getHeight() == 0)
4362     {
4363       final String msg = MessageManager
4364               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4365       final String errorTitle = MessageManager
4366               .getString("label.translation_failed");
4367       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4368               JvOptionPane.WARNING_MESSAGE);
4369     }
4370     else
4371     {
4372       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4373       af.setFileFormat(this.currentFileFormat);
4374       final String newTitle = MessageManager.formatMessage(
4375               "label.translation_of_params",
4376               new Object[] { this.getTitle() });
4377       af.setTitle(newTitle);
4378       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4379       {
4380         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4381         viewport.openSplitFrame(af, new Alignment(seqs));
4382       }
4383       else
4384       {
4385         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4386                 DEFAULT_HEIGHT);
4387       }
4388     }
4389   }
4390
4391   /**
4392    * Set the file format
4393    *
4394    * @param format
4395    */
4396   public void setFileFormat(FileFormatI format)
4397   {
4398     this.currentFileFormat = format;
4399   }
4400
4401   /**
4402    * Try to load a features file onto the alignment.
4403    *
4404    * @param file
4405    *          contents or path to retrieve file
4406    * @param sourceType
4407    *          access mode of file (see jalview.io.AlignFile)
4408    * @return true if features file was parsed correctly.
4409    */
4410   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4411   {
4412     return avc.parseFeaturesFile(file, sourceType,
4413             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4414
4415   }
4416
4417   @Override
4418   public void refreshFeatureUI(boolean enableIfNecessary)
4419   {
4420     // note - currently this is only still here rather than in the controller
4421     // because of the featureSettings hard reference that is yet to be
4422     // abstracted
4423     if (enableIfNecessary)
4424     {
4425       viewport.setShowSequenceFeatures(true);
4426       showSeqFeatures.setSelected(true);
4427     }
4428
4429   }
4430
4431   @Override
4432   public void dragEnter(DropTargetDragEvent evt)
4433   {
4434   }
4435
4436   @Override
4437   public void dragExit(DropTargetEvent evt)
4438   {
4439   }
4440
4441   @Override
4442   public void dragOver(DropTargetDragEvent evt)
4443   {
4444   }
4445
4446   @Override
4447   public void dropActionChanged(DropTargetDragEvent evt)
4448   {
4449   }
4450
4451   @Override
4452   public void drop(DropTargetDropEvent evt)
4453   {
4454     // JAL-1552 - acceptDrop required before getTransferable call for
4455     // Java's Transferable for native dnd
4456     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4457     Transferable t = evt.getTransferable();
4458     List<String> files = new ArrayList<String>();
4459     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4460
4461     try
4462     {
4463       Desktop.transferFromDropTarget(files, protocols, evt, t);
4464     } catch (Exception e)
4465     {
4466       e.printStackTrace();
4467     }
4468     if (files != null)
4469     {
4470       try
4471       {
4472         // check to see if any of these files have names matching sequences in
4473         // the alignment
4474         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4475                 .getAlignment().getSequencesArray());
4476         /**
4477          * Object[] { String,SequenceI}
4478          */
4479         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4480         ArrayList<String> filesnotmatched = new ArrayList<String>();
4481         for (int i = 0; i < files.size(); i++)
4482         {
4483           String file = files.get(i).toString();
4484           String pdbfn = "";
4485           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4486           if (protocol == DataSourceType.FILE)
4487           {
4488             File fl = new File(file);
4489             pdbfn = fl.getName();
4490           }
4491           else if (protocol == DataSourceType.URL)
4492           {
4493             URL url = new URL(file);
4494             pdbfn = url.getFile();
4495           }
4496           if (pdbfn.length() > 0)
4497           {
4498             // attempt to find a match in the alignment
4499             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4500             int l = 0, c = pdbfn.indexOf(".");
4501             while (mtch == null && c != -1)
4502             {
4503               do
4504               {
4505                 l = c;
4506               } while ((c = pdbfn.indexOf(".", l)) > l);
4507               if (l > -1)
4508               {
4509                 pdbfn = pdbfn.substring(0, l);
4510               }
4511               mtch = idm.findAllIdMatches(pdbfn);
4512             }
4513             if (mtch != null)
4514             {
4515               FileFormatI type = null;
4516               try
4517               {
4518                 type = new IdentifyFile().identify(file, protocol);
4519               } catch (Exception ex)
4520               {
4521                 type = null;
4522               }
4523               if (type != null && type.isStructureFile())
4524               {
4525                 filesmatched.add(new Object[] { file, protocol, mtch });
4526                 continue;
4527               }
4528             }
4529             // File wasn't named like one of the sequences or wasn't a PDB file.
4530             filesnotmatched.add(file);
4531           }
4532         }
4533         int assocfiles = 0;
4534         if (filesmatched.size() > 0)
4535         {
4536           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4537                   || JvOptionPane
4538                           .showConfirmDialog(
4539                                   this,
4540                                   MessageManager
4541                                           .formatMessage(
4542                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4543                                                   new Object[] { Integer
4544                                                           .valueOf(
4545                                                                   filesmatched
4546                                                                           .size())
4547                                                           .toString() }),
4548                                   MessageManager
4549                                           .getString("label.automatically_associate_structure_files_by_name"),
4550                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4551
4552           {
4553             for (Object[] fm : filesmatched)
4554             {
4555               // try and associate
4556               // TODO: may want to set a standard ID naming formalism for
4557               // associating PDB files which have no IDs.
4558               for (SequenceI toassoc : (SequenceI[]) fm[2])
4559               {
4560                 PDBEntry pe = new AssociatePdbFileWithSeq()
4561                         .associatePdbWithSeq((String) fm[0],
4562                                 (DataSourceType) fm[1], toassoc, false,
4563                                 Desktop.instance);
4564                 if (pe != null)
4565                 {
4566                   System.err.println("Associated file : "
4567                           + ((String) fm[0]) + " with "
4568                           + toassoc.getDisplayId(true));
4569                   assocfiles++;
4570                 }
4571               }
4572               alignPanel.paintAlignment(true);
4573             }
4574           }
4575         }
4576         if (filesnotmatched.size() > 0)
4577         {
4578           if (assocfiles > 0
4579                   && (Cache.getDefault(
4580                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4581                           .showConfirmDialog(
4582                                   this,
4583                                   "<html>"
4584                                           + MessageManager
4585                                                   .formatMessage(
4586                                                           "label.ignore_unmatched_dropped_files_info",
4587                                                           new Object[] { Integer
4588                                                                   .valueOf(
4589                                                                           filesnotmatched
4590                                                                                   .size())
4591                                                                   .toString() })
4592                                           + "</html>",
4593                                   MessageManager
4594                                           .getString("label.ignore_unmatched_dropped_files"),
4595                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4596           {
4597             return;
4598           }
4599           for (String fn : filesnotmatched)
4600           {
4601             loadJalviewDataFile(fn, null, null, null);
4602           }
4603
4604         }
4605       } catch (Exception ex)
4606       {
4607         ex.printStackTrace();
4608       }
4609     }
4610   }
4611
4612   /**
4613    * Attempt to load a "dropped" file or URL string, by testing in turn for
4614    * <ul>
4615    * <li>an Annotation file</li>
4616    * <li>a JNet file</li>
4617    * <li>a features file</li>
4618    * <li>else try to interpret as an alignment file</li>
4619    * </ul>
4620    *
4621    * @param file
4622    *          either a filename or a URL string.
4623    */
4624   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4625           FileFormatI format, SequenceI assocSeq)
4626   {
4627     try
4628     {
4629       if (sourceType == null)
4630       {
4631         sourceType = FormatAdapter.checkProtocol(file);
4632       }
4633       // if the file isn't identified, or not positively identified as some
4634       // other filetype (PFAM is default unidentified alignment file type) then
4635       // try to parse as annotation.
4636       boolean isAnnotation = (format == null || FileFormat.Pfam
4637               .equals(format)) ? new AnnotationFile()
4638               .annotateAlignmentView(viewport, file, sourceType) : false;
4639
4640       if (!isAnnotation)
4641       {
4642         // first see if its a T-COFFEE score file
4643         TCoffeeScoreFile tcf = null;
4644         try
4645         {
4646           tcf = new TCoffeeScoreFile(file, sourceType);
4647           if (tcf.isValid())
4648           {
4649             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4650             {
4651               buildColourMenu();
4652               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4653               isAnnotation = true;
4654               statusBar
4655                       .setText(MessageManager
4656                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4657             }
4658             else
4659             {
4660               // some problem - if no warning its probable that the ID matching
4661               // process didn't work
4662               JvOptionPane
4663                       .showMessageDialog(
4664                               Desktop.desktop,
4665                               tcf.getWarningMessage() == null ? MessageManager
4666                                       .getString("label.check_file_matches_sequence_ids_alignment")
4667                                       : tcf.getWarningMessage(),
4668                               MessageManager
4669                                       .getString("label.problem_reading_tcoffee_score_file"),
4670                               JvOptionPane.WARNING_MESSAGE);
4671             }
4672           }
4673           else
4674           {
4675             tcf = null;
4676           }
4677         } catch (Exception x)
4678         {
4679           Cache.log
4680                   .debug("Exception when processing data source as T-COFFEE score file",
4681                           x);
4682           tcf = null;
4683         }
4684         if (tcf == null)
4685         {
4686           // try to see if its a JNet 'concise' style annotation file *before*
4687           // we
4688           // try to parse it as a features file
4689           if (format == null)
4690           {
4691             format = new IdentifyFile().identify(file, sourceType);
4692           }
4693           if (FileFormat.ScoreMatrix == format)
4694           {
4695             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4696                     sourceType));
4697             sm.parse();
4698             // todo: i18n this message
4699             statusBar
4700                     .setText(MessageManager.formatMessage(
4701                             "label.successfully_loaded_matrix",
4702                             sm.getMatrixName()));
4703           }
4704           else if (FileFormat.Jnet.equals(format))
4705           {
4706             JPredFile predictions = new JPredFile(file, sourceType);
4707             new JnetAnnotationMaker();
4708             JnetAnnotationMaker.add_annotation(predictions,
4709                     viewport.getAlignment(), 0, false);
4710             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4711             viewport.getAlignment().setSeqrep(repseq);
4712             ColumnSelection cs = new ColumnSelection();
4713             cs.hideInsertionsFor(repseq);
4714             viewport.setColumnSelection(cs);
4715             isAnnotation = true;
4716           }
4717           // else if (IdentifyFile.FeaturesFile.equals(format))
4718           else if (FileFormat.Features.equals(format))
4719           {
4720             if (parseFeaturesFile(file, sourceType))
4721             {
4722               alignPanel.paintAlignment(true);
4723             }
4724           }
4725           else
4726           {
4727             new FileLoader().LoadFile(viewport, file, sourceType, format);
4728           }
4729         }
4730       }
4731       if (isAnnotation)
4732       {
4733
4734         alignPanel.adjustAnnotationHeight();
4735         viewport.updateSequenceIdColours();
4736         buildSortByAnnotationScoresMenu();
4737         alignPanel.paintAlignment(true);
4738       }
4739     } catch (Exception ex)
4740     {
4741       ex.printStackTrace();
4742     } catch (OutOfMemoryError oom)
4743     {
4744       try
4745       {
4746         System.gc();
4747       } catch (Exception x)
4748       {
4749       }
4750       new OOMWarning(
4751               "loading data "
4752                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4753                               : "using " + sourceType + " from " + file)
4754                               : ".")
4755                       + (format != null ? "(parsing as '" + format
4756                               + "' file)" : ""), oom, Desktop.desktop);
4757     }
4758   }
4759
4760   /**
4761    * Method invoked by the ChangeListener on the tabbed pane, in other words
4762    * when a different tabbed pane is selected by the user or programmatically.
4763    */
4764   @Override
4765   public void tabSelectionChanged(int index)
4766   {
4767     if (index > -1)
4768     {
4769       alignPanel = alignPanels.get(index);
4770       viewport = alignPanel.av;
4771       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4772       setMenusFromViewport(viewport);
4773     }
4774
4775     /*
4776      * 'focus' any colour slider that is open to the selected viewport
4777      */
4778     if (viewport.getConservationSelected())
4779     {
4780       SliderPanel.setConservationSlider(alignPanel,
4781               viewport.getResidueShading(), alignPanel.getViewName());
4782     }
4783     else
4784     {
4785       SliderPanel.hideConservationSlider();
4786     }
4787     if (viewport.getAbovePIDThreshold())
4788     {
4789       SliderPanel.setPIDSliderSource(alignPanel,
4790               viewport.getResidueShading(), alignPanel.getViewName());
4791     }
4792     else
4793     {
4794       SliderPanel.hidePIDSlider();
4795     }
4796
4797     /*
4798      * If there is a frame linked to this one in a SplitPane, switch it to the
4799      * same view tab index. No infinite recursion of calls should happen, since
4800      * tabSelectionChanged() should not get invoked on setting the selected
4801      * index to an unchanged value. Guard against setting an invalid index
4802      * before the new view peer tab has been created.
4803      */
4804     final AlignViewportI peer = viewport.getCodingComplement();
4805     if (peer != null)
4806     {
4807       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4808       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4809       {
4810         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4811       }
4812     }
4813   }
4814
4815   /**
4816    * On right mouse click on view tab, prompt for and set new view name.
4817    */
4818   @Override
4819   public void tabbedPane_mousePressed(MouseEvent e)
4820   {
4821     if (e.isPopupTrigger())
4822     {
4823       String msg = MessageManager.getString("label.enter_view_name");
4824       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4825               JvOptionPane.QUESTION_MESSAGE);
4826
4827       if (reply != null)
4828       {
4829         viewport.viewName = reply;
4830         // TODO warn if reply is in getExistingViewNames()?
4831         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4832       }
4833     }
4834   }
4835
4836   public AlignViewport getCurrentView()
4837   {
4838     return viewport;
4839   }
4840
4841   /**
4842    * Open the dialog for regex description parsing.
4843    */
4844   @Override
4845   protected void extractScores_actionPerformed(ActionEvent e)
4846   {
4847     ParseProperties pp = new jalview.analysis.ParseProperties(
4848             viewport.getAlignment());
4849     // TODO: verify regex and introduce GUI dialog for version 2.5
4850     // if (pp.getScoresFromDescription("col", "score column ",
4851     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4852     // true)>0)
4853     if (pp.getScoresFromDescription("description column",
4854             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4855     {
4856       buildSortByAnnotationScoresMenu();
4857     }
4858   }
4859
4860   /*
4861    * (non-Javadoc)
4862    *
4863    * @see
4864    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4865    * )
4866    */
4867   @Override
4868   protected void showDbRefs_actionPerformed(ActionEvent e)
4869   {
4870     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4871   }
4872
4873   /*
4874    * (non-Javadoc)
4875    *
4876    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4877    * ActionEvent)
4878    */
4879   @Override
4880   protected void showNpFeats_actionPerformed(ActionEvent e)
4881   {
4882     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4883   }
4884
4885   /**
4886    * find the viewport amongst the tabs in this alignment frame and close that
4887    * tab
4888    *
4889    * @param av
4890    */
4891   public boolean closeView(AlignViewportI av)
4892   {
4893     if (viewport == av)
4894     {
4895       this.closeMenuItem_actionPerformed(false);
4896       return true;
4897     }
4898     Component[] comp = tabbedPane.getComponents();
4899     for (int i = 0; comp != null && i < comp.length; i++)
4900     {
4901       if (comp[i] instanceof AlignmentPanel)
4902       {
4903         if (((AlignmentPanel) comp[i]).av == av)
4904         {
4905           // close the view.
4906           closeView((AlignmentPanel) comp[i]);
4907           return true;
4908         }
4909       }
4910     }
4911     return false;
4912   }
4913
4914   protected void build_fetchdbmenu(JMenu webService)
4915   {
4916     // Temporary hack - DBRef Fetcher always top level ws entry.
4917     // TODO We probably want to store a sequence database checklist in
4918     // preferences and have checkboxes.. rather than individual sources selected
4919     // here
4920     final JMenu rfetch = new JMenu(
4921             MessageManager.getString("action.fetch_db_references"));
4922     rfetch.setToolTipText(MessageManager
4923             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4924     webService.add(rfetch);
4925
4926     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4927             MessageManager.getString("option.trim_retrieved_seqs"));
4928     trimrs.setToolTipText(MessageManager
4929             .getString("label.trim_retrieved_sequences"));
4930     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4931     trimrs.addActionListener(new ActionListener()
4932     {
4933       @Override
4934       public void actionPerformed(ActionEvent e)
4935       {
4936         trimrs.setSelected(trimrs.isSelected());
4937         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4938                 Boolean.valueOf(trimrs.isSelected()).toString());
4939       };
4940     });
4941     rfetch.add(trimrs);
4942     JMenuItem fetchr = new JMenuItem(
4943             MessageManager.getString("label.standard_databases"));
4944     fetchr.setToolTipText(MessageManager
4945             .getString("label.fetch_embl_uniprot"));
4946     fetchr.addActionListener(new ActionListener()
4947     {
4948
4949       @Override
4950       public void actionPerformed(ActionEvent e)
4951       {
4952         new Thread(new Runnable()
4953         {
4954           @Override
4955           public void run()
4956           {
4957             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4958                     .getAlignment().isNucleotide();
4959             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4960                     .getSequenceSelection(), alignPanel.alignFrame, null,
4961                     alignPanel.alignFrame.featureSettings, isNucleotide);
4962             dbRefFetcher.addListener(new FetchFinishedListenerI()
4963             {
4964               @Override
4965               public void finished()
4966               {
4967                 AlignFrame.this.setMenusForViewport();
4968               }
4969             });
4970             dbRefFetcher.fetchDBRefs(false);
4971           }
4972         }).start();
4973
4974       }
4975
4976     });
4977     rfetch.add(fetchr);
4978     final AlignFrame me = this;
4979     new Thread(new Runnable()
4980     {
4981       @Override
4982       public void run()
4983       {
4984         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4985                 .getSequenceFetcherSingleton(me);
4986         javax.swing.SwingUtilities.invokeLater(new Runnable()
4987         {
4988           @Override
4989           public void run()
4990           {
4991             String[] dbclasses = sf.getOrderedSupportedSources();
4992             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4993             // jalview.util.QuickSort.sort(otherdb, otherdb);
4994             List<DbSourceProxy> otherdb;
4995             JMenu dfetch = new JMenu();
4996             JMenu ifetch = new JMenu();
4997             JMenuItem fetchr = null;
4998             int comp = 0, icomp = 0, mcomp = 15;
4999             String mname = null;
5000             int dbi = 0;
5001             for (String dbclass : dbclasses)
5002             {
5003               otherdb = sf.getSourceProxy(dbclass);
5004               // add a single entry for this class, or submenu allowing 'fetch
5005               // all' or pick one
5006               if (otherdb == null || otherdb.size() < 1)
5007               {
5008                 continue;
5009               }
5010               // List<DbSourceProxy> dbs=otherdb;
5011               // otherdb=new ArrayList<DbSourceProxy>();
5012               // for (DbSourceProxy db:dbs)
5013               // {
5014               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5015               // }
5016               if (mname == null)
5017               {
5018                 mname = "From " + dbclass;
5019               }
5020               if (otherdb.size() == 1)
5021               {
5022                 final DbSourceProxy[] dassource = otherdb
5023                         .toArray(new DbSourceProxy[0]);
5024                 DbSourceProxy src = otherdb.get(0);
5025                 fetchr = new JMenuItem(src.getDbSource());
5026                 fetchr.addActionListener(new ActionListener()
5027                 {
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",
5064                                 new Object[] { src.getDbName() })));
5065                 dfetch.add(fetchr);
5066                 comp++;
5067               }
5068               else
5069               {
5070                 final DbSourceProxy[] dassource = otherdb
5071                         .toArray(new DbSourceProxy[0]);
5072                 // fetch all entry
5073                 DbSourceProxy src = otherdb.get(0);
5074                 fetchr = new JMenuItem(MessageManager.formatMessage(
5075                         "label.fetch_all_param",
5076                         new Object[] { src.getDbSource() }));
5077                 fetchr.addActionListener(new ActionListener()
5078                 {
5079                   @Override
5080                   public void actionPerformed(ActionEvent e)
5081                   {
5082                     new Thread(new Runnable()
5083                     {
5084
5085                       @Override
5086                       public void run()
5087                       {
5088                         boolean isNucleotide = alignPanel.alignFrame
5089                                 .getViewport().getAlignment()
5090                                 .isNucleotide();
5091                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5092                                 alignPanel.av.getSequenceSelection(),
5093                                 alignPanel.alignFrame, dassource,
5094                                 alignPanel.alignFrame.featureSettings,
5095                                 isNucleotide);
5096                         dbRefFetcher
5097                                 .addListener(new FetchFinishedListenerI()
5098                                 {
5099                                   @Override
5100                                   public void finished()
5101                                   {
5102                                     AlignFrame.this.setMenusForViewport();
5103                                   }
5104                                 });
5105                         dbRefFetcher.fetchDBRefs(false);
5106                       }
5107                     }).start();
5108                   }
5109                 });
5110
5111                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5112                         MessageManager.formatMessage(
5113                                 "label.fetch_retrieve_from_all_sources",
5114                                 new Object[] {
5115                                     Integer.valueOf(otherdb.size())
5116                                             .toString(), src.getDbSource(),
5117                                     src.getDbName() })));
5118                 dfetch.add(fetchr);
5119                 comp++;
5120                 // and then build the rest of the individual menus
5121                 ifetch = new JMenu(MessageManager.formatMessage(
5122                         "label.source_from_db_source",
5123                         new Object[] { src.getDbSource() }));
5124                 icomp = 0;
5125                 String imname = null;
5126                 int i = 0;
5127                 for (DbSourceProxy sproxy : otherdb)
5128                 {
5129                   String dbname = sproxy.getDbName();
5130                   String sname = dbname.length() > 5 ? dbname.substring(0,
5131                           5) + "..." : dbname;
5132                   String msname = dbname.length() > 10 ? dbname.substring(
5133                           0, 10) + "..." : dbname;
5134                   if (imname == null)
5135                   {
5136                     imname = MessageManager.formatMessage(
5137                             "label.from_msname", new Object[] { sname });
5138                   }
5139                   fetchr = new JMenuItem(msname);
5140                   final DbSourceProxy[] dassrc = { sproxy };
5141                   fetchr.addActionListener(new ActionListener()
5142                   {
5143
5144                     @Override
5145                     public void actionPerformed(ActionEvent e)
5146                     {
5147                       new Thread(new Runnable()
5148                       {
5149
5150                         @Override
5151                         public void run()
5152                         {
5153                           boolean isNucleotide = alignPanel.alignFrame
5154                                   .getViewport().getAlignment()
5155                                   .isNucleotide();
5156                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5157                                   alignPanel.av.getSequenceSelection(),
5158                                   alignPanel.alignFrame, dassrc,
5159                                   alignPanel.alignFrame.featureSettings,
5160                                   isNucleotide);
5161                           dbRefFetcher
5162                                   .addListener(new FetchFinishedListenerI()
5163                                   {
5164                                     @Override
5165                                     public void finished()
5166                                     {
5167                                       AlignFrame.this.setMenusForViewport();
5168                                     }
5169                                   });
5170                           dbRefFetcher.fetchDBRefs(false);
5171                         }
5172                       }).start();
5173                     }
5174
5175                   });
5176                   fetchr.setToolTipText("<html>"
5177                           + MessageManager.formatMessage(
5178                                   "label.fetch_retrieve_from", new Object[]
5179                                   { dbname }));
5180                   ifetch.add(fetchr);
5181                   ++i;
5182                   if (++icomp >= mcomp || i == (otherdb.size()))
5183                   {
5184                     ifetch.setText(MessageManager.formatMessage(
5185                             "label.source_to_target", imname, sname));
5186                     dfetch.add(ifetch);
5187                     ifetch = new JMenu();
5188                     imname = null;
5189                     icomp = 0;
5190                     comp++;
5191                   }
5192                 }
5193               }
5194               ++dbi;
5195               if (comp >= mcomp || dbi >= (dbclasses.length))
5196               {
5197                 dfetch.setText(MessageManager.formatMessage(
5198                         "label.source_to_target", mname, dbclass));
5199                 rfetch.add(dfetch);
5200                 dfetch = new JMenu();
5201                 mname = null;
5202                 comp = 0;
5203               }
5204             }
5205           }
5206         });
5207       }
5208     }).start();
5209
5210   }
5211
5212   /**
5213    * Left justify the whole alignment.
5214    */
5215   @Override
5216   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5217   {
5218     AlignmentI al = viewport.getAlignment();
5219     al.justify(false);
5220     viewport.firePropertyChange("alignment", null, al);
5221   }
5222
5223   /**
5224    * Right justify the whole alignment.
5225    */
5226   @Override
5227   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5228   {
5229     AlignmentI al = viewport.getAlignment();
5230     al.justify(true);
5231     viewport.firePropertyChange("alignment", null, al);
5232   }
5233
5234   @Override
5235   public void setShowSeqFeatures(boolean b)
5236   {
5237     showSeqFeatures.setSelected(b);
5238     viewport.setShowSequenceFeatures(b);
5239   }
5240
5241   /*
5242    * (non-Javadoc)
5243    *
5244    * @see
5245    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5246    * awt.event.ActionEvent)
5247    */
5248   @Override
5249   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5250   {
5251     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5252     alignPanel.paintAlignment(true);
5253   }
5254
5255   /*
5256    * (non-Javadoc)
5257    *
5258    * @see
5259    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5260    * .ActionEvent)
5261    */
5262   @Override
5263   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5264   {
5265     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5266     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5267
5268   }
5269
5270   /*
5271    * (non-Javadoc)
5272    *
5273    * @see
5274    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5275    * .event.ActionEvent)
5276    */
5277   @Override
5278   protected void showGroupConservation_actionPerformed(ActionEvent e)
5279   {
5280     viewport.setShowGroupConservation(showGroupConservation.getState());
5281     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5282   }
5283
5284   /*
5285    * (non-Javadoc)
5286    *
5287    * @see
5288    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5289    * .event.ActionEvent)
5290    */
5291   @Override
5292   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5293   {
5294     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5295     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5296   }
5297
5298   /*
5299    * (non-Javadoc)
5300    *
5301    * @see
5302    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5303    * .event.ActionEvent)
5304    */
5305   @Override
5306   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5307   {
5308     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5309     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310   }
5311
5312   @Override
5313   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5314   {
5315     showSequenceLogo.setState(true);
5316     viewport.setShowSequenceLogo(true);
5317     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5318     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5319   }
5320
5321   @Override
5322   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5323   {
5324     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5325   }
5326
5327   /*
5328    * (non-Javadoc)
5329    *
5330    * @see
5331    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5332    * .event.ActionEvent)
5333    */
5334   @Override
5335   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5336   {
5337     if (avc.makeGroupsFromSelection())
5338     {
5339       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5340       alignPanel.updateAnnotation();
5341       alignPanel.paintAlignment(true);
5342     }
5343   }
5344
5345   public void clearAlignmentSeqRep()
5346   {
5347     // TODO refactor alignmentseqrep to controller
5348     if (viewport.getAlignment().hasSeqrep())
5349     {
5350       viewport.getAlignment().setSeqrep(null);
5351       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5352       alignPanel.updateAnnotation();
5353       alignPanel.paintAlignment(true);
5354     }
5355   }
5356
5357   @Override
5358   protected void createGroup_actionPerformed(ActionEvent e)
5359   {
5360     if (avc.createGroup())
5361     {
5362       alignPanel.alignmentChanged();
5363     }
5364   }
5365
5366   @Override
5367   protected void unGroup_actionPerformed(ActionEvent e)
5368   {
5369     if (avc.unGroup())
5370     {
5371       alignPanel.alignmentChanged();
5372     }
5373   }
5374
5375   /**
5376    * make the given alignmentPanel the currently selected tab
5377    *
5378    * @param alignmentPanel
5379    */
5380   public void setDisplayedView(AlignmentPanel alignmentPanel)
5381   {
5382     if (!viewport.getSequenceSetId().equals(
5383             alignmentPanel.av.getSequenceSetId()))
5384     {
5385       throw new Error(
5386               MessageManager
5387                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5388     }
5389     if (tabbedPane != null
5390             && tabbedPane.getTabCount() > 0
5391             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5392                     .getSelectedIndex())
5393     {
5394       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5395     }
5396   }
5397
5398   /**
5399    * Action on selection of menu options to Show or Hide annotations.
5400    *
5401    * @param visible
5402    * @param forSequences
5403    *          update sequence-related annotations
5404    * @param forAlignment
5405    *          update non-sequence-related annotations
5406    */
5407   @Override
5408   protected void setAnnotationsVisibility(boolean visible,
5409           boolean forSequences, boolean forAlignment)
5410   {
5411     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5412             .getAlignmentAnnotation();
5413     if (anns == null)
5414     {
5415       return;
5416     }
5417     for (AlignmentAnnotation aa : anns)
5418     {
5419       /*
5420        * don't display non-positional annotations on an alignment
5421        */
5422       if (aa.annotations == null)
5423       {
5424         continue;
5425       }
5426       boolean apply = (aa.sequenceRef == null && forAlignment)
5427               || (aa.sequenceRef != null && forSequences);
5428       if (apply)
5429       {
5430         aa.visible = visible;
5431       }
5432     }
5433     alignPanel.validateAnnotationDimensions(true);
5434     alignPanel.alignmentChanged();
5435   }
5436
5437   /**
5438    * Store selected annotation sort order for the view and repaint.
5439    */
5440   @Override
5441   protected void sortAnnotations_actionPerformed()
5442   {
5443     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5444     this.alignPanel.av
5445             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5446     alignPanel.paintAlignment(true);
5447   }
5448
5449   /**
5450    *
5451    * @return alignment panels in this alignment frame
5452    */
5453   public List<? extends AlignmentViewPanel> getAlignPanels()
5454   {
5455     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5456   }
5457
5458   /**
5459    * Open a new alignment window, with the cDNA associated with this (protein)
5460    * alignment, aligned as is the protein.
5461    */
5462   protected void viewAsCdna_actionPerformed()
5463   {
5464     // TODO no longer a menu action - refactor as required
5465     final AlignmentI alignment = getViewport().getAlignment();
5466     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5467     if (mappings == null)
5468     {
5469       return;
5470     }
5471     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5472     for (SequenceI aaSeq : alignment.getSequences())
5473     {
5474       for (AlignedCodonFrame acf : mappings)
5475       {
5476         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5477         if (dnaSeq != null)
5478         {
5479           /*
5480            * There is a cDNA mapping for this protein sequence - add to new
5481            * alignment. It will share the same dataset sequence as other mapped
5482            * cDNA (no new mappings need to be created).
5483            */
5484           final Sequence newSeq = new Sequence(dnaSeq);
5485           newSeq.setDatasetSequence(dnaSeq);
5486           cdnaSeqs.add(newSeq);
5487         }
5488       }
5489     }
5490     if (cdnaSeqs.size() == 0)
5491     {
5492       // show a warning dialog no mapped cDNA
5493       return;
5494     }
5495     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5496             .size()]));
5497     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5498             AlignFrame.DEFAULT_HEIGHT);
5499     cdna.alignAs(alignment);
5500     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5501             + this.title;
5502     Desktop.addInternalFrame(alignFrame, newtitle,
5503             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5504   }
5505
5506   /**
5507    * Set visibility of dna/protein complement view (available when shown in a
5508    * split frame).
5509    *
5510    * @param show
5511    */
5512   @Override
5513   protected void showComplement_actionPerformed(boolean show)
5514   {
5515     SplitContainerI sf = getSplitViewContainer();
5516     if (sf != null)
5517     {
5518       sf.setComplementVisible(this, show);
5519     }
5520   }
5521
5522   /**
5523    * Generate the reverse (optionally complemented) of the selected sequences,
5524    * and add them to the alignment
5525    */
5526   @Override
5527   protected void showReverse_actionPerformed(boolean complement)
5528   {
5529     AlignmentI al = null;
5530     try
5531     {
5532       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5533       al = dna.reverseCdna(complement);
5534       viewport.addAlignment(al, "");
5535       addHistoryItem(new EditCommand(
5536               MessageManager.getString("label.add_sequences"),
5537               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5538               viewport.getAlignment()));
5539     } catch (Exception ex)
5540     {
5541       System.err.println(ex.getMessage());
5542       return;
5543     }
5544   }
5545
5546   /**
5547    * Try to run a script in the Groovy console, having first ensured that this
5548    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5549    * be targeted at this alignment.
5550    */
5551   @Override
5552   protected void runGroovy_actionPerformed()
5553   {
5554     Jalview.setCurrentAlignFrame(this);
5555     groovy.ui.Console console = Desktop.getGroovyConsole();
5556     if (console != null)
5557     {
5558       try
5559       {
5560         console.runScript();
5561       } catch (Exception ex)
5562       {
5563         System.err.println((ex.toString()));
5564         JvOptionPane
5565                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5566                         .getString("label.couldnt_run_groovy_script"),
5567                         MessageManager
5568                                 .getString("label.groovy_support_failed"),
5569                         JvOptionPane.ERROR_MESSAGE);
5570       }
5571     }
5572     else
5573     {
5574       System.err.println("Can't run Groovy script as console not found");
5575     }
5576   }
5577
5578   /**
5579    * Hides columns containing (or not containing) a specified feature, provided
5580    * that would not leave all columns hidden
5581    *
5582    * @param featureType
5583    * @param columnsContaining
5584    * @return
5585    */
5586   public boolean hideFeatureColumns(String featureType,
5587           boolean columnsContaining)
5588   {
5589     boolean notForHiding = avc.markColumnsContainingFeatures(
5590             columnsContaining, false, false, featureType);
5591     if (notForHiding)
5592     {
5593       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5594               false, featureType))
5595       {
5596         getViewport().hideSelectedColumns();
5597         return true;
5598       }
5599     }
5600     return false;
5601   }
5602
5603   @Override
5604   protected void selectHighlightedColumns_actionPerformed(
5605           ActionEvent actionEvent)
5606   {
5607     // include key modifier check in case user selects from menu
5608     avc.markHighlightedColumns(
5609             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5610             true,
5611             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5612   }
5613
5614   /**
5615    * Rebuilds the Colour menu, including any user-defined colours which have
5616    * been loaded either on startup or during the session
5617    */
5618   public void buildColourMenu()
5619   {
5620     colourMenu.removeAll();
5621
5622     colourMenu.add(applyToAllGroups);
5623     colourMenu.add(textColour);
5624     colourMenu.addSeparator();
5625
5626     ColourMenuHelper.addMenuItems(colourMenu, this,
5627             viewport.getAlignment(), false);
5628
5629     colourMenu.addSeparator();
5630     colourMenu.add(conservationMenuItem);
5631     colourMenu.add(modifyConservation);
5632     colourMenu.add(abovePIDThreshold);
5633     colourMenu.add(modifyPID);
5634     colourMenu.add(annotationColour);
5635
5636     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5637     String schemeName = colourScheme == null ? null : colourScheme
5638             .getSchemeName();
5639
5640     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5641   }
5642 }
5643
5644 class PrintThread extends Thread
5645 {
5646   AlignmentPanel ap;
5647
5648   public PrintThread(AlignmentPanel ap)
5649   {
5650     this.ap = ap;
5651   }
5652
5653   static PageFormat pf;
5654
5655   @Override
5656   public void run()
5657   {
5658     PrinterJob printJob = PrinterJob.getPrinterJob();
5659
5660     if (pf != null)
5661     {
5662       printJob.setPrintable(ap, pf);
5663     }
5664     else
5665     {
5666       printJob.setPrintable(ap);
5667     }
5668
5669     if (printJob.printDialog())
5670     {
5671       try
5672       {
5673         printJob.print();
5674       } catch (Exception PrintException)
5675       {
5676         PrintException.printStackTrace();
5677       }
5678     }
5679   }
5680 }