src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenMarkovModel;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.hmmer.HMMAlign;
  67 import jalview.hmmer.HMMBuild;
  68 import jalview.hmmer.HMMERParamStore;
  69 import jalview.hmmer.HMMERPreset;
  70 import jalview.hmmer.HMMSearch;
  71 import jalview.hmmer.HmmerCommand;
  72 import jalview.io.AlignmentProperties;
  73 import jalview.io.AnnotationFile;
  74 import jalview.io.BioJsHTMLOutput;
  75 import jalview.io.DataSourceType;
  76 import jalview.io.FileFormat;
  77 import jalview.io.FileFormatI;
  78 import jalview.io.FileFormats;
  79 import jalview.io.FileLoader;
  80 import jalview.io.FileParse;
  81 import jalview.io.FormatAdapter;
  82 import jalview.io.HtmlSvgOutput;
  83 import jalview.io.IdentifyFile;
  84 import jalview.io.JPredFile;
  85 import jalview.io.JalviewFileChooser;
  86 import jalview.io.JalviewFileView;
  87 import jalview.io.JnetAnnotationMaker;
  88 import jalview.io.NewickFile;
  89 import jalview.io.ScoreMatrixFile;
  90 import jalview.io.TCoffeeScoreFile;
  91 import jalview.io.vcf.VCFLoader;
  92 import jalview.jbgui.GAlignFrame;
  93 import jalview.schemes.ColourSchemeI;
  94 import jalview.schemes.ColourSchemes;
  95 import jalview.schemes.ResidueColourScheme;
  96 import jalview.schemes.TCoffeeColourScheme;
  97 import jalview.util.MessageManager;
  98 import jalview.util.StringUtils;
  99 import jalview.viewmodel.AlignmentViewport;
 100 import jalview.viewmodel.ViewportRanges;
 101 import jalview.ws.DBRefFetcher;
 102 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 103 import jalview.ws.jws1.Discoverer;
 104 import jalview.ws.jws2.Jws2Discoverer;
 105 import jalview.ws.jws2.jabaws2.Jws2Instance;
 106 import jalview.ws.params.ArgumentI;
 107 import jalview.ws.params.ParamDatastoreI;
 108 import jalview.ws.params.WsParamSetI;
 109 import jalview.ws.seqfetcher.DbSourceProxy;
 110
 111 import java.awt.BorderLayout;
 112 import java.awt.Component;
 113 import java.awt.Rectangle;
 114 import java.awt.Toolkit;
 115 import java.awt.datatransfer.Clipboard;
 116 import java.awt.datatransfer.DataFlavor;
 117 import java.awt.datatransfer.StringSelection;
 118 import java.awt.datatransfer.Transferable;
 119 import java.awt.dnd.DnDConstants;
 120 import java.awt.dnd.DropTargetDragEvent;
 121 import java.awt.dnd.DropTargetDropEvent;
 122 import java.awt.dnd.DropTargetEvent;
 123 import java.awt.dnd.DropTargetListener;
 124 import java.awt.event.ActionEvent;
 125 import java.awt.event.ActionListener;
 126 import java.awt.event.FocusAdapter;
 127 import java.awt.event.FocusEvent;
 128 import java.awt.event.ItemEvent;
 129 import java.awt.event.ItemListener;
 130 import java.awt.event.KeyAdapter;
 131 import java.awt.event.KeyEvent;
 132 import java.awt.event.MouseEvent;
 133 import java.awt.print.PageFormat;
 134 import java.awt.print.PrinterJob;
 135 import java.beans.PropertyChangeEvent;
 136 import java.io.File;
 137 import java.io.FileWriter;
 138 import java.io.IOException;
 139 import java.io.PrintWriter;
 140 import java.net.URL;
 141 import java.util.ArrayList;
 142 import java.util.Arrays;
 143 import java.util.Deque;
 144 import java.util.Enumeration;
 145 import java.util.HashMap;
 146 import java.util.Hashtable;
 147 import java.util.List;
 148 import java.util.Map;
 149 import java.util.Scanner;
 150 import java.util.Vector;
 151
 152 import javax.swing.JCheckBoxMenuItem;
 153 import javax.swing.JEditorPane;
 154 import javax.swing.JFileChooser;
 155 import javax.swing.JFrame;
 156 import javax.swing.JInternalFrame;
 157 import javax.swing.JLayeredPane;
 158 import javax.swing.JMenu;
 159 import javax.swing.JMenuItem;
 160 import javax.swing.JOptionPane;
 161 import javax.swing.JScrollPane;
 162 import javax.swing.SwingUtilities;
 163
 164 /**
 165  * DOCUMENT ME!
 166  *
 167  * @author $author$
 168  * @version $Revision$
 169  */
 170 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 171         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 172 {
 173
 174   Map<String, Float> distribution = new HashMap<>(); // temporary
 175
 176   public static final int DEFAULT_WIDTH = 700;
 177
 178   public static final int DEFAULT_HEIGHT = 500;
 179
 180   /*
 181    * The currently displayed panel (selected tabbed view if more than one)
 182    */
 183   public AlignmentPanel alignPanel;
 184
 185   AlignViewport viewport;
 186
 187   public AlignViewControllerI avc;
 188   /*
 189    * The selected HMM for this align frame
 190    */
 191   SequenceI selectedHMMSequence;
 192
 193   List<AlignmentPanel> alignPanels = new ArrayList<>();
 194
 195   /**
 196    * Last format used to load or save alignments in this window
 197    */
 198   FileFormatI currentFileFormat = null;
 199
 200   /**
 201    * Current filename for this alignment
 202    */
 203   String fileName = null;
 204
 205
 206   /**
 207    * Creates a new AlignFrame object with specific width and height.
 208    *
 209    * @param al
 210    * @param width
 211    * @param height
 212    */
 213   public AlignFrame(AlignmentI al, int width, int height)
 214   {
 215     this(al, null, width, height);
 216   }
 217
 218   /**
 219    * Creates a new AlignFrame object with specific width, height and
 220    * sequenceSetId
 221    *
 222    * @param al
 223    * @param width
 224    * @param height
 225    * @param sequenceSetId
 226    */
 227   public AlignFrame(AlignmentI al, int width, int height,
 228           String sequenceSetId)
 229   {
 230     this(al, null, width, height, sequenceSetId);
 231   }
 232
 233   /**
 234    * Creates a new AlignFrame object with specific width, height and
 235    * sequenceSetId
 236    *
 237    * @param al
 238    * @param width
 239    * @param height
 240    * @param sequenceSetId
 241    * @param viewId
 242    */
 243   public AlignFrame(AlignmentI al, int width, int height,
 244           String sequenceSetId, String viewId)
 245   {
 246     this(al, null, width, height, sequenceSetId, viewId);
 247   }
 248
 249   /**
 250    * new alignment window with hidden columns
 251    *
 252    * @param al
 253    *          AlignmentI
 254    * @param hiddenColumns
 255    *          ColumnSelection or null
 256    * @param width
 257    *          Width of alignment frame
 258    * @param height
 259    *          height of frame.
 260    */
 261   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 262           int height)
 263   {
 264     this(al, hiddenColumns, width, height, null);
 265   }
 266
 267   /**
 268    * Create alignment frame for al with hiddenColumns, a specific width and
 269    * height, and specific sequenceId
 270    *
 271    * @param al
 272    * @param hiddenColumns
 273    * @param width
 274    * @param height
 275    * @param sequenceSetId
 276    *          (may be null)
 277    */
 278   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 279           int height, String sequenceSetId)
 280   {
 281     this(al, hiddenColumns, width, height, sequenceSetId, null);
 282   }
 283
 284   /**
 285    * Create alignment frame for al with hiddenColumns, a specific width and
 286    * height, and specific sequenceId
 287    *
 288    * @param al
 289    * @param hiddenColumns
 290    * @param width
 291    * @param height
 292    * @param sequenceSetId
 293    *          (may be null)
 294    * @param viewId
 295    *          (may be null)
 296    */
 297   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 298           int height, String sequenceSetId, String viewId)
 299   {
 300     setSize(width, height);
 301
 302     if (al.getDataset() == null)
 303     {
 304       al.setDataset(null);
 305     }
 306
 307     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 308
 309     alignPanel = new AlignmentPanel(this, viewport);
 310
 311     addAlignmentPanel(alignPanel, true);
 312     init();
 313   }
 314
 315   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 316           HiddenColumns hiddenColumns, int width, int height)
 317   {
 318     setSize(width, height);
 319
 320     if (al.getDataset() == null)
 321     {
 322       al.setDataset(null);
 323     }
 324
 325     viewport = new AlignViewport(al, hiddenColumns);
 326
 327     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 328     {
 329       viewport.hideSequence(hiddenSeqs);
 330     }
 331     alignPanel = new AlignmentPanel(this, viewport);
 332     addAlignmentPanel(alignPanel, true);
 333     init();
 334   }
 335
 336   /**
 337    * Make a new AlignFrame from existing alignmentPanels
 338    *
 339    * @param ap
 340    *          AlignmentPanel
 341    * @param av
 342    *          AlignViewport
 343    */
 344   public AlignFrame(AlignmentPanel ap)
 345   {
 346     viewport = ap.av;
 347     alignPanel = ap;
 348     addAlignmentPanel(ap, false);
 349     init();
 350   }
 351
 352   /**
 353    * initalise the alignframe from the underlying viewport data and the
 354    * configurations
 355    */
 356   void init()
 357   {
 358     if (!Jalview.isHeadlessMode())
 359     {
 360       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 361     }
 362
 363     avc = new jalview.controller.AlignViewController(this, viewport,
 364             alignPanel);
 365     if (viewport.getAlignmentConservationAnnotation() == null)
 366     {
 367       // BLOSUM62Colour.setEnabled(false);
 368       conservationMenuItem.setEnabled(false);
 369       modifyConservation.setEnabled(false);
 370       // PIDColour.setEnabled(false);
 371       // abovePIDThreshold.setEnabled(false);
 372       // modifyPID.setEnabled(false);
 373     }
 374
 375     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 376             "No sort");
 377
 378     if (sortby.equals("Id"))
 379     {
 380       sortIDMenuItem_actionPerformed(null);
 381     }
 382     else if (sortby.equals("Pairwise Identity"))
 383     {
 384       sortPairwiseMenuItem_actionPerformed(null);
 385     }
 386
 387     this.alignPanel.av
 388             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 389
 390     setMenusFromViewport(viewport);
 391     buildSortByAnnotationScoresMenu();
 392     calculateTree.addActionListener(new ActionListener()
 393     {
 394
 395       @Override
 396       public void actionPerformed(ActionEvent e)
 397       {
 398         openTreePcaDialog();
 399       }
 400     });
 401     buildColourMenu();
 402
 403     if (Desktop.desktop != null)
 404     {
 405       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 406       addServiceListeners();
 407       setGUINucleotide();
 408     }
 409
 410     if (viewport.getWrapAlignment())
 411     {
 412       wrapMenuItem_actionPerformed(null);
 413     }
 414
 415     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 416     {
 417       this.overviewMenuItem_actionPerformed(null);
 418     }
 419
 420     addKeyListener();
 421
 422     final List<AlignmentPanel> selviews = new ArrayList<>();
 423     final List<AlignmentPanel> origview = new ArrayList<>();
 424     final String menuLabel = MessageManager
 425             .getString("label.copy_format_from");
 426     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 427             new ViewSetProvider()
 428             {
 429
 430               @Override
 431               public AlignmentPanel[] getAllAlignmentPanels()
 432               {
 433                 origview.clear();
 434                 origview.add(alignPanel);
 435                 // make an array of all alignment panels except for this one
 436                 List<AlignmentPanel> aps = new ArrayList<>(
 437                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 438                 aps.remove(AlignFrame.this.alignPanel);
 439                 return aps.toArray(new AlignmentPanel[aps.size()]);
 440               }
 441             }, selviews, new ItemListener()
 442             {
 443
 444               @Override
 445               public void itemStateChanged(ItemEvent e)
 446               {
 447                 if (origview.size() > 0)
 448                 {
 449                   final AlignmentPanel ap = origview.get(0);
 450
 451                   /*
 452                    * Copy the ViewStyle of the selected panel to 'this one'.
 453                    * Don't change value of 'scaleProteinAsCdna' unless copying
 454                    * from a SplitFrame.
 455                    */
 456                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 457                           .getViewStyle();
 458                   boolean fromSplitFrame = selviews.get(0)
 459                           .getAlignViewport().getCodingComplement() != null;
 460                   if (!fromSplitFrame)
 461                   {
 462                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 463                             .getViewStyle().isScaleProteinAsCdna());
 464                   }
 465                   ap.getAlignViewport().setViewStyle(vs);
 466
 467                   /*
 468                    * Also rescale ViewStyle of SplitFrame complement if there is
 469                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 470                    * the whole ViewStyle (allow cDNA protein to have different
 471                    * fonts)
 472                    */
 473                   AlignViewportI complement = ap.getAlignViewport()
 474                           .getCodingComplement();
 475                   if (complement != null && vs.isScaleProteinAsCdna())
 476                   {
 477                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 478                     ((SplitFrame) af.getSplitViewContainer())
 479                             .adjustLayout();
 480                     af.setMenusForViewport();
 481                   }
 482
 483                   ap.updateLayout();
 484                   ap.setSelected(true);
 485                   ap.alignFrame.setMenusForViewport();
 486
 487                 }
 488               }
 489             });
 490     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 491             .indexOf("devel") > -1
 492             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 493                     .indexOf("test") > -1)
 494     {
 495       formatMenu.add(vsel);
 496     }
 497     addFocusListener(new FocusAdapter()
 498     {
 499       @Override
 500       public void focusGained(FocusEvent e)
 501       {
 502         Jalview.setCurrentAlignFrame(AlignFrame.this);
 503       }
 504     });
 505
 506   }
 507
 508   /**
 509    * Change the filename and format for the alignment, and enable the 'reload'
 510    * button functionality.
 511    *
 512    * @param file
 513    *          valid filename
 514    * @param format
 515    *          format of file
 516    */
 517   public void setFileName(String file, FileFormatI format)
 518   {
 519     fileName = file;
 520     setFileFormat(format);
 521     reload.setEnabled(true);
 522   }
 523
 524   /**
 525    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 526    * events
 527    */
 528   void addKeyListener()
 529   {
 530     addKeyListener(new KeyAdapter()
 531     {
 532       @Override
 533       public void keyPressed(KeyEvent evt)
 534       {
 535         if (viewport.cursorMode
 536                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 537                         && evt.getKeyCode() <= KeyEvent.VK_9)
 538                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 539                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 540                 && Character.isDigit(evt.getKeyChar()))
 541         {
 542           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 543         }
 544
 545         switch (evt.getKeyCode())
 546         {
 547
 548         case 27: // escape key
 549           deselectAllSequenceMenuItem_actionPerformed(null);
 550
 551           break;
 552
 553         case KeyEvent.VK_DOWN:
 554           if (evt.isAltDown() || !viewport.cursorMode)
 555           {
 556             moveSelectedSequences(false);
 557           }
 558           if (viewport.cursorMode)
 559           {
 560             alignPanel.getSeqPanel().moveCursor(0, 1);
 561           }
 562           break;
 563
 564         case KeyEvent.VK_UP:
 565           if (evt.isAltDown() || !viewport.cursorMode)
 566           {
 567             moveSelectedSequences(true);
 568           }
 569           if (viewport.cursorMode)
 570           {
 571             alignPanel.getSeqPanel().moveCursor(0, -1);
 572           }
 573
 574           break;
 575
 576         case KeyEvent.VK_LEFT:
 577           if (evt.isAltDown() || !viewport.cursorMode)
 578           {
 579             slideSequences(false,
 580                     alignPanel.getSeqPanel().getKeyboardNo1());
 581           }
 582           else
 583           {
 584             alignPanel.getSeqPanel().moveCursor(-1, 0);
 585           }
 586
 587           break;
 588
 589         case KeyEvent.VK_RIGHT:
 590           if (evt.isAltDown() || !viewport.cursorMode)
 591           {
 592             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 593           }
 594           else
 595           {
 596             alignPanel.getSeqPanel().moveCursor(1, 0);
 597           }
 598           break;
 599
 600         case KeyEvent.VK_SPACE:
 601           if (viewport.cursorMode)
 602           {
 603             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 604                     || evt.isShiftDown() || evt.isAltDown());
 605           }
 606           break;
 607
 608         // case KeyEvent.VK_A:
 609         // if (viewport.cursorMode)
 610         // {
 611         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 612         // //System.out.println("A");
 613         // }
 614         // break;
 615         /*
 616          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 617          * System.out.println("closing bracket"); } break;
 618          */
 619         case KeyEvent.VK_DELETE:
 620         case KeyEvent.VK_BACK_SPACE:
 621           if (!viewport.cursorMode)
 622           {
 623             cut_actionPerformed(null);
 624           }
 625           else
 626           {
 627             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 628                     || evt.isShiftDown() || evt.isAltDown());
 629           }
 630
 631           break;
 632
 633         case KeyEvent.VK_S:
 634           if (viewport.cursorMode)
 635           {
 636             alignPanel.getSeqPanel().setCursorRow();
 637           }
 638           break;
 639         case KeyEvent.VK_C:
 640           if (viewport.cursorMode && !evt.isControlDown())
 641           {
 642             alignPanel.getSeqPanel().setCursorColumn();
 643           }
 644           break;
 645         case KeyEvent.VK_P:
 646           if (viewport.cursorMode)
 647           {
 648             alignPanel.getSeqPanel().setCursorPosition();
 649           }
 650           break;
 651
 652         case KeyEvent.VK_ENTER:
 653         case KeyEvent.VK_COMMA:
 654           if (viewport.cursorMode)
 655           {
 656             alignPanel.getSeqPanel().setCursorRowAndColumn();
 657           }
 658           break;
 659
 660         case KeyEvent.VK_Q:
 661           if (viewport.cursorMode)
 662           {
 663             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 664           }
 665           break;
 666         case KeyEvent.VK_M:
 667           if (viewport.cursorMode)
 668           {
 669             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 670           }
 671           break;
 672
 673         case KeyEvent.VK_F2:
 674           viewport.cursorMode = !viewport.cursorMode;
 675           statusBar.setText(MessageManager
 676                   .formatMessage("label.keyboard_editing_mode", new String[]
 677                   { (viewport.cursorMode ? "on" : "off") }));
 678           if (viewport.cursorMode)
 679           {
 680             ViewportRanges ranges = viewport.getRanges();
 681             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 682                     .getStartRes();
 683             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 684                     .getStartSeq();
 685           }
 686           alignPanel.getSeqPanel().seqCanvas.repaint();
 687           break;
 688
 689         case KeyEvent.VK_F1:
 690           try
 691           {
 692             Help.showHelpWindow();
 693           } catch (Exception ex)
 694           {
 695             ex.printStackTrace();
 696           }
 697           break;
 698         case KeyEvent.VK_H:
 699         {
 700           boolean toggleSeqs = !evt.isControlDown();
 701           boolean toggleCols = !evt.isShiftDown();
 702           toggleHiddenRegions(toggleSeqs, toggleCols);
 703           break;
 704         }
 705         case KeyEvent.VK_B:
 706         {
 707           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 708           boolean modifyExisting = true; // always modify, don't clear
 709                                          // evt.isShiftDown();
 710           boolean invertHighlighted = evt.isAltDown();
 711           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 712                   toggleSel);
 713           break;
 714         }
 715         case KeyEvent.VK_PAGE_UP:
 716           viewport.getRanges().pageUp();
 717           break;
 718         case KeyEvent.VK_PAGE_DOWN:
 719           viewport.getRanges().pageDown();
 720           break;
 721         }
 722       }
 723
 724       @Override
 725       public void keyReleased(KeyEvent evt)
 726       {
 727         switch (evt.getKeyCode())
 728         {
 729         case KeyEvent.VK_LEFT:
 730           if (evt.isAltDown() || !viewport.cursorMode)
 731           {
 732             viewport.firePropertyChange("alignment", null,
 733                     viewport.getAlignment().getSequences());
 734           }
 735           break;
 736
 737         case KeyEvent.VK_RIGHT:
 738           if (evt.isAltDown() || !viewport.cursorMode)
 739           {
 740             viewport.firePropertyChange("alignment", null,
 741                     viewport.getAlignment().getSequences());
 742           }
 743           break;
 744         }
 745       }
 746     });
 747   }
 748
 749   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 750   {
 751     ap.alignFrame = this;
 752     avc = new jalview.controller.AlignViewController(this, viewport,
 753             alignPanel);
 754
 755     alignPanels.add(ap);
 756
 757     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 758
 759     int aSize = alignPanels.size();
 760
 761     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 762
 763     if (aSize == 1 && ap.av.viewName == null)
 764     {
 765       this.getContentPane().add(ap, BorderLayout.CENTER);
 766     }
 767     else
 768     {
 769       if (aSize == 2)
 770       {
 771         setInitialTabVisible();
 772       }
 773
 774       expandViews.setEnabled(true);
 775       gatherViews.setEnabled(true);
 776       tabbedPane.addTab(ap.av.viewName, ap);
 777
 778       ap.setVisible(false);
 779     }
 780
 781     if (newPanel)
 782     {
 783       if (ap.av.isPadGaps())
 784       {
 785         ap.av.getAlignment().padGaps();
 786       }
 787       ap.av.updateConservation(ap);
 788       ap.av.updateConsensus(ap);
 789       ap.av.updateStrucConsensus(ap);
 790       ap.av.updateInformation(ap);
 791     }
 792   }
 793
 794   public void setInitialTabVisible()
 795   {
 796     expandViews.setEnabled(true);
 797     gatherViews.setEnabled(true);
 798     tabbedPane.setVisible(true);
 799     AlignmentPanel first = alignPanels.get(0);
 800     tabbedPane.addTab(first.av.viewName, first);
 801     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 802   }
 803
 804   public AlignViewport getViewport()
 805   {
 806     return viewport;
 807   }
 808
 809   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 810   private void addServiceListeners()
 811   {
 812     final java.beans.PropertyChangeListener thisListener;
 813     Desktop.instance.addJalviewPropertyChangeListener("services",
 814             thisListener = new java.beans.PropertyChangeListener()
 815             {
 816               @Override
 817               public void propertyChange(PropertyChangeEvent evt)
 818               {
 819                 // // System.out.println("Discoverer property change.");
 820                 // if (evt.getPropertyName().equals("services"))
 821                 {
 822                   SwingUtilities.invokeLater(new Runnable()
 823                   {
 824
 825                     @Override
 826                     public void run()
 827                     {
 828                       System.err.println(
 829                               "Rebuild WS Menu for service change");
 830                       BuildWebServiceMenu();
 831                     }
 832
 833                   });
 834                 }
 835               }
 836             });
 837     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 838     {
 839       @Override
 840       public void internalFrameClosed(
 841               javax.swing.event.InternalFrameEvent evt)
 842       {
 843         // System.out.println("deregistering discoverer listener");
 844         Desktop.instance.removeJalviewPropertyChangeListener("services",
 845                 thisListener);
 846         closeMenuItem_actionPerformed(true);
 847       };
 848     });
 849     // Finally, build the menu once to get current service state
 850     new Thread(new Runnable()
 851     {
 852       @Override
 853       public void run()
 854       {
 855         BuildWebServiceMenu();
 856       }
 857     }).start();
 858   }
 859
 860   /**
 861    * Configure menu items that vary according to whether the alignment is
 862    * nucleotide or protein
 863    */
 864   public void setGUINucleotide()
 865   {
 866     AlignmentI al = getViewport().getAlignment();
 867     boolean nucleotide = al.isNucleotide();
 868
 869     loadVcf.setVisible(nucleotide);
 870     showTranslation.setVisible(nucleotide);
 871     showReverse.setVisible(nucleotide);
 872     showReverseComplement.setVisible(nucleotide);
 873     conservationMenuItem.setEnabled(!nucleotide);
 874     modifyConservation
 875             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 876     showGroupConservation.setEnabled(!nucleotide);
 877
 878     showComplementMenuItem
 879             .setText(nucleotide ? MessageManager.getString("label.protein")
 880                     : MessageManager.getString("label.nucleotide"));
 881   }
 882
 883   /**
 884    * set up menus for the current viewport. This may be called after any
 885    * operation that affects the data in the current view (selection changed,
 886    * etc) to update the menus to reflect the new state.
 887    */
 888   @Override
 889   public void setMenusForViewport()
 890   {
 891     setMenusFromViewport(viewport);
 892   }
 893
 894   /**
 895    * Need to call this method when tabs are selected for multiple views, or when
 896    * loading from Jalview2XML.java
 897    *
 898    * @param av
 899    *          AlignViewport
 900    */
 901   void setMenusFromViewport(AlignViewport av)
 902   {
 903     padGapsMenuitem.setSelected(av.isPadGaps());
 904     colourTextMenuItem.setSelected(av.isShowColourText());
 905     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 906     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 907     conservationMenuItem.setSelected(av.getConservationSelected());
 908     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 909     seqLimits.setSelected(av.getShowJVSuffix());
 910     idRightAlign.setSelected(av.isRightAlignIds());
 911     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 912     renderGapsMenuItem.setSelected(av.isRenderGaps());
 913     wrapMenuItem.setSelected(av.getWrapAlignment());
 914     scaleAbove.setVisible(av.getWrapAlignment());
 915     scaleLeft.setVisible(av.getWrapAlignment());
 916     scaleRight.setVisible(av.getWrapAlignment());
 917     annotationPanelMenuItem.setState(av.isShowAnnotation());
 918     /*
 919      * Show/hide annotations only enabled if annotation panel is shown
 920      */
 921     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 922     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 923     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 924     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 925     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 926     viewTextMenuItem.setSelected(av.getShowText());
 927     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 928     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 929     showGroupConservation.setSelected(av.isShowGroupConservation());
 930     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 931     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 932     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 933     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 934     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 935     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 936
 937     ColourMenuHelper.setColourSelected(colourMenu,
 938             av.getGlobalColourScheme());
 939
 940     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 941     hiddenMarkers.setState(av.getShowHiddenMarkers());
 942     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 943     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 944     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 945     autoCalculate.setSelected(av.autoCalculateConsensus);
 946     sortByTree.setSelected(av.sortByTree);
 947     listenToViewSelections.setSelected(av.followSelection);
 948
 949     showProducts.setEnabled(canShowProducts());
 950     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 951
 952     updateEditMenuBar();
 953   }
 954
 955   /**
 956    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 957    *
 958    * @param b
 959    */
 960   public void setGroovyEnabled(boolean b)
 961   {
 962     runGroovy.setEnabled(b);
 963   }
 964
 965   private IProgressIndicator progressBar;
 966
 967   /*
 968    * (non-Javadoc)
 969    *
 970    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 971    */
 972   @Override
 973   public void setProgressBar(String message, long id)
 974   {
 975     progressBar.setProgressBar(message, id);
 976   }
 977
 978   @Override
 979   public void registerHandler(final long id,
 980           final IProgressIndicatorHandler handler)
 981   {
 982     progressBar.registerHandler(id, handler);
 983   }
 984
 985   /**
 986    *
 987    * @return true if any progress bars are still active
 988    */
 989   @Override
 990   public boolean operationInProgress()
 991   {
 992     return progressBar.operationInProgress();
 993   }
 994
 995   @Override
 996   public void setStatus(String text)
 997   {
 998     statusBar.setText(text);
 999   }
1000
1001   /*
1002    * Added so Castor Mapping file can obtain Jalview Version
1003    */
1004   public String getVersion()
1005   {
1006     return jalview.bin.Cache.getProperty("VERSION");
1007   }
1008
1009   public FeatureRenderer getFeatureRenderer()
1010   {
1011     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1012   }
1013
1014   @Override
1015   public void fetchSequence_actionPerformed(ActionEvent e)
1016   {
1017     new jalview.gui.SequenceFetcher(this);
1018   }
1019
1020   @Override
1021   public void addFromFile_actionPerformed(ActionEvent e)
1022   {
1023     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1024   }
1025
1026   @Override
1027   public void hmmBuildSettings_actionPerformed()
1028   {
1029     if (!(alignmentIsSufficient(1)))
1030     {
1031       return;
1032     }
1033     WsParamSetI set = new HMMERPreset();
1034     List<ArgumentI> args = new ArrayList<>();
1035     ParamDatastoreI store = new HMMERParamStore("hmmbuild");
1036     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1037             args);
1038     if (params.showRunDialog())
1039     {
1040       new Thread(new HMMBuild(this, params.getJobParams())).start();
1041     }
1042     alignPanel.repaint();
1043
1044   }
1045
1046   @Override
1047   public void hmmAlignSettings_actionPerformed()
1048   {
1049     if (!(checkForHMM() && alignmentIsSufficient(2)))
1050     {
1051       return;
1052     }
1053     WsParamSetI set = new HMMERPreset();
1054     List<ArgumentI> args = new ArrayList<>();
1055     ParamDatastoreI store = new HMMERParamStore("hmmalign");
1056     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1057             args);
1058     if (params.showRunDialog())
1059     {
1060       new Thread(new HMMAlign(this, params.getJobParams()))
1061             .start();
1062     }
1063     alignPanel.repaint();
1064   }
1065
1066   @Override
1067   public void hmmSearchSettings_actionPerformed()
1068   {
1069     if (!checkForHMM())
1070     {
1071       return;
1072     }
1073     WsParamSetI set = new HMMERPreset();
1074     List<ArgumentI> args = new ArrayList<>();
1075     ParamDatastoreI store = new HMMERParamStore("hmmsearch");
1076     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1077             args);
1078     if (params.showRunDialog())
1079     {
1080       new Thread(new HMMSearch(this, params.getJobParams()))
1081             .start();
1082     }
1083     alignPanel.repaint();
1084   }
1085
1086   @Override
1087   public void hmmBuildRun_actionPerformed()
1088   {
1089     if (!alignmentIsSufficient(1))
1090     {
1091       return;
1092     }
1093     new Thread(new HMMBuild(this, null))
1094             .start();
1095   }
1096
1097   @Override
1098   public void hmmAlignRun_actionPerformed()
1099   {
1100     if (!(checkForHMM() && alignmentIsSufficient(2)))
1101     {
1102       return;
1103     }
1104     new Thread(new HMMAlign(this, null)).start();
1105   }
1106
1107   @Override
1108   public void hmmSearchRun_actionPerformed()
1109   {
1110     if (!checkForHMM())
1111     {
1112       return;
1113     }
1114     new Thread(new HMMSearch(this, null)).start();
1115   }
1116
1117   /**
1118    * Checks if the frame has a selected hidden Markov model
1119    *
1120    * @return
1121    */
1122   private boolean checkForHMM()
1123   {
1124     if (getSelectedHMM() == null)
1125     {
1126       JOptionPane.showMessageDialog(this,
1127               MessageManager.getString("warn.no_selected_hmm"));
1128       return false;
1129     }
1130     return true;
1131   }
1132
1133   /**
1134    * Checks if the alignment contains the required number of sequences.
1135    *
1136    * @param required
1137    * @return
1138    */
1139   public boolean alignmentIsSufficient(int required)
1140   {
1141     if (getViewport().getAlignment().getSequences().size() < required)
1142     {
1143       JOptionPane.showMessageDialog(this,
1144               MessageManager.getString("warn.not_enough_sequences"));
1145       return false;
1146     }
1147     return true;
1148   }
1149
1150   @Override
1151   public void addDatabase_actionPerformed() throws IOException
1152   {
1153     if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
1154     {
1155       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1156       Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
1157     }
1158
1159     String path = openFileChooser(false);
1160     if (new File(path).exists())
1161     {
1162       IdentifyFile identifier = new IdentifyFile();
1163       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1164       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1165               || format == FileFormat.Pfam)
1166       {
1167         String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
1168         String currentDbPaths = Cache
1169                 .getProperty(Preferences.HMMSEARCH_DB_PATHS);
1170         currentDbPaths += " " + path;
1171
1172         String fileName = StringUtils.getLastToken(path, File.separator);
1173         Scanner scanner = new Scanner(fileName).useDelimiter(".");
1174         String name = scanner.next();
1175         scanner.close();
1176         currentDbs += " " + path; // TODO remove path from file name
1177         scanner.close();
1178
1179         Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
1180         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1181       }
1182       else
1183       {
1184         JOptionPane.showMessageDialog(this,
1185                 MessageManager.getString("warn.invalid_format"));
1186       }
1187     }
1188     else
1189     {
1190       JOptionPane.showMessageDialog(this,
1191               MessageManager.getString("warn.not_enough_sequences"));
1192     }
1193   }
1194
1195   /**
1196    * Opens a file chooser
1197    *
1198    * @param forFolder
1199    * @return
1200    */
1201   protected String openFileChooser(boolean forFolder)
1202   {
1203     String choice = null;
1204     JFileChooser chooser = new JFileChooser();
1205     if (forFolder)
1206     {
1207       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1208     }
1209     chooser.setDialogTitle(
1210             MessageManager.getString("label.open_local_file"));
1211     chooser.setToolTipText(MessageManager.getString("action.open"));
1212
1213     int value = chooser.showOpenDialog(this);
1214
1215     if (value == JFileChooser.APPROVE_OPTION)
1216     {
1217       choice = chooser.getSelectedFile().getPath();
1218     }
1219     return choice;
1220   }
1221
1222   @Override
1223   public void reload_actionPerformed(ActionEvent e)
1224   {
1225     if (fileName != null)
1226     {
1227       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1228       // originating file's format
1229       // TODO: work out how to recover feature settings for correct view(s) when
1230       // file is reloaded.
1231       if (FileFormat.Jalview.equals(currentFileFormat))
1232       {
1233         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1234         for (int i = 0; i < frames.length; i++)
1235         {
1236           if (frames[i] instanceof AlignFrame && frames[i] != this
1237                   && ((AlignFrame) frames[i]).fileName != null
1238                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1239           {
1240             try
1241             {
1242               frames[i].setSelected(true);
1243               Desktop.instance.closeAssociatedWindows();
1244             } catch (java.beans.PropertyVetoException ex)
1245             {
1246             }
1247           }
1248
1249         }
1250         Desktop.instance.closeAssociatedWindows();
1251
1252         FileLoader loader = new FileLoader();
1253         DataSourceType protocol = fileName.startsWith("http:")
1254                 ? DataSourceType.URL
1255                 : DataSourceType.FILE;
1256         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1257       }
1258       else
1259       {
1260         Rectangle bounds = this.getBounds();
1261
1262         FileLoader loader = new FileLoader();
1263         DataSourceType protocol = fileName.startsWith("http:")
1264                 ? DataSourceType.URL
1265                 : DataSourceType.FILE;
1266         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1267                 protocol, currentFileFormat);
1268
1269         newframe.setBounds(bounds);
1270         if (featureSettings != null && featureSettings.isShowing())
1271         {
1272           final Rectangle fspos = featureSettings.frame.getBounds();
1273           // TODO: need a 'show feature settings' function that takes bounds -
1274           // need to refactor Desktop.addFrame
1275           newframe.featureSettings_actionPerformed(null);
1276           final FeatureSettings nfs = newframe.featureSettings;
1277           SwingUtilities.invokeLater(new Runnable()
1278           {
1279             @Override
1280             public void run()
1281             {
1282               nfs.frame.setBounds(fspos);
1283             }
1284           });
1285           this.featureSettings.close();
1286           this.featureSettings = null;
1287         }
1288         this.closeMenuItem_actionPerformed(true);
1289       }
1290     }
1291   }
1292
1293   @Override
1294   public void addFromText_actionPerformed(ActionEvent e)
1295   {
1296     Desktop.instance
1297             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1298   }
1299
1300   @Override
1301   public void addFromURL_actionPerformed(ActionEvent e)
1302   {
1303     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1304   }
1305
1306   @Override
1307   public void save_actionPerformed(ActionEvent e)
1308   {
1309     if (fileName == null || (currentFileFormat == null)
1310             || fileName.startsWith("http"))
1311     {
1312       saveAs_actionPerformed(null);
1313     }
1314     else
1315     {
1316       saveAlignment(fileName, currentFileFormat);
1317     }
1318   }
1319
1320   /**
1321    * DOCUMENT ME!
1322    *
1323    * @param e
1324    *          DOCUMENT ME!
1325    */
1326   @Override
1327   public void saveAs_actionPerformed(ActionEvent e)
1328   {
1329     String format = currentFileFormat == null ? null
1330             : currentFileFormat.getName();
1331     JalviewFileChooser chooser = JalviewFileChooser
1332             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1333
1334     chooser.setFileView(new JalviewFileView());
1335     chooser.setDialogTitle(
1336             MessageManager.getString("label.save_alignment_to_file"));
1337     chooser.setToolTipText(MessageManager.getString("action.save"));
1338
1339     int value = chooser.showSaveDialog(this);
1340
1341     if (value == JalviewFileChooser.APPROVE_OPTION)
1342     {
1343       currentFileFormat = chooser.getSelectedFormat();
1344       while (currentFileFormat == null)
1345       {
1346         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1347                 MessageManager.getString(
1348                         "label.select_file_format_before_saving"),
1349                 MessageManager.getString("label.file_format_not_specified"),
1350                 JvOptionPane.WARNING_MESSAGE);
1351         currentFileFormat = chooser.getSelectedFormat();
1352         value = chooser.showSaveDialog(this);
1353         if (value != JalviewFileChooser.APPROVE_OPTION)
1354         {
1355           return;
1356         }
1357       }
1358
1359       fileName = chooser.getSelectedFile().getPath();
1360
1361       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1362
1363       Cache.setProperty("LAST_DIRECTORY", fileName);
1364       saveAlignment(fileName, currentFileFormat);
1365     }
1366   }
1367
1368   public boolean saveAlignment(String file, FileFormatI format)
1369   {
1370     boolean success = true;
1371
1372     if (FileFormat.Jalview.equals(format))
1373     {
1374       String shortName = title;
1375
1376       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1377       {
1378         shortName = shortName.substring(
1379                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1380       }
1381
1382       success = new Jalview2XML().saveAlignment(this, file, shortName);
1383
1384       statusBar.setText(MessageManager.formatMessage(
1385               "label.successfully_saved_to_file_in_format", new Object[]
1386               { fileName, format }));
1387
1388     }
1389     else
1390     {
1391       AlignmentExportData exportData = getAlignmentForExport(format,
1392               viewport, null);
1393       if (exportData.getSettings().isCancelled())
1394       {
1395         return false;
1396       }
1397       FormatAdapter f = new FormatAdapter(alignPanel,
1398               exportData.getSettings());
1399       String output = f.formatSequences(format, exportData.getAlignment(), // class
1400                                                                            // cast
1401                                                                            // exceptions
1402                                                                            // will
1403               // occur in the distant future
1404               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1405               f.getCacheSuffixDefault(format),
1406               viewport.getAlignment().getHiddenColumns());
1407
1408       if (output == null)
1409       {
1410         success = false;
1411       }
1412       else
1413       {
1414         try
1415         {
1416           PrintWriter out = new PrintWriter(new FileWriter(file));
1417
1418           out.print(output);
1419           out.close();
1420           this.setTitle(file);
1421           statusBar.setText(MessageManager.formatMessage(
1422                   "label.successfully_saved_to_file_in_format", new Object[]
1423                   { fileName, format.getName() }));
1424         } catch (Exception ex)
1425         {
1426           success = false;
1427           ex.printStackTrace();
1428         }
1429       }
1430     }
1431
1432     if (!success)
1433     {
1434       JvOptionPane.showInternalMessageDialog(this, MessageManager
1435               .formatMessage("label.couldnt_save_file", new Object[]
1436               { fileName }),
1437               MessageManager.getString("label.error_saving_file"),
1438               JvOptionPane.WARNING_MESSAGE);
1439     }
1440
1441     return success;
1442   }
1443
1444   private void warningMessage(String warning, String title)
1445   {
1446     if (new jalview.util.Platform().isHeadless())
1447     {
1448       System.err.println("Warning: " + title + "\nWarning: " + warning);
1449
1450     }
1451     else
1452     {
1453       JvOptionPane.showInternalMessageDialog(this, warning, title,
1454               JvOptionPane.WARNING_MESSAGE);
1455     }
1456     return;
1457   }
1458
1459   /**
1460    * DOCUMENT ME!
1461    *
1462    * @param e
1463    *          DOCUMENT ME!
1464    */
1465   @Override
1466   protected void outputText_actionPerformed(ActionEvent e)
1467   {
1468     FileFormatI fileFormat = FileFormats.getInstance()
1469             .forName(e.getActionCommand());
1470     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1471             viewport, null);
1472     if (exportData.getSettings().isCancelled())
1473     {
1474       return;
1475     }
1476     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1477     cap.setForInput(null);
1478     try
1479     {
1480       FileFormatI format = fileFormat;
1481       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1482               .formatSequences(format, exportData.getAlignment(),
1483                       exportData.getOmitHidden(),
1484                       exportData.getStartEndPostions(),
1485                       viewport.getAlignment().getHiddenColumns()));
1486       Desktop.addInternalFrame(cap, MessageManager
1487               .formatMessage("label.alignment_output_command", new Object[]
1488               { e.getActionCommand() }), 600, 500);
1489     } catch (OutOfMemoryError oom)
1490     {
1491       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1492               oom);
1493       cap.dispose();
1494     }
1495
1496   }
1497
1498   public static AlignmentExportData getAlignmentForExport(
1499           FileFormatI format, AlignViewportI viewport,
1500           AlignExportSettingI exportSettings)
1501   {
1502     AlignmentI alignmentToExport = null;
1503     AlignExportSettingI settings = exportSettings;
1504     String[] omitHidden = null;
1505
1506     HiddenSequences hiddenSeqs = viewport.getAlignment()
1507             .getHiddenSequences();
1508
1509     alignmentToExport = viewport.getAlignment();
1510
1511     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1512     if (settings == null)
1513     {
1514       settings = new AlignExportSettings(hasHiddenSeqs,
1515               viewport.hasHiddenColumns(), format);
1516     }
1517     // settings.isExportAnnotations();
1518
1519     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1520     {
1521       omitHidden = viewport.getViewAsString(false,
1522               settings.isExportHiddenSequences());
1523     }
1524
1525     int[] alignmentStartEnd = new int[2];
1526     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1527     {
1528       alignmentToExport = hiddenSeqs.getFullAlignment();
1529     }
1530     else
1531     {
1532       alignmentToExport = viewport.getAlignment();
1533     }
1534     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1535             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1536     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1537             omitHidden, alignmentStartEnd, settings);
1538     return ed;
1539   }
1540
1541   /**
1542    * DOCUMENT ME!
1543    *
1544    * @param e
1545    *          DOCUMENT ME!
1546    */
1547   @Override
1548   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1549   {
1550     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1551     htmlSVG.exportHTML(null);
1552   }
1553
1554   @Override
1555   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1556   {
1557     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1558     bjs.exportHTML(null);
1559   }
1560
1561   public void createImageMap(File file, String image)
1562   {
1563     alignPanel.makePNGImageMap(file, image);
1564   }
1565
1566   /**
1567    * DOCUMENT ME!
1568    *
1569    * @param e
1570    *          DOCUMENT ME!
1571    */
1572   @Override
1573   public void createPNG(File f)
1574   {
1575     alignPanel.makePNG(f);
1576   }
1577
1578   /**
1579    * DOCUMENT ME!
1580    *
1581    * @param e
1582    *          DOCUMENT ME!
1583    */
1584   @Override
1585   public void createEPS(File f)
1586   {
1587     alignPanel.makeEPS(f);
1588   }
1589
1590   @Override
1591   public void createSVG(File f)
1592   {
1593     alignPanel.makeSVG(f);
1594   }
1595
1596   @Override
1597   public void pageSetup_actionPerformed(ActionEvent e)
1598   {
1599     PrinterJob printJob = PrinterJob.getPrinterJob();
1600     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1601   }
1602
1603   /**
1604    * DOCUMENT ME!
1605    *
1606    * @param e
1607    *          DOCUMENT ME!
1608    */
1609   @Override
1610   public void printMenuItem_actionPerformed(ActionEvent e)
1611   {
1612     // Putting in a thread avoids Swing painting problems
1613     PrintThread thread = new PrintThread(alignPanel);
1614     thread.start();
1615   }
1616
1617   @Override
1618   public void exportFeatures_actionPerformed(ActionEvent e)
1619   {
1620     new AnnotationExporter(alignPanel).exportFeatures();
1621   }
1622
1623   @Override
1624   public void exportAnnotations_actionPerformed(ActionEvent e)
1625   {
1626     new AnnotationExporter(alignPanel).exportAnnotations();
1627   }
1628
1629   @Override
1630   public void associatedData_actionPerformed(ActionEvent e)
1631           throws IOException, InterruptedException
1632   {
1633     // Pick the tree file
1634     JalviewFileChooser chooser = new JalviewFileChooser(
1635             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1636     chooser.setFileView(new JalviewFileView());
1637     chooser.setDialogTitle(
1638             MessageManager.getString("label.load_jalview_annotations"));
1639     chooser.setToolTipText(
1640             MessageManager.getString("label.load_jalview_annotations"));
1641
1642     int value = chooser.showOpenDialog(null);
1643
1644     if (value == JalviewFileChooser.APPROVE_OPTION)
1645     {
1646       String choice = chooser.getSelectedFile().getPath();
1647       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1648       loadJalviewDataFile(choice, null, null, null);
1649     }
1650
1651   }
1652
1653   /**
1654    * Close the current view or all views in the alignment frame. If the frame
1655    * only contains one view then the alignment will be removed from memory.
1656    *
1657    * @param closeAllTabs
1658    */
1659   @Override
1660   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1661   {
1662     if (alignPanels != null && alignPanels.size() < 2)
1663     {
1664       closeAllTabs = true;
1665     }
1666
1667     try
1668     {
1669       if (alignPanels != null)
1670       {
1671         if (closeAllTabs)
1672         {
1673           if (this.isClosed())
1674           {
1675             // really close all the windows - otherwise wait till
1676             // setClosed(true) is called
1677             for (int i = 0; i < alignPanels.size(); i++)
1678             {
1679               AlignmentPanel ap = alignPanels.get(i);
1680               ap.closePanel();
1681             }
1682           }
1683         }
1684         else
1685         {
1686           closeView(alignPanel);
1687         }
1688       }
1689
1690       if (closeAllTabs)
1691       {
1692         /*
1693          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1694          * be called recursively, with the frame now in 'closed' state
1695          */
1696         this.setClosed(true);
1697       }
1698     } catch (Exception ex)
1699     {
1700       ex.printStackTrace();
1701     }
1702   }
1703
1704   /**
1705    * Close the specified panel and close up tabs appropriately.
1706    *
1707    * @param panelToClose
1708    */
1709   public void closeView(AlignmentPanel panelToClose)
1710   {
1711     int index = tabbedPane.getSelectedIndex();
1712     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1713     alignPanels.remove(panelToClose);
1714     panelToClose.closePanel();
1715     panelToClose = null;
1716
1717     tabbedPane.removeTabAt(closedindex);
1718     tabbedPane.validate();
1719
1720     if (index > closedindex || index == tabbedPane.getTabCount())
1721     {
1722       // modify currently selected tab index if necessary.
1723       index--;
1724     }
1725
1726     this.tabSelectionChanged(index);
1727   }
1728
1729   /**
1730    * DOCUMENT ME!
1731    */
1732   void updateEditMenuBar()
1733   {
1734
1735     if (viewport.getHistoryList().size() > 0)
1736     {
1737       undoMenuItem.setEnabled(true);
1738       CommandI command = viewport.getHistoryList().peek();
1739       undoMenuItem.setText(MessageManager
1740               .formatMessage("label.undo_command", new Object[]
1741               { command.getDescription() }));
1742     }
1743     else
1744     {
1745       undoMenuItem.setEnabled(false);
1746       undoMenuItem.setText(MessageManager.getString("action.undo"));
1747     }
1748
1749     if (viewport.getRedoList().size() > 0)
1750     {
1751       redoMenuItem.setEnabled(true);
1752
1753       CommandI command = viewport.getRedoList().peek();
1754       redoMenuItem.setText(MessageManager
1755               .formatMessage("label.redo_command", new Object[]
1756               { command.getDescription() }));
1757     }
1758     else
1759     {
1760       redoMenuItem.setEnabled(false);
1761       redoMenuItem.setText(MessageManager.getString("action.redo"));
1762     }
1763   }
1764
1765   @Override
1766   public void addHistoryItem(CommandI command)
1767   {
1768     if (command.getSize() > 0)
1769     {
1770       viewport.addToHistoryList(command);
1771       viewport.clearRedoList();
1772       updateEditMenuBar();
1773       viewport.updateHiddenColumns();
1774       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1775       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1776       // viewport.getColumnSelection()
1777       // .getHiddenColumns().size() > 0);
1778     }
1779   }
1780
1781   /**
1782    *
1783    * @return alignment objects for all views
1784    */
1785   AlignmentI[] getViewAlignments()
1786   {
1787     if (alignPanels != null)
1788     {
1789       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1790       int i = 0;
1791       for (AlignmentPanel ap : alignPanels)
1792       {
1793         als[i++] = ap.av.getAlignment();
1794       }
1795       return als;
1796     }
1797     if (viewport != null)
1798     {
1799       return new AlignmentI[] { viewport.getAlignment() };
1800     }
1801     return null;
1802   }
1803
1804   /**
1805    * DOCUMENT ME!
1806    *
1807    * @param e
1808    *          DOCUMENT ME!
1809    */
1810   @Override
1811   protected void undoMenuItem_actionPerformed(ActionEvent e)
1812   {
1813     if (viewport.getHistoryList().isEmpty())
1814     {
1815       return;
1816     }
1817     CommandI command = viewport.getHistoryList().pop();
1818     viewport.addToRedoList(command);
1819     command.undoCommand(getViewAlignments());
1820
1821     AlignmentViewport originalSource = getOriginatingSource(command);
1822     updateEditMenuBar();
1823
1824     if (originalSource != null)
1825     {
1826       if (originalSource != viewport)
1827       {
1828         Cache.log.warn(
1829                 "Implementation worry: mismatch of viewport origin for undo");
1830       }
1831       originalSource.updateHiddenColumns();
1832       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1833       // null
1834       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1835       // viewport.getColumnSelection()
1836       // .getHiddenColumns().size() > 0);
1837       originalSource.firePropertyChange("alignment", null,
1838               originalSource.getAlignment().getSequences());
1839     }
1840   }
1841
1842   /**
1843    * DOCUMENT ME!
1844    *
1845    * @param e
1846    *          DOCUMENT ME!
1847    */
1848   @Override
1849   protected void redoMenuItem_actionPerformed(ActionEvent e)
1850   {
1851     if (viewport.getRedoList().size() < 1)
1852     {
1853       return;
1854     }
1855
1856     CommandI command = viewport.getRedoList().pop();
1857     viewport.addToHistoryList(command);
1858     command.doCommand(getViewAlignments());
1859
1860     AlignmentViewport originalSource = getOriginatingSource(command);
1861     updateEditMenuBar();
1862
1863     if (originalSource != null)
1864     {
1865
1866       if (originalSource != viewport)
1867       {
1868         Cache.log.warn(
1869                 "Implementation worry: mismatch of viewport origin for redo");
1870       }
1871       originalSource.updateHiddenColumns();
1872       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1873       // null
1874       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1875       // viewport.getColumnSelection()
1876       // .getHiddenColumns().size() > 0);
1877       originalSource.firePropertyChange("alignment", null,
1878               originalSource.getAlignment().getSequences());
1879     }
1880   }
1881
1882   AlignmentViewport getOriginatingSource(CommandI command)
1883   {
1884     AlignmentViewport originalSource = null;
1885     // For sequence removal and addition, we need to fire
1886     // the property change event FROM the viewport where the
1887     // original alignment was altered
1888     AlignmentI al = null;
1889     if (command instanceof EditCommand)
1890     {
1891       EditCommand editCommand = (EditCommand) command;
1892       al = editCommand.getAlignment();
1893       List<Component> comps = PaintRefresher.components
1894               .get(viewport.getSequenceSetId());
1895
1896       for (Component comp : comps)
1897       {
1898         if (comp instanceof AlignmentPanel)
1899         {
1900           if (al == ((AlignmentPanel) comp).av.getAlignment())
1901           {
1902             originalSource = ((AlignmentPanel) comp).av;
1903             break;
1904           }
1905         }
1906       }
1907     }
1908
1909     if (originalSource == null)
1910     {
1911       // The original view is closed, we must validate
1912       // the current view against the closed view first
1913       if (al != null)
1914       {
1915         PaintRefresher.validateSequences(al, viewport.getAlignment());
1916       }
1917
1918       originalSource = viewport;
1919     }
1920
1921     return originalSource;
1922   }
1923
1924   /**
1925    * DOCUMENT ME!
1926    *
1927    * @param up
1928    *          DOCUMENT ME!
1929    */
1930   public void moveSelectedSequences(boolean up)
1931   {
1932     SequenceGroup sg = viewport.getSelectionGroup();
1933
1934     if (sg == null)
1935     {
1936       return;
1937     }
1938     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1939             viewport.getHiddenRepSequences(), up);
1940     alignPanel.paintAlignment(true, false);
1941   }
1942
1943   synchronized void slideSequences(boolean right, int size)
1944   {
1945     List<SequenceI> sg = new ArrayList<>();
1946     if (viewport.cursorMode)
1947     {
1948       sg.add(viewport.getAlignment()
1949               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1950     }
1951     else if (viewport.getSelectionGroup() != null
1952             && viewport.getSelectionGroup().getSize() != viewport
1953                     .getAlignment().getHeight())
1954     {
1955       sg = viewport.getSelectionGroup()
1956               .getSequences(viewport.getHiddenRepSequences());
1957     }
1958
1959     if (sg.size() < 1)
1960     {
1961       return;
1962     }
1963
1964     List<SequenceI> invertGroup = new ArrayList<>();
1965
1966     for (SequenceI seq : viewport.getAlignment().getSequences())
1967     {
1968       if (!sg.contains(seq))
1969       {
1970         invertGroup.add(seq);
1971       }
1972     }
1973
1974     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1975
1976     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1977     for (int i = 0; i < invertGroup.size(); i++)
1978     {
1979       seqs2[i] = invertGroup.get(i);
1980     }
1981
1982     SlideSequencesCommand ssc;
1983     if (right)
1984     {
1985       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1986               viewport.getGapCharacter());
1987     }
1988     else
1989     {
1990       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1991               viewport.getGapCharacter());
1992     }
1993
1994     int groupAdjustment = 0;
1995     if (ssc.getGapsInsertedBegin() && right)
1996     {
1997       if (viewport.cursorMode)
1998       {
1999         alignPanel.getSeqPanel().moveCursor(size, 0);
2000       }
2001       else
2002       {
2003         groupAdjustment = size;
2004       }
2005     }
2006     else if (!ssc.getGapsInsertedBegin() && !right)
2007     {
2008       if (viewport.cursorMode)
2009       {
2010         alignPanel.getSeqPanel().moveCursor(-size, 0);
2011       }
2012       else
2013       {
2014         groupAdjustment = -size;
2015       }
2016     }
2017
2018     if (groupAdjustment != 0)
2019     {
2020       viewport.getSelectionGroup().setStartRes(
2021               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2022       viewport.getSelectionGroup().setEndRes(
2023               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2024     }
2025
2026     /*
2027      * just extend the last slide command if compatible; but not if in
2028      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2029      */
2030     boolean appendHistoryItem = false;
2031     Deque<CommandI> historyList = viewport.getHistoryList();
2032     boolean inSplitFrame = getSplitViewContainer() != null;
2033     if (!inSplitFrame && historyList != null && historyList.size() > 0
2034             && historyList.peek() instanceof SlideSequencesCommand)
2035     {
2036       appendHistoryItem = ssc.appendSlideCommand(
2037               (SlideSequencesCommand) historyList.peek());
2038     }
2039
2040     if (!appendHistoryItem)
2041     {
2042       addHistoryItem(ssc);
2043     }
2044
2045     repaint();
2046   }
2047
2048   /**
2049    * DOCUMENT ME!
2050    *
2051    * @param e
2052    *          DOCUMENT ME!
2053    */
2054   @Override
2055   protected void copy_actionPerformed(ActionEvent e)
2056   {
2057     if (viewport.getSelectionGroup() == null)
2058     {
2059       return;
2060     }
2061     // TODO: preserve the ordering of displayed alignment annotation in any
2062     // internal paste (particularly sequence associated annotation)
2063     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2064     String[] omitHidden = null;
2065
2066     if (viewport.hasHiddenColumns())
2067     {
2068       omitHidden = viewport.getViewAsString(true);
2069     }
2070
2071     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2072             seqs, omitHidden, null);
2073
2074     StringSelection ss = new StringSelection(output);
2075
2076     try
2077     {
2078       jalview.gui.Desktop.internalCopy = true;
2079       // Its really worth setting the clipboard contents
2080       // to empty before setting the large StringSelection!!
2081       Toolkit.getDefaultToolkit().getSystemClipboard()
2082               .setContents(new StringSelection(""), null);
2083
2084       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2085               Desktop.instance);
2086     } catch (OutOfMemoryError er)
2087     {
2088       new OOMWarning("copying region", er);
2089       return;
2090     }
2091
2092     HiddenColumns hiddenColumns = null;
2093     if (viewport.hasHiddenColumns())
2094     {
2095       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2096       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2097
2098       // create new HiddenColumns object with copy of hidden regions
2099       // between startRes and endRes, offset by startRes
2100       hiddenColumns = new HiddenColumns(
2101               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2102               hiddenCutoff, hiddenOffset);
2103     }
2104
2105     Desktop.jalviewClipboard = new Object[] { seqs,
2106         viewport.getAlignment().getDataset(), hiddenColumns };
2107     statusBar.setText(MessageManager.formatMessage(
2108             "label.copied_sequences_to_clipboard", new Object[]
2109             { Integer.valueOf(seqs.length).toString() }));
2110   }
2111
2112   /**
2113    * DOCUMENT ME!
2114    *
2115    * @param e
2116    *          DOCUMENT ME!
2117    * @throws InterruptedException
2118    * @throws IOException
2119    */
2120   @Override
2121   protected void pasteNew_actionPerformed(ActionEvent e)
2122           throws IOException, InterruptedException
2123   {
2124     paste(true);
2125   }
2126
2127   /**
2128    * DOCUMENT ME!
2129    *
2130    * @param e
2131    *          DOCUMENT ME!
2132    * @throws InterruptedException
2133    * @throws IOException
2134    */
2135   @Override
2136   protected void pasteThis_actionPerformed(ActionEvent e)
2137           throws IOException, InterruptedException
2138   {
2139     paste(false);
2140   }
2141
2142   /**
2143    * Paste contents of Jalview clipboard
2144    *
2145    * @param newAlignment
2146    *          true to paste to a new alignment, otherwise add to this.
2147    * @throws InterruptedException
2148    * @throws IOException
2149    */
2150   void paste(boolean newAlignment) throws IOException, InterruptedException
2151   {
2152     boolean externalPaste = true;
2153     try
2154     {
2155       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2156       Transferable contents = c.getContents(this);
2157
2158       if (contents == null)
2159       {
2160         return;
2161       }
2162
2163       String str;
2164       FileFormatI format;
2165       try
2166       {
2167         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2168         if (str.length() < 1)
2169         {
2170           return;
2171         }
2172
2173         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2174
2175       } catch (OutOfMemoryError er)
2176       {
2177         new OOMWarning("Out of memory pasting sequences!!", er);
2178         return;
2179       }
2180
2181       SequenceI[] sequences;
2182       boolean annotationAdded = false;
2183       AlignmentI alignment = null;
2184
2185       if (Desktop.jalviewClipboard != null)
2186       {
2187         // The clipboard was filled from within Jalview, we must use the
2188         // sequences
2189         // And dataset from the copied alignment
2190         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2191         // be doubly sure that we create *new* sequence objects.
2192         sequences = new SequenceI[newseq.length];
2193         for (int i = 0; i < newseq.length; i++)
2194         {
2195           sequences[i] = new Sequence(newseq[i]);
2196         }
2197         alignment = new Alignment(sequences);
2198         externalPaste = false;
2199       }
2200       else
2201       {
2202         // parse the clipboard as an alignment.
2203         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2204                 format);
2205         sequences = alignment.getSequencesArray();
2206       }
2207
2208       int alwidth = 0;
2209       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2210       int fgroup = -1;
2211
2212       if (newAlignment)
2213       {
2214
2215         if (Desktop.jalviewClipboard != null)
2216         {
2217           // dataset is inherited
2218           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2219         }
2220         else
2221         {
2222           // new dataset is constructed
2223           alignment.setDataset(null);
2224         }
2225         alwidth = alignment.getWidth() + 1;
2226       }
2227       else
2228       {
2229         AlignmentI pastedal = alignment; // preserve pasted alignment object
2230         // Add pasted sequences and dataset into existing alignment.
2231         alignment = viewport.getAlignment();
2232         alwidth = alignment.getWidth() + 1;
2233         // decide if we need to import sequences from an existing dataset
2234         boolean importDs = Desktop.jalviewClipboard != null
2235                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2236         // importDs==true instructs us to copy over new dataset sequences from
2237         // an existing alignment
2238         Vector newDs = (importDs) ? new Vector() : null; // used to create
2239         // minimum dataset set
2240
2241         for (int i = 0; i < sequences.length; i++)
2242         {
2243           if (importDs)
2244           {
2245             newDs.addElement(null);
2246           }
2247           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2248           // paste
2249           if (importDs && ds != null)
2250           {
2251             if (!newDs.contains(ds))
2252             {
2253               newDs.setElementAt(ds, i);
2254               ds = new Sequence(ds);
2255               // update with new dataset sequence
2256               sequences[i].setDatasetSequence(ds);
2257             }
2258             else
2259             {
2260               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2261             }
2262           }
2263           else
2264           {
2265             // copy and derive new dataset sequence
2266             sequences[i] = sequences[i].deriveSequence();
2267             alignment.getDataset()
2268                     .addSequence(sequences[i].getDatasetSequence());
2269             // TODO: avoid creation of duplicate dataset sequences with a
2270             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2271           }
2272           alignment.addSequence(sequences[i]); // merges dataset
2273         }
2274         if (newDs != null)
2275         {
2276           newDs.clear(); // tidy up
2277         }
2278         if (alignment.getAlignmentAnnotation() != null)
2279         {
2280           for (AlignmentAnnotation alan : alignment
2281                   .getAlignmentAnnotation())
2282           {
2283             if (alan.graphGroup > fgroup)
2284             {
2285               fgroup = alan.graphGroup;
2286             }
2287           }
2288         }
2289         if (pastedal.getAlignmentAnnotation() != null)
2290         {
2291           // Add any annotation attached to alignment.
2292           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2293           for (int i = 0; i < alann.length; i++)
2294           {
2295             annotationAdded = true;
2296             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2297             {
2298               AlignmentAnnotation newann = new AlignmentAnnotation(
2299                       alann[i]);
2300               if (newann.graphGroup > -1)
2301               {
2302                 if (newGraphGroups.size() <= newann.graphGroup
2303                         || newGraphGroups.get(newann.graphGroup) == null)
2304                 {
2305                   for (int q = newGraphGroups
2306                           .size(); q <= newann.graphGroup; q++)
2307                   {
2308                     newGraphGroups.add(q, null);
2309                   }
2310                   newGraphGroups.set(newann.graphGroup,
2311                           new Integer(++fgroup));
2312                 }
2313                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2314                         .intValue();
2315               }
2316
2317               newann.padAnnotation(alwidth);
2318               alignment.addAnnotation(newann);
2319             }
2320           }
2321         }
2322       }
2323       if (!newAlignment)
2324       {
2325         // /////
2326         // ADD HISTORY ITEM
2327         //
2328         addHistoryItem(new EditCommand(
2329                 MessageManager.getString("label.add_sequences"),
2330                 Action.PASTE, sequences, 0, alignment.getWidth(),
2331                 alignment));
2332       }
2333       // Add any annotations attached to sequences
2334       for (int i = 0; i < sequences.length; i++)
2335       {
2336         if (sequences[i].getAnnotation() != null)
2337         {
2338           AlignmentAnnotation newann;
2339           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2340           {
2341             annotationAdded = true;
2342             newann = sequences[i].getAnnotation()[a];
2343             newann.adjustForAlignment();
2344             newann.padAnnotation(alwidth);
2345             if (newann.graphGroup > -1)
2346             {
2347               if (newann.graphGroup > -1)
2348               {
2349                 if (newGraphGroups.size() <= newann.graphGroup
2350                         || newGraphGroups.get(newann.graphGroup) == null)
2351                 {
2352                   for (int q = newGraphGroups
2353                           .size(); q <= newann.graphGroup; q++)
2354                   {
2355                     newGraphGroups.add(q, null);
2356                   }
2357                   newGraphGroups.set(newann.graphGroup,
2358                           new Integer(++fgroup));
2359                 }
2360                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2361                         .intValue();
2362               }
2363             }
2364             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2365             // was
2366             // duplicated
2367             // earlier
2368             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2369                     a);
2370           }
2371         }
2372       }
2373       if (!newAlignment)
2374       {
2375
2376         // propagate alignment changed.
2377         viewport.getRanges().setEndSeq(alignment.getHeight());
2378         if (annotationAdded)
2379         {
2380           // Duplicate sequence annotation in all views.
2381           AlignmentI[] alview = this.getViewAlignments();
2382           for (int i = 0; i < sequences.length; i++)
2383           {
2384             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2385             if (sann == null)
2386             {
2387               continue;
2388             }
2389             for (int avnum = 0; avnum < alview.length; avnum++)
2390             {
2391               if (alview[avnum] != alignment)
2392               {
2393                 // duplicate in a view other than the one with input focus
2394                 int avwidth = alview[avnum].getWidth() + 1;
2395                 // this relies on sann being preserved after we
2396                 // modify the sequence's annotation array for each duplication
2397                 for (int a = 0; a < sann.length; a++)
2398                 {
2399                   AlignmentAnnotation newann = new AlignmentAnnotation(
2400                           sann[a]);
2401                   sequences[i].addAlignmentAnnotation(newann);
2402                   newann.padAnnotation(avwidth);
2403                   alview[avnum].addAnnotation(newann); // annotation was
2404                   // duplicated earlier
2405                   // TODO JAL-1145 graphGroups are not updated for sequence
2406                   // annotation added to several views. This may cause
2407                   // strangeness
2408                   alview[avnum].setAnnotationIndex(newann, a);
2409                 }
2410               }
2411             }
2412           }
2413           buildSortByAnnotationScoresMenu();
2414         }
2415         viewport.firePropertyChange("alignment", null,
2416                 alignment.getSequences());
2417         if (alignPanels != null)
2418         {
2419           for (AlignmentPanel ap : alignPanels)
2420           {
2421             ap.validateAnnotationDimensions(false);
2422           }
2423         }
2424         else
2425         {
2426           alignPanel.validateAnnotationDimensions(false);
2427         }
2428
2429       }
2430       else
2431       {
2432         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2433                 DEFAULT_HEIGHT);
2434         String newtitle = new String("Copied sequences");
2435
2436         if (Desktop.jalviewClipboard != null
2437                 && Desktop.jalviewClipboard[2] != null)
2438         {
2439           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2440           af.viewport.setHiddenColumns(hc);
2441         }
2442
2443         // >>>This is a fix for the moment, until a better solution is
2444         // found!!<<<
2445         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2446                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2447                         .getFeatureRenderer());
2448
2449         // TODO: maintain provenance of an alignment, rather than just make the
2450         // title a concatenation of operations.
2451         if (!externalPaste)
2452         {
2453           if (title.startsWith("Copied sequences"))
2454           {
2455             newtitle = title;
2456           }
2457           else
2458           {
2459             newtitle = newtitle.concat("- from " + title);
2460           }
2461         }
2462         else
2463         {
2464           newtitle = new String("Pasted sequences");
2465         }
2466
2467         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2468                 DEFAULT_HEIGHT);
2469
2470       }
2471
2472     } catch (Exception ex)
2473     {
2474       ex.printStackTrace();
2475       System.out.println("Exception whilst pasting: " + ex);
2476       // could be anything being pasted in here
2477     }
2478   }
2479
2480   @Override
2481   protected void expand_newalign(ActionEvent e)
2482   {
2483     try
2484     {
2485       AlignmentI alignment = AlignmentUtils
2486               .expandContext(getViewport().getAlignment(), -1);
2487       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2488               DEFAULT_HEIGHT);
2489       String newtitle = new String("Flanking alignment");
2490
2491       if (Desktop.jalviewClipboard != null
2492               && Desktop.jalviewClipboard[2] != null)
2493       {
2494         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2495         af.viewport.setHiddenColumns(hc);
2496       }
2497
2498       // >>>This is a fix for the moment, until a better solution is
2499       // found!!<<<
2500       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2501               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2502                       .getFeatureRenderer());
2503
2504       // TODO: maintain provenance of an alignment, rather than just make the
2505       // title a concatenation of operations.
2506       {
2507         if (title.startsWith("Copied sequences"))
2508         {
2509           newtitle = title;
2510         }
2511         else
2512         {
2513           newtitle = newtitle.concat("- from " + title);
2514         }
2515       }
2516
2517       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2518
2519     } catch (Exception ex)
2520     {
2521       ex.printStackTrace();
2522       System.out.println("Exception whilst pasting: " + ex);
2523       // could be anything being pasted in here
2524     } catch (OutOfMemoryError oom)
2525     {
2526       new OOMWarning("Viewing flanking region of alignment", oom);
2527     }
2528   }
2529
2530   /**
2531    * DOCUMENT ME!
2532    *
2533    * @param e
2534    *          DOCUMENT ME!
2535    */
2536   @Override
2537   protected void cut_actionPerformed(ActionEvent e)
2538   {
2539     copy_actionPerformed(null);
2540     delete_actionPerformed(null);
2541   }
2542
2543   /**
2544    * DOCUMENT ME!
2545    *
2546    * @param e
2547    *          DOCUMENT ME!
2548    */
2549   @Override
2550   protected void delete_actionPerformed(ActionEvent evt)
2551   {
2552
2553     SequenceGroup sg = viewport.getSelectionGroup();
2554     if (sg == null)
2555     {
2556       return;
2557     }
2558
2559     /*
2560      * If the cut affects all sequences, warn, remove highlighted columns
2561      */
2562     if (sg.getSize() == viewport.getAlignment().getHeight())
2563     {
2564       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2565               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2566       if (isEntireAlignWidth)
2567       {
2568         int confirm = JvOptionPane.showConfirmDialog(this,
2569                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2570                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2571                 JvOptionPane.OK_CANCEL_OPTION);
2572
2573         if (confirm == JvOptionPane.CANCEL_OPTION
2574                 || confirm == JvOptionPane.CLOSED_OPTION)
2575         {
2576           return;
2577         }
2578       }
2579       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2580               sg.getEndRes() + 1);
2581     }
2582     SequenceI[] cut = sg.getSequences()
2583             .toArray(new SequenceI[sg.getSize()]);
2584
2585     addHistoryItem(new EditCommand(
2586             MessageManager.getString("label.cut_sequences"), Action.CUT,
2587             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2588             viewport.getAlignment()));
2589
2590     viewport.setSelectionGroup(null);
2591     viewport.sendSelection();
2592     viewport.getAlignment().deleteGroup(sg);
2593
2594     viewport.firePropertyChange("alignment", null,
2595             viewport.getAlignment().getSequences());
2596     if (viewport.getAlignment().getHeight() < 1)
2597     {
2598       try
2599       {
2600         this.setClosed(true);
2601       } catch (Exception ex)
2602       {
2603       }
2604     }
2605   }
2606
2607   /**
2608    * DOCUMENT ME!
2609    *
2610    * @param e
2611    *          DOCUMENT ME!
2612    */
2613   @Override
2614   protected void deleteGroups_actionPerformed(ActionEvent e)
2615   {
2616     if (avc.deleteGroups())
2617     {
2618       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2619       alignPanel.updateAnnotation();
2620       alignPanel.paintAlignment(true, true);
2621     }
2622   }
2623
2624   /**
2625    * DOCUMENT ME!
2626    *
2627    * @param e
2628    *          DOCUMENT ME!
2629    */
2630   @Override
2631   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2632   {
2633     SequenceGroup sg = new SequenceGroup();
2634
2635     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2636     {
2637       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2638     }
2639
2640     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2641     viewport.setSelectionGroup(sg);
2642     viewport.sendSelection();
2643     // JAL-2034 - should delegate to
2644     // alignPanel to decide if overview needs
2645     // updating.
2646     alignPanel.paintAlignment(false, false);
2647     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2648   }
2649
2650   /**
2651    * DOCUMENT ME!
2652    *
2653    * @param e
2654    *          DOCUMENT ME!
2655    */
2656   @Override
2657   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2658   {
2659     if (viewport.cursorMode)
2660     {
2661       alignPanel.getSeqPanel().keyboardNo1 = null;
2662       alignPanel.getSeqPanel().keyboardNo2 = null;
2663     }
2664     viewport.setSelectionGroup(null);
2665     viewport.getColumnSelection().clear();
2666     viewport.setSelectionGroup(null);
2667     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2668     // JAL-2034 - should delegate to
2669     // alignPanel to decide if overview needs
2670     // updating.
2671     alignPanel.paintAlignment(false, false);
2672     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2673     viewport.sendSelection();
2674   }
2675
2676   /**
2677    * DOCUMENT ME!
2678    *
2679    * @param e
2680    *          DOCUMENT ME!
2681    */
2682   @Override
2683   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2684   {
2685     SequenceGroup sg = viewport.getSelectionGroup();
2686
2687     if (sg == null)
2688     {
2689       selectAllSequenceMenuItem_actionPerformed(null);
2690
2691       return;
2692     }
2693
2694     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2695     {
2696       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2697     }
2698     // JAL-2034 - should delegate to
2699     // alignPanel to decide if overview needs
2700     // updating.
2701
2702     alignPanel.paintAlignment(true, false);
2703     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2704     viewport.sendSelection();
2705   }
2706
2707   @Override
2708   public void invertColSel_actionPerformed(ActionEvent e)
2709   {
2710     viewport.invertColumnSelection();
2711     alignPanel.paintAlignment(true, false);
2712     viewport.sendSelection();
2713   }
2714
2715   /**
2716    * DOCUMENT ME!
2717    *
2718    * @param e
2719    *          DOCUMENT ME!
2720    */
2721   @Override
2722   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2723   {
2724     trimAlignment(true);
2725   }
2726
2727   /**
2728    * DOCUMENT ME!
2729    *
2730    * @param e
2731    *          DOCUMENT ME!
2732    */
2733   @Override
2734   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2735   {
2736     trimAlignment(false);
2737   }
2738
2739   void trimAlignment(boolean trimLeft)
2740   {
2741     ColumnSelection colSel = viewport.getColumnSelection();
2742     int column;
2743
2744     if (!colSel.isEmpty())
2745     {
2746       if (trimLeft)
2747       {
2748         column = colSel.getMin();
2749       }
2750       else
2751       {
2752         column = colSel.getMax();
2753       }
2754
2755       SequenceI[] seqs;
2756       if (viewport.getSelectionGroup() != null)
2757       {
2758         seqs = viewport.getSelectionGroup()
2759                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2760       }
2761       else
2762       {
2763         seqs = viewport.getAlignment().getSequencesArray();
2764       }
2765
2766       TrimRegionCommand trimRegion;
2767       if (trimLeft)
2768       {
2769         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2770                 column, viewport.getAlignment());
2771         viewport.getRanges().setStartRes(0);
2772       }
2773       else
2774       {
2775         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2776                 column, viewport.getAlignment());
2777       }
2778
2779       statusBar.setText(MessageManager
2780               .formatMessage("label.removed_columns", new String[]
2781               { Integer.valueOf(trimRegion.getSize()).toString() }));
2782
2783       addHistoryItem(trimRegion);
2784
2785       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2786       {
2787         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2788                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2789         {
2790           viewport.getAlignment().deleteGroup(sg);
2791         }
2792       }
2793
2794       viewport.firePropertyChange("alignment", null,
2795               viewport.getAlignment().getSequences());
2796     }
2797   }
2798
2799   /**
2800    * DOCUMENT ME!
2801    *
2802    * @param e
2803    *          DOCUMENT ME!
2804    */
2805   @Override
2806   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2807   {
2808     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2809
2810     SequenceI[] seqs;
2811     if (viewport.getSelectionGroup() != null)
2812     {
2813       seqs = viewport.getSelectionGroup()
2814               .getSequencesAsArray(viewport.getHiddenRepSequences());
2815       start = viewport.getSelectionGroup().getStartRes();
2816       end = viewport.getSelectionGroup().getEndRes();
2817     }
2818     else
2819     {
2820       seqs = viewport.getAlignment().getSequencesArray();
2821     }
2822
2823     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2824             "Remove Gapped Columns", seqs, start, end,
2825             viewport.getAlignment());
2826
2827     addHistoryItem(removeGapCols);
2828
2829     statusBar.setText(MessageManager
2830             .formatMessage("label.removed_empty_columns", new Object[]
2831             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2832
2833     // This is to maintain viewport position on first residue
2834     // of first sequence
2835     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2836     ViewportRanges ranges = viewport.getRanges();
2837     int startRes = seq.findPosition(ranges.getStartRes());
2838     // ShiftList shifts;
2839     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2840     // edit.alColumnChanges=shifts.getInverse();
2841     // if (viewport.hasHiddenColumns)
2842     // viewport.getColumnSelection().compensateForEdits(shifts);
2843     ranges.setStartRes(seq.findIndex(startRes) - 1);
2844     viewport.firePropertyChange("alignment", null,
2845             viewport.getAlignment().getSequences());
2846
2847   }
2848
2849   /**
2850    * DOCUMENT ME!
2851    *
2852    * @param e
2853    *          DOCUMENT ME!
2854    */
2855   @Override
2856   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2857   {
2858     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2859
2860     SequenceI[] seqs;
2861     if (viewport.getSelectionGroup() != null)
2862     {
2863       seqs = viewport.getSelectionGroup()
2864               .getSequencesAsArray(viewport.getHiddenRepSequences());
2865       start = viewport.getSelectionGroup().getStartRes();
2866       end = viewport.getSelectionGroup().getEndRes();
2867     }
2868     else
2869     {
2870       seqs = viewport.getAlignment().getSequencesArray();
2871     }
2872
2873     // This is to maintain viewport position on first residue
2874     // of first sequence
2875     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2876     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2877
2878     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2879             viewport.getAlignment()));
2880
2881     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2882
2883     viewport.firePropertyChange("alignment", null,
2884             viewport.getAlignment().getSequences());
2885
2886   }
2887
2888   /**
2889    * DOCUMENT ME!
2890    *
2891    * @param e
2892    *          DOCUMENT ME!
2893    */
2894   @Override
2895   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2896   {
2897     viewport.setPadGaps(padGapsMenuitem.isSelected());
2898     viewport.firePropertyChange("alignment", null,
2899             viewport.getAlignment().getSequences());
2900   }
2901
2902   /**
2903    * DOCUMENT ME!
2904    *
2905    * @param e
2906    *          DOCUMENT ME!
2907    */
2908   @Override
2909   public void findMenuItem_actionPerformed(ActionEvent e)
2910   {
2911     new Finder();
2912   }
2913
2914   /**
2915    * Create a new view of the current alignment.
2916    */
2917   @Override
2918   public void newView_actionPerformed(ActionEvent e)
2919   {
2920     newView(null, true);
2921   }
2922
2923   /**
2924    * Creates and shows a new view of the current alignment.
2925    *
2926    * @param viewTitle
2927    *          title of newly created view; if null, one will be generated
2928    * @param copyAnnotation
2929    *          if true then duplicate all annnotation, groups and settings
2930    * @return new alignment panel, already displayed.
2931    */
2932   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2933   {
2934     /*
2935      * Create a new AlignmentPanel (with its own, new Viewport)
2936      */
2937     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2938     if (!copyAnnotation)
2939     {
2940       /*
2941        * remove all groups and annotation except for the automatic stuff
2942        */
2943       newap.av.getAlignment().deleteAllGroups();
2944       newap.av.getAlignment().deleteAllAnnotations(false);
2945     }
2946
2947     newap.av.setGatherViewsHere(false);
2948
2949     if (viewport.viewName == null)
2950     {
2951       viewport.viewName = MessageManager
2952               .getString("label.view_name_original");
2953     }
2954
2955     /*
2956      * Views share the same edits undo and redo stacks
2957      */
2958     newap.av.setHistoryList(viewport.getHistoryList());
2959     newap.av.setRedoList(viewport.getRedoList());
2960
2961     /*
2962      * Views share the same mappings; need to deregister any new mappings
2963      * created by copyAlignPanel, and register the new reference to the shared
2964      * mappings
2965      */
2966     newap.av.replaceMappings(viewport.getAlignment());
2967
2968     /*
2969      * start up cDNA consensus (if applicable) now mappings are in place
2970      */
2971     if (newap.av.initComplementConsensus())
2972     {
2973       newap.refresh(true); // adjust layout of annotations
2974     }
2975
2976     newap.av.viewName = getNewViewName(viewTitle);
2977
2978     addAlignmentPanel(newap, true);
2979     newap.alignmentChanged();
2980
2981     if (alignPanels.size() == 2)
2982     {
2983       viewport.setGatherViewsHere(true);
2984     }
2985     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2986     return newap;
2987   }
2988
2989   /**
2990    * Make a new name for the view, ensuring it is unique within the current
2991    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2992    * these now use viewId. Unique view names are still desirable for usability.)
2993    *
2994    * @param viewTitle
2995    * @return
2996    */
2997   protected String getNewViewName(String viewTitle)
2998   {
2999     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3000     boolean addFirstIndex = false;
3001     if (viewTitle == null || viewTitle.trim().length() == 0)
3002     {
3003       viewTitle = MessageManager.getString("action.view");
3004       addFirstIndex = true;
3005     }
3006     else
3007     {
3008       index = 1;// we count from 1 if given a specific name
3009     }
3010     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3011
3012     List<Component> comps = PaintRefresher.components
3013             .get(viewport.getSequenceSetId());
3014
3015     List<String> existingNames = getExistingViewNames(comps);
3016
3017     while (existingNames.contains(newViewName))
3018     {
3019       newViewName = viewTitle + " " + (++index);
3020     }
3021     return newViewName;
3022   }
3023
3024   /**
3025    * Returns a list of distinct view names found in the given list of
3026    * components. View names are held on the viewport of an AlignmentPanel.
3027    *
3028    * @param comps
3029    * @return
3030    */
3031   protected List<String> getExistingViewNames(List<Component> comps)
3032   {
3033     List<String> existingNames = new ArrayList<>();
3034     for (Component comp : comps)
3035     {
3036       if (comp instanceof AlignmentPanel)
3037       {
3038         AlignmentPanel ap = (AlignmentPanel) comp;
3039         if (!existingNames.contains(ap.av.viewName))
3040         {
3041           existingNames.add(ap.av.viewName);
3042         }
3043       }
3044     }
3045     return existingNames;
3046   }
3047
3048   /**
3049    * Explode tabbed views into separate windows.
3050    */
3051   @Override
3052   public void expandViews_actionPerformed(ActionEvent e)
3053   {
3054     Desktop.explodeViews(this);
3055   }
3056
3057   /**
3058    * Gather views in separate windows back into a tabbed presentation.
3059    */
3060   @Override
3061   public void gatherViews_actionPerformed(ActionEvent e)
3062   {
3063     Desktop.instance.gatherViews(this);
3064   }
3065
3066   /**
3067    * DOCUMENT ME!
3068    *
3069    * @param e
3070    *          DOCUMENT ME!
3071    */
3072   @Override
3073   public void font_actionPerformed(ActionEvent e)
3074   {
3075     new FontChooser(alignPanel);
3076   }
3077
3078   /**
3079    * DOCUMENT ME!
3080    *
3081    * @param e
3082    *          DOCUMENT ME!
3083    */
3084   @Override
3085   protected void seqLimit_actionPerformed(ActionEvent e)
3086   {
3087     viewport.setShowJVSuffix(seqLimits.isSelected());
3088
3089     alignPanel.getIdPanel().getIdCanvas()
3090             .setPreferredSize(alignPanel.calculateIdWidth());
3091     alignPanel.paintAlignment(true, false);
3092   }
3093
3094   @Override
3095   public void idRightAlign_actionPerformed(ActionEvent e)
3096   {
3097     viewport.setRightAlignIds(idRightAlign.isSelected());
3098     alignPanel.paintAlignment(false, false);
3099   }
3100
3101   @Override
3102   public void centreColumnLabels_actionPerformed(ActionEvent e)
3103   {
3104     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3105     alignPanel.paintAlignment(false, false);
3106   }
3107
3108   /*
3109    * (non-Javadoc)
3110    *
3111    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3112    */
3113   @Override
3114   protected void followHighlight_actionPerformed()
3115   {
3116     /*
3117      * Set the 'follow' flag on the Viewport (and scroll to position if now
3118      * true).
3119      */
3120     final boolean state = this.followHighlightMenuItem.getState();
3121     viewport.setFollowHighlight(state);
3122     if (state)
3123     {
3124       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3125     }
3126   }
3127
3128   /**
3129    * DOCUMENT ME!
3130    *
3131    * @param e
3132    *          DOCUMENT ME!
3133    */
3134   @Override
3135   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3136   {
3137     viewport.setColourText(colourTextMenuItem.isSelected());
3138     alignPanel.paintAlignment(false, false);
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   public void wrapMenuItem_actionPerformed(ActionEvent e)
3149   {
3150     scaleAbove.setVisible(wrapMenuItem.isSelected());
3151     scaleLeft.setVisible(wrapMenuItem.isSelected());
3152     scaleRight.setVisible(wrapMenuItem.isSelected());
3153     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3154     alignPanel.updateLayout();
3155   }
3156
3157   @Override
3158   public void showAllSeqs_actionPerformed(ActionEvent e)
3159   {
3160     viewport.showAllHiddenSeqs();
3161   }
3162
3163   @Override
3164   public void showAllColumns_actionPerformed(ActionEvent e)
3165   {
3166     viewport.showAllHiddenColumns();
3167     alignPanel.paintAlignment(true, true);
3168     viewport.sendSelection();
3169   }
3170
3171   @Override
3172   public void hideSelSequences_actionPerformed(ActionEvent e)
3173   {
3174     viewport.hideAllSelectedSeqs();
3175   }
3176
3177   /**
3178    * called by key handler and the hide all/show all menu items
3179    *
3180    * @param toggleSeqs
3181    * @param toggleCols
3182    */
3183   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3184   {
3185
3186     boolean hide = false;
3187     SequenceGroup sg = viewport.getSelectionGroup();
3188     if (!toggleSeqs && !toggleCols)
3189     {
3190       // Hide everything by the current selection - this is a hack - we do the
3191       // invert and then hide
3192       // first check that there will be visible columns after the invert.
3193       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3194               && sg.getStartRes() <= sg.getEndRes()))
3195       {
3196         // now invert the sequence set, if required - empty selection implies
3197         // that no hiding is required.
3198         if (sg != null)
3199         {
3200           invertSequenceMenuItem_actionPerformed(null);
3201           sg = viewport.getSelectionGroup();
3202           toggleSeqs = true;
3203
3204         }
3205         viewport.expandColSelection(sg, true);
3206         // finally invert the column selection and get the new sequence
3207         // selection.
3208         invertColSel_actionPerformed(null);
3209         toggleCols = true;
3210       }
3211     }
3212
3213     if (toggleSeqs)
3214     {
3215       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3216       {
3217         hideSelSequences_actionPerformed(null);
3218         hide = true;
3219       }
3220       else if (!(toggleCols && viewport.hasSelectedColumns()))
3221       {
3222         showAllSeqs_actionPerformed(null);
3223       }
3224     }
3225
3226     if (toggleCols)
3227     {
3228       if (viewport.hasSelectedColumns())
3229       {
3230         hideSelColumns_actionPerformed(null);
3231         if (!toggleSeqs)
3232         {
3233           viewport.setSelectionGroup(sg);
3234         }
3235       }
3236       else if (!hide)
3237       {
3238         showAllColumns_actionPerformed(null);
3239       }
3240     }
3241   }
3242
3243   /*
3244    * (non-Javadoc)
3245    *
3246    * @see
3247    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3248    * event.ActionEvent)
3249    */
3250   @Override
3251   public void hideAllButSelection_actionPerformed(ActionEvent e)
3252   {
3253     toggleHiddenRegions(false, false);
3254     viewport.sendSelection();
3255   }
3256
3257   /*
3258    * (non-Javadoc)
3259    *
3260    * @see
3261    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3262    * .ActionEvent)
3263    */
3264   @Override
3265   public void hideAllSelection_actionPerformed(ActionEvent e)
3266   {
3267     SequenceGroup sg = viewport.getSelectionGroup();
3268     viewport.expandColSelection(sg, false);
3269     viewport.hideAllSelectedSeqs();
3270     viewport.hideSelectedColumns();
3271     alignPanel.paintAlignment(true, true);
3272     viewport.sendSelection();
3273   }
3274
3275   /*
3276    * (non-Javadoc)
3277    *
3278    * @see
3279    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3280    * ActionEvent)
3281    */
3282   @Override
3283   public void showAllhidden_actionPerformed(ActionEvent e)
3284   {
3285     viewport.showAllHiddenColumns();
3286     viewport.showAllHiddenSeqs();
3287     alignPanel.paintAlignment(true, true);
3288     viewport.sendSelection();
3289   }
3290
3291   @Override
3292   public void hideSelColumns_actionPerformed(ActionEvent e)
3293   {
3294     viewport.hideSelectedColumns();
3295     alignPanel.paintAlignment(true, true);
3296     viewport.sendSelection();
3297   }
3298
3299   @Override
3300   public void hiddenMarkers_actionPerformed(ActionEvent e)
3301   {
3302     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3303     repaint();
3304   }
3305
3306   /**
3307    * DOCUMENT ME!
3308    *
3309    * @param e
3310    *          DOCUMENT ME!
3311    */
3312   @Override
3313   protected void scaleAbove_actionPerformed(ActionEvent e)
3314   {
3315     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3316     // TODO: do we actually need to update overview for scale above change ?
3317     alignPanel.paintAlignment(true, false);
3318   }
3319
3320   /**
3321    * DOCUMENT ME!
3322    *
3323    * @param e
3324    *          DOCUMENT ME!
3325    */
3326   @Override
3327   protected void scaleLeft_actionPerformed(ActionEvent e)
3328   {
3329     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3330     alignPanel.paintAlignment(true, false);
3331   }
3332
3333   /**
3334    * DOCUMENT ME!
3335    *
3336    * @param e
3337    *          DOCUMENT ME!
3338    */
3339   @Override
3340   protected void scaleRight_actionPerformed(ActionEvent e)
3341   {
3342     viewport.setScaleRightWrapped(scaleRight.isSelected());
3343     alignPanel.paintAlignment(true, false);
3344   }
3345
3346   /**
3347    * DOCUMENT ME!
3348    *
3349    * @param e
3350    *          DOCUMENT ME!
3351    */
3352   @Override
3353   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3354   {
3355     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3356     alignPanel.paintAlignment(false, false);
3357   }
3358
3359   /**
3360    * DOCUMENT ME!
3361    *
3362    * @param e
3363    *          DOCUMENT ME!
3364    */
3365   @Override
3366   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3367   {
3368     viewport.setShowText(viewTextMenuItem.isSelected());
3369     alignPanel.paintAlignment(false, false);
3370   }
3371
3372   /**
3373    * DOCUMENT ME!
3374    *
3375    * @param e
3376    *          DOCUMENT ME!
3377    */
3378   @Override
3379   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3380   {
3381     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3382     alignPanel.paintAlignment(false, false);
3383   }
3384
3385   public FeatureSettings featureSettings;
3386
3387   @Override
3388   public FeatureSettingsControllerI getFeatureSettingsUI()
3389   {
3390     return featureSettings;
3391   }
3392
3393   @Override
3394   public void featureSettings_actionPerformed(ActionEvent e)
3395   {
3396     if (featureSettings != null)
3397     {
3398       featureSettings.close();
3399       featureSettings = null;
3400     }
3401     if (!showSeqFeatures.isSelected())
3402     {
3403       // make sure features are actually displayed
3404       showSeqFeatures.setSelected(true);
3405       showSeqFeatures_actionPerformed(null);
3406     }
3407     featureSettings = new FeatureSettings(this);
3408   }
3409
3410   /**
3411    * Set or clear 'Show Sequence Features'
3412    *
3413    * @param evt
3414    *          DOCUMENT ME!
3415    */
3416   @Override
3417   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3418   {
3419     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3420     alignPanel.paintAlignment(true, true);
3421   }
3422
3423   /**
3424    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3425    * the annotations panel as a whole.
3426    *
3427    * The options to show/hide all annotations should be enabled when the panel
3428    * is shown, and disabled when the panel is hidden.
3429    *
3430    * @param e
3431    */
3432   @Override
3433   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3434   {
3435     final boolean setVisible = annotationPanelMenuItem.isSelected();
3436     viewport.setShowAnnotation(setVisible);
3437     this.showAllSeqAnnotations.setEnabled(setVisible);
3438     this.hideAllSeqAnnotations.setEnabled(setVisible);
3439     this.showAllAlAnnotations.setEnabled(setVisible);
3440     this.hideAllAlAnnotations.setEnabled(setVisible);
3441     alignPanel.updateLayout();
3442   }
3443
3444   @Override
3445   public void alignmentProperties()
3446   {
3447     JEditorPane editPane = new JEditorPane("text/html", "");
3448     editPane.setEditable(false);
3449     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3450             .formatAsHtml();
3451     editPane.setText(
3452             MessageManager.formatMessage("label.html_content", new Object[]
3453             { contents.toString() }));
3454     JInternalFrame frame = new JInternalFrame();
3455     frame.getContentPane().add(new JScrollPane(editPane));
3456
3457     Desktop.addInternalFrame(frame, MessageManager
3458             .formatMessage("label.alignment_properties", new Object[]
3459             { getTitle() }), 500, 400);
3460   }
3461
3462   /**
3463    * DOCUMENT ME!
3464    *
3465    * @param e
3466    *          DOCUMENT ME!
3467    */
3468   @Override
3469   public void overviewMenuItem_actionPerformed(ActionEvent e)
3470   {
3471     if (alignPanel.overviewPanel != null)
3472     {
3473       return;
3474     }
3475
3476     JInternalFrame frame = new JInternalFrame();
3477     final OverviewPanel overview = new OverviewPanel(alignPanel);
3478     frame.setContentPane(overview);
3479     Desktop.addInternalFrame(frame, MessageManager
3480             .formatMessage("label.overview_params", new Object[]
3481             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3482             true, true);
3483     frame.pack();
3484     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3485     frame.addInternalFrameListener(
3486             new javax.swing.event.InternalFrameAdapter()
3487             {
3488               @Override
3489               public void internalFrameClosed(
3490                       javax.swing.event.InternalFrameEvent evt)
3491               {
3492                 overview.dispose();
3493                 alignPanel.setOverviewPanel(null);
3494               };
3495             });
3496
3497     alignPanel.setOverviewPanel(overview);
3498   }
3499
3500   @Override
3501   public void textColour_actionPerformed()
3502   {
3503     new TextColourChooser().chooseColour(alignPanel, null);
3504   }
3505
3506   /*
3507    * public void covariationColour_actionPerformed() {
3508    * changeColour(new
3509    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3510    * ()[0])); }
3511    */
3512   @Override
3513   public void annotationColour_actionPerformed()
3514   {
3515     new AnnotationColourChooser(viewport, alignPanel);
3516   }
3517
3518   @Override
3519   public void annotationColumn_actionPerformed(ActionEvent e)
3520   {
3521     new AnnotationColumnChooser(viewport, alignPanel);
3522   }
3523
3524   /**
3525    * Action on the user checking or unchecking the option to apply the selected
3526    * colour scheme to all groups. If unchecked, groups may have their own
3527    * independent colour schemes.
3528    *
3529    * @param selected
3530    */
3531   @Override
3532   public void applyToAllGroups_actionPerformed(boolean selected)
3533   {
3534     viewport.setColourAppliesToAllGroups(selected);
3535   }
3536
3537   /**
3538    * Action on user selecting a colour from the colour menu
3539    *
3540    * @param name
3541    *          the name (not the menu item label!) of the colour scheme
3542    */
3543   @Override
3544   public void changeColour_actionPerformed(String name)
3545   {
3546     /*
3547      * 'User Defined' opens a panel to configure or load a
3548      * user-defined colour scheme
3549      */
3550     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3551     {
3552       new UserDefinedColours(alignPanel);
3553       return;
3554     }
3555
3556     /*
3557      * otherwise set the chosen colour scheme (or null for 'None')
3558      */
3559     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3560             viewport.getAlignment(), viewport.getHiddenRepSequences());
3561     changeColour(cs);
3562   }
3563
3564   /**
3565    * Actions on setting or changing the alignment colour scheme
3566    *
3567    * @param cs
3568    */
3569   @Override
3570   public void changeColour(ColourSchemeI cs)
3571   {
3572     // TODO: pull up to controller method
3573     ColourMenuHelper.setColourSelected(colourMenu, cs);
3574
3575     viewport.setGlobalColourScheme(cs);
3576
3577     alignPanel.paintAlignment(true, true);
3578   }
3579
3580   /**
3581    * Show the PID threshold slider panel
3582    */
3583   @Override
3584   protected void modifyPID_actionPerformed()
3585   {
3586     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3587             alignPanel.getViewName());
3588     SliderPanel.showPIDSlider();
3589   }
3590
3591   /**
3592    * Show the Conservation slider panel
3593    */
3594   @Override
3595   protected void modifyConservation_actionPerformed()
3596   {
3597     SliderPanel.setConservationSlider(alignPanel,
3598             viewport.getResidueShading(), alignPanel.getViewName());
3599     SliderPanel.showConservationSlider();
3600   }
3601
3602   /**
3603    * Action on selecting or deselecting (Colour) By Conservation
3604    */
3605   @Override
3606   public void conservationMenuItem_actionPerformed(boolean selected)
3607   {
3608     modifyConservation.setEnabled(selected);
3609     viewport.setConservationSelected(selected);
3610     viewport.getResidueShading().setConservationApplied(selected);
3611
3612     changeColour(viewport.getGlobalColourScheme());
3613     if (selected)
3614     {
3615       modifyConservation_actionPerformed();
3616     }
3617     else
3618     {
3619       SliderPanel.hideConservationSlider();
3620     }
3621   }
3622
3623   /**
3624    * Action on selecting or deselecting (Colour) Above PID Threshold
3625    */
3626   @Override
3627   public void abovePIDThreshold_actionPerformed(boolean selected)
3628   {
3629     modifyPID.setEnabled(selected);
3630     viewport.setAbovePIDThreshold(selected);
3631     if (!selected)
3632     {
3633       viewport.getResidueShading().setThreshold(0,
3634               viewport.isIgnoreGapsConsensus());
3635     }
3636
3637     changeColour(viewport.getGlobalColourScheme());
3638     if (selected)
3639     {
3640       modifyPID_actionPerformed();
3641     }
3642     else
3643     {
3644       SliderPanel.hidePIDSlider();
3645     }
3646   }
3647
3648   /**
3649    * DOCUMENT ME!
3650    *
3651    * @param e
3652    *          DOCUMENT ME!
3653    */
3654   @Override
3655   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3656   {
3657     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3658     AlignmentSorter.sortByPID(viewport.getAlignment(),
3659             viewport.getAlignment().getSequenceAt(0));
3660     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3661             viewport.getAlignment()));
3662     alignPanel.paintAlignment(true, false);
3663   }
3664
3665   /**
3666    * DOCUMENT ME!
3667    *
3668    * @param e
3669    *          DOCUMENT ME!
3670    */
3671   @Override
3672   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3673   {
3674     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3675     AlignmentSorter.sortByID(viewport.getAlignment());
3676     addHistoryItem(
3677             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3678     alignPanel.paintAlignment(true, false);
3679   }
3680
3681   /**
3682    * DOCUMENT ME!
3683    *
3684    * @param e
3685    *          DOCUMENT ME!
3686    */
3687   @Override
3688   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3689   {
3690     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3691     AlignmentSorter.sortByLength(viewport.getAlignment());
3692     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3693             viewport.getAlignment()));
3694     alignPanel.paintAlignment(true, false);
3695   }
3696
3697   /**
3698    * DOCUMENT ME!
3699    *
3700    * @param e
3701    *          DOCUMENT ME!
3702    */
3703   @Override
3704   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3705   {
3706     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3707     AlignmentSorter.sortByGroup(viewport.getAlignment());
3708     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3709             viewport.getAlignment()));
3710
3711     alignPanel.paintAlignment(true, false);
3712   }
3713
3714   /**
3715    * DOCUMENT ME!
3716    *
3717    * @param e
3718    *          DOCUMENT ME!
3719    */
3720   @Override
3721   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3722   {
3723     new RedundancyPanel(alignPanel, this);
3724   }
3725
3726   /**
3727    * DOCUMENT ME!
3728    *
3729    * @param e
3730    *          DOCUMENT ME!
3731    */
3732   @Override
3733   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3734   {
3735     if ((viewport.getSelectionGroup() == null)
3736             || (viewport.getSelectionGroup().getSize() < 2))
3737     {
3738       JvOptionPane.showInternalMessageDialog(this,
3739               MessageManager.getString(
3740                       "label.you_must_select_least_two_sequences"),
3741               MessageManager.getString("label.invalid_selection"),
3742               JvOptionPane.WARNING_MESSAGE);
3743     }
3744     else
3745     {
3746       JInternalFrame frame = new JInternalFrame();
3747       frame.setContentPane(new PairwiseAlignPanel(viewport));
3748       Desktop.addInternalFrame(frame,
3749               MessageManager.getString("action.pairwise_alignment"), 600,
3750               500);
3751     }
3752   }
3753
3754   @Override
3755   public void autoCalculate_actionPerformed(ActionEvent e)
3756   {
3757     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3758     if (viewport.autoCalculateConsensus)
3759     {
3760       viewport.firePropertyChange("alignment", null,
3761               viewport.getAlignment().getSequences());
3762     }
3763   }
3764
3765   @Override
3766   public void sortByTreeOption_actionPerformed(ActionEvent e)
3767   {
3768     viewport.sortByTree = sortByTree.isSelected();
3769   }
3770
3771   @Override
3772   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3773   {
3774     viewport.followSelection = listenToViewSelections.isSelected();
3775   }
3776
3777   /**
3778    * Constructs a tree panel and adds it to the desktop
3779    *
3780    * @param type
3781    *          tree type (NJ or AV)
3782    * @param modelName
3783    *          name of score model used to compute the tree
3784    * @param options
3785    *          parameters for the distance or similarity calculation
3786    */
3787   void newTreePanel(String type, String modelName,
3788           SimilarityParamsI options)
3789   {
3790     String frameTitle = "";
3791     TreePanel tp;
3792
3793     boolean onSelection = false;
3794     if (viewport.getSelectionGroup() != null
3795             && viewport.getSelectionGroup().getSize() > 0)
3796     {
3797       SequenceGroup sg = viewport.getSelectionGroup();
3798
3799       /* Decide if the selection is a column region */
3800       for (SequenceI _s : sg.getSequences())
3801       {
3802         if (_s.getLength() < sg.getEndRes())
3803         {
3804           JvOptionPane.showMessageDialog(Desktop.desktop,
3805                   MessageManager.getString(
3806                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3807                   MessageManager.getString(
3808                           "label.sequences_selection_not_aligned"),
3809                   JvOptionPane.WARNING_MESSAGE);
3810
3811           return;
3812         }
3813       }
3814       onSelection = true;
3815     }
3816     else
3817     {
3818       if (viewport.getAlignment().getHeight() < 2)
3819       {
3820         return;
3821       }
3822     }
3823
3824     tp = new TreePanel(alignPanel, type, modelName, options);
3825     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3826
3827     frameTitle += " from ";
3828
3829     if (viewport.viewName != null)
3830     {
3831       frameTitle += viewport.viewName + " of ";
3832     }
3833
3834     frameTitle += this.title;
3835
3836     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3837   }
3838
3839   /**
3840    * DOCUMENT ME!
3841    *
3842    * @param title
3843    *          DOCUMENT ME!
3844    * @param order
3845    *          DOCUMENT ME!
3846    */
3847   public void addSortByOrderMenuItem(String title,
3848           final AlignmentOrder order)
3849   {
3850     final JMenuItem item = new JMenuItem(MessageManager
3851             .formatMessage("action.by_title_param", new Object[]
3852             { title }));
3853     sort.add(item);
3854     item.addActionListener(new java.awt.event.ActionListener()
3855     {
3856       @Override
3857       public void actionPerformed(ActionEvent e)
3858       {
3859         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3860
3861         // TODO: JBPNote - have to map order entries to curent SequenceI
3862         // pointers
3863         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3864
3865         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3866                 viewport.getAlignment()));
3867
3868         alignPanel.paintAlignment(true, false);
3869       }
3870     });
3871   }
3872
3873   /**
3874    * Add a new sort by annotation score menu item
3875    *
3876    * @param sort
3877    *          the menu to add the option to
3878    * @param scoreLabel
3879    *          the label used to retrieve scores for each sequence on the
3880    *          alignment
3881    */
3882   public void addSortByAnnotScoreMenuItem(JMenu sort,
3883           final String scoreLabel)
3884   {
3885     final JMenuItem item = new JMenuItem(scoreLabel);
3886     sort.add(item);
3887     item.addActionListener(new java.awt.event.ActionListener()
3888     {
3889       @Override
3890       public void actionPerformed(ActionEvent e)
3891       {
3892         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3893         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3894                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3895         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3896                 viewport.getAlignment()));
3897         alignPanel.paintAlignment(true, false);
3898       }
3899     });
3900   }
3901
3902   /**
3903    * last hash for alignment's annotation array - used to minimise cost of
3904    * rebuild.
3905    */
3906   protected int _annotationScoreVectorHash;
3907
3908   /**
3909    * search the alignment and rebuild the sort by annotation score submenu the
3910    * last alignment annotation vector hash is stored to minimize cost of
3911    * rebuilding in subsequence calls.
3912    *
3913    */
3914   @Override
3915   public void buildSortByAnnotationScoresMenu()
3916   {
3917     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3918     {
3919       return;
3920     }
3921
3922     if (viewport.getAlignment().getAlignmentAnnotation()
3923             .hashCode() != _annotationScoreVectorHash)
3924     {
3925       sortByAnnotScore.removeAll();
3926       // almost certainly a quicker way to do this - but we keep it simple
3927       Hashtable scoreSorts = new Hashtable();
3928       AlignmentAnnotation aann[];
3929       for (SequenceI sqa : viewport.getAlignment().getSequences())
3930       {
3931         aann = sqa.getAnnotation();
3932         for (int i = 0; aann != null && i < aann.length; i++)
3933         {
3934           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3935           {
3936             scoreSorts.put(aann[i].label, aann[i].label);
3937           }
3938         }
3939       }
3940       Enumeration labels = scoreSorts.keys();
3941       while (labels.hasMoreElements())
3942       {
3943         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3944                 (String) labels.nextElement());
3945       }
3946       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3947       scoreSorts.clear();
3948
3949       _annotationScoreVectorHash = viewport.getAlignment()
3950               .getAlignmentAnnotation().hashCode();
3951     }
3952   }
3953
3954   /**
3955    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3956    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3957    * call. Listeners are added to remove the menu item when the treePanel is
3958    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3959    * modified.
3960    */
3961   @Override
3962   public void buildTreeSortMenu()
3963   {
3964     sortByTreeMenu.removeAll();
3965
3966     List<Component> comps = PaintRefresher.components
3967             .get(viewport.getSequenceSetId());
3968     List<TreePanel> treePanels = new ArrayList<>();
3969     for (Component comp : comps)
3970     {
3971       if (comp instanceof TreePanel)
3972       {
3973         treePanels.add((TreePanel) comp);
3974       }
3975     }
3976
3977     if (treePanels.size() < 1)
3978     {
3979       sortByTreeMenu.setVisible(false);
3980       return;
3981     }
3982
3983     sortByTreeMenu.setVisible(true);
3984
3985     for (final TreePanel tp : treePanels)
3986     {
3987       final JMenuItem item = new JMenuItem(tp.getTitle());
3988       item.addActionListener(new java.awt.event.ActionListener()
3989       {
3990         @Override
3991         public void actionPerformed(ActionEvent e)
3992         {
3993           tp.sortByTree_actionPerformed();
3994           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3995
3996         }
3997       });
3998
3999       sortByTreeMenu.add(item);
4000     }
4001   }
4002
4003   public boolean sortBy(AlignmentOrder alorder, String undoname)
4004   {
4005     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4006     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4007     if (undoname != null)
4008     {
4009       addHistoryItem(new OrderCommand(undoname, oldOrder,
4010               viewport.getAlignment()));
4011     }
4012     alignPanel.paintAlignment(true, false);
4013     return true;
4014   }
4015
4016   /**
4017    * Work out whether the whole set of sequences or just the selected set will
4018    * be submitted for multiple alignment.
4019    *
4020    */
4021   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4022   {
4023     // Now, check we have enough sequences
4024     AlignmentView msa = null;
4025
4026     if ((viewport.getSelectionGroup() != null)
4027             && (viewport.getSelectionGroup().getSize() > 1))
4028     {
4029       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4030       // some common interface!
4031       /*
4032        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4033        * SequenceI[sz = seqs.getSize(false)];
4034        *
4035        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4036        * seqs.getSequenceAt(i); }
4037        */
4038       msa = viewport.getAlignmentView(true);
4039     }
4040     else if (viewport.getSelectionGroup() != null
4041             && viewport.getSelectionGroup().getSize() == 1)
4042     {
4043       int option = JvOptionPane.showConfirmDialog(this,
4044               MessageManager.getString("warn.oneseq_msainput_selection"),
4045               MessageManager.getString("label.invalid_selection"),
4046               JvOptionPane.OK_CANCEL_OPTION);
4047       if (option == JvOptionPane.OK_OPTION)
4048       {
4049         msa = viewport.getAlignmentView(false);
4050       }
4051     }
4052     else
4053     {
4054       msa = viewport.getAlignmentView(false);
4055     }
4056     return msa;
4057   }
4058
4059   /**
4060    * Decides what is submitted to a secondary structure prediction service: the
4061    * first sequence in the alignment, or in the current selection, or, if the
4062    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4063    * region or the whole alignment. (where the first sequence in the set is the
4064    * one that the prediction will be for).
4065    */
4066   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4067   {
4068     AlignmentView seqs = null;
4069
4070     if ((viewport.getSelectionGroup() != null)
4071             && (viewport.getSelectionGroup().getSize() > 0))
4072     {
4073       seqs = viewport.getAlignmentView(true);
4074     }
4075     else
4076     {
4077       seqs = viewport.getAlignmentView(false);
4078     }
4079     // limit sequences - JBPNote in future - could spawn multiple prediction
4080     // jobs
4081     // TODO: viewport.getAlignment().isAligned is a global state - the local
4082     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4083     if (!viewport.getAlignment().isAligned(false))
4084     {
4085       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4086       // TODO: if seqs.getSequences().length>1 then should really have warned
4087       // user!
4088
4089     }
4090     return seqs;
4091   }
4092
4093   /**
4094    * DOCUMENT ME!
4095    *
4096    * @param e
4097    *          DOCUMENT ME!
4098    */
4099   @Override
4100   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4101   {
4102     // Pick the tree file
4103     JalviewFileChooser chooser = new JalviewFileChooser(
4104             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4105     chooser.setFileView(new JalviewFileView());
4106     chooser.setDialogTitle(
4107             MessageManager.getString("label.select_newick_like_tree_file"));
4108     chooser.setToolTipText(
4109             MessageManager.getString("label.load_tree_file"));
4110
4111     int value = chooser.showOpenDialog(null);
4112
4113     if (value == JalviewFileChooser.APPROVE_OPTION)
4114     {
4115       String filePath = chooser.getSelectedFile().getPath();
4116       Cache.setProperty("LAST_DIRECTORY", filePath);
4117       NewickFile fin = null;
4118       try
4119       {
4120         fin = new NewickFile(filePath, DataSourceType.FILE);
4121         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4122       } catch (Exception ex)
4123       {
4124         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4125                 MessageManager.getString("label.problem_reading_tree_file"),
4126                 JvOptionPane.WARNING_MESSAGE);
4127         ex.printStackTrace();
4128       }
4129       if (fin != null && fin.hasWarningMessage())
4130       {
4131         JvOptionPane.showMessageDialog(Desktop.desktop,
4132                 fin.getWarningMessage(),
4133                 MessageManager
4134                         .getString("label.possible_problem_with_tree_file"),
4135                 JvOptionPane.WARNING_MESSAGE);
4136       }
4137     }
4138   }
4139
4140   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4141   {
4142     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4143   }
4144
4145   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4146           int h, int x, int y)
4147   {
4148     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4149   }
4150
4151   /**
4152    * Add a treeviewer for the tree extracted from a Newick file object to the
4153    * current alignment view
4154    *
4155    * @param nf
4156    *          the tree
4157    * @param title
4158    *          tree viewer title
4159    * @param input
4160    *          Associated alignment input data (or null)
4161    * @param w
4162    *          width
4163    * @param h
4164    *          height
4165    * @param x
4166    *          position
4167    * @param y
4168    *          position
4169    * @return TreePanel handle
4170    */
4171   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4172           AlignmentView input, int w, int h, int x, int y)
4173   {
4174     TreePanel tp = null;
4175
4176     try
4177     {
4178       nf.parse();
4179
4180       if (nf.getTree() != null)
4181       {
4182         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4183
4184         tp.setSize(w, h);
4185
4186         if (x > 0 && y > 0)
4187         {
4188           tp.setLocation(x, y);
4189         }
4190
4191         Desktop.addInternalFrame(tp, treeTitle, w, h);
4192       }
4193     } catch (Exception ex)
4194     {
4195       ex.printStackTrace();
4196     }
4197
4198     return tp;
4199   }
4200
4201   private boolean buildingMenu = false;
4202
4203   /**
4204    * Generates menu items and listener event actions for web service clients
4205    *
4206    */
4207   public void BuildWebServiceMenu()
4208   {
4209     while (buildingMenu)
4210     {
4211       try
4212       {
4213         System.err.println("Waiting for building menu to finish.");
4214         Thread.sleep(10);
4215       } catch (Exception e)
4216       {
4217       }
4218     }
4219     final AlignFrame me = this;
4220     buildingMenu = true;
4221     new Thread(new Runnable()
4222     {
4223       @Override
4224       public void run()
4225       {
4226         final List<JMenuItem> legacyItems = new ArrayList<>();
4227         try
4228         {
4229           // System.err.println("Building ws menu again "
4230           // + Thread.currentThread());
4231           // TODO: add support for context dependent disabling of services based
4232           // on
4233           // alignment and current selection
4234           // TODO: add additional serviceHandle parameter to specify abstract
4235           // handler
4236           // class independently of AbstractName
4237           // TODO: add in rediscovery GUI function to restart discoverer
4238           // TODO: group services by location as well as function and/or
4239           // introduce
4240           // object broker mechanism.
4241           final Vector<JMenu> wsmenu = new Vector<>();
4242           final IProgressIndicator af = me;
4243
4244           /*
4245            * do not i18n these strings - they are hard-coded in class
4246            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4247            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4248            */
4249           final JMenu msawsmenu = new JMenu("Alignment");
4250           final JMenu secstrmenu = new JMenu(
4251                   "Secondary Structure Prediction");
4252           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4253           final JMenu analymenu = new JMenu("Analysis");
4254           final JMenu dismenu = new JMenu("Protein Disorder");
4255           // JAL-940 - only show secondary structure prediction services from
4256           // the legacy server
4257           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4258               // &&
4259           Discoverer.services != null && (Discoverer.services.size() > 0))
4260           {
4261             // TODO: refactor to allow list of AbstractName/Handler bindings to
4262             // be
4263             // stored or retrieved from elsewhere
4264             // No MSAWS used any more:
4265             // Vector msaws = null; // (Vector)
4266             // Discoverer.services.get("MsaWS");
4267             Vector secstrpr = (Vector) Discoverer.services
4268                     .get("SecStrPred");
4269             if (secstrpr != null)
4270             {
4271               // Add any secondary structure prediction services
4272               for (int i = 0, j = secstrpr.size(); i < j; i++)
4273               {
4274                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4275                         .get(i);
4276                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4277                         .getServiceClient(sh);
4278                 int p = secstrmenu.getItemCount();
4279                 impl.attachWSMenuEntry(secstrmenu, me);
4280                 int q = secstrmenu.getItemCount();
4281                 for (int litm = p; litm < q; litm++)
4282                 {
4283                   legacyItems.add(secstrmenu.getItem(litm));
4284                 }
4285               }
4286             }
4287           }
4288
4289           // Add all submenus in the order they should appear on the web
4290           // services menu
4291           wsmenu.add(msawsmenu);
4292           wsmenu.add(secstrmenu);
4293           wsmenu.add(dismenu);
4294           wsmenu.add(analymenu);
4295           // No search services yet
4296           // wsmenu.add(seqsrchmenu);
4297
4298           javax.swing.SwingUtilities.invokeLater(new Runnable()
4299           {
4300             @Override
4301             public void run()
4302             {
4303               try
4304               {
4305                 webService.removeAll();
4306                 // first, add discovered services onto the webservices menu
4307                 if (wsmenu.size() > 0)
4308                 {
4309                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4310                   {
4311                     webService.add(wsmenu.get(i));
4312                   }
4313                 }
4314                 else
4315                 {
4316                   webService.add(me.webServiceNoServices);
4317                 }
4318                 // TODO: move into separate menu builder class.
4319                 boolean new_sspred = false;
4320                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4321                 {
4322                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4323                   if (jws2servs != null)
4324                   {
4325                     if (jws2servs.hasServices())
4326                     {
4327                       jws2servs.attachWSMenuEntry(webService, me);
4328                       for (Jws2Instance sv : jws2servs.getServices())
4329                       {
4330                         if (sv.description.toLowerCase().contains("jpred"))
4331                         {
4332                           for (JMenuItem jmi : legacyItems)
4333                           {
4334                             jmi.setVisible(false);
4335                           }
4336                         }
4337                       }
4338
4339                     }
4340                     if (jws2servs.isRunning())
4341                     {
4342                       JMenuItem tm = new JMenuItem(
4343                               "Still discovering JABA Services");
4344                       tm.setEnabled(false);
4345                       webService.add(tm);
4346                     }
4347                   }
4348                 }
4349                 build_urlServiceMenu(me.webService);
4350                 build_fetchdbmenu(webService);
4351                 for (JMenu item : wsmenu)
4352                 {
4353                   if (item.getItemCount() == 0)
4354                   {
4355                     item.setEnabled(false);
4356                   }
4357                   else
4358                   {
4359                     item.setEnabled(true);
4360                   }
4361                 }
4362               } catch (Exception e)
4363               {
4364                 Cache.log.debug(
4365                         "Exception during web service menu building process.",
4366                         e);
4367               }
4368             }
4369           });
4370         } catch (Exception e)
4371         {
4372         }
4373         buildingMenu = false;
4374       }
4375     }).start();
4376
4377   }
4378
4379   /**
4380    * construct any groupURL type service menu entries.
4381    *
4382    * @param webService
4383    */
4384   private void build_urlServiceMenu(JMenu webService)
4385   {
4386     // TODO: remove this code when 2.7 is released
4387     // DEBUG - alignmentView
4388     /*
4389      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4390      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4391      *
4392      * @Override public void actionPerformed(ActionEvent e) {
4393      * jalview.datamodel.AlignmentView
4394      * .testSelectionViews(af.viewport.getAlignment(),
4395      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4396      *
4397      * }); webService.add(testAlView);
4398      */
4399     // TODO: refactor to RestClient discoverer and merge menu entries for
4400     // rest-style services with other types of analysis/calculation service
4401     // SHmmr test client - still being implemented.
4402     // DEBUG - alignmentView
4403
4404     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4405             .getRestClients())
4406     {
4407       client.attachWSMenuEntry(
4408               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4409               this);
4410     }
4411   }
4412
4413   /**
4414    * Searches the alignment sequences for xRefs and builds the Show
4415    * Cross-References menu (formerly called Show Products), with database
4416    * sources for which cross-references are found (protein sources for a
4417    * nucleotide alignment and vice versa)
4418    *
4419    * @return true if Show Cross-references menu should be enabled
4420    */
4421   public boolean canShowProducts()
4422   {
4423     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4424     AlignmentI dataset = viewport.getAlignment().getDataset();
4425
4426     showProducts.removeAll();
4427     final boolean dna = viewport.getAlignment().isNucleotide();
4428
4429     if (seqs == null || seqs.length == 0)
4430     {
4431       // nothing to see here.
4432       return false;
4433     }
4434
4435     boolean showp = false;
4436     try
4437     {
4438       List<String> ptypes = new CrossRef(seqs, dataset)
4439               .findXrefSourcesForSequences(dna);
4440
4441       for (final String source : ptypes)
4442       {
4443         showp = true;
4444         final AlignFrame af = this;
4445         JMenuItem xtype = new JMenuItem(source);
4446         xtype.addActionListener(new ActionListener()
4447         {
4448           @Override
4449           public void actionPerformed(ActionEvent e)
4450           {
4451             showProductsFor(af.viewport.getSequenceSelection(), dna,
4452                     source);
4453           }
4454         });
4455         showProducts.add(xtype);
4456       }
4457       showProducts.setVisible(showp);
4458       showProducts.setEnabled(showp);
4459     } catch (Exception e)
4460     {
4461       Cache.log.warn(
4462               "canShowProducts threw an exception - please report to help@jalview.org",
4463               e);
4464       return false;
4465     }
4466     return showp;
4467   }
4468
4469   /**
4470    * Finds and displays cross-references for the selected sequences (protein
4471    * products for nucleotide sequences, dna coding sequences for peptides).
4472    *
4473    * @param sel
4474    *          the sequences to show cross-references for
4475    * @param dna
4476    *          true if from a nucleotide alignment (so showing proteins)
4477    * @param source
4478    *          the database to show cross-references for
4479    */
4480   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4481           final String source)
4482   {
4483     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4484             .start();
4485   }
4486
4487   /**
4488    * Construct and display a new frame containing the translation of this
4489    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4490    */
4491   @Override
4492   public void showTranslation_actionPerformed(ActionEvent e)
4493   {
4494     AlignmentI al = null;
4495     try
4496     {
4497       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4498
4499       al = dna.translateCdna();
4500     } catch (Exception ex)
4501     {
4502       jalview.bin.Cache.log.error(
4503               "Exception during translation. Please report this !", ex);
4504       final String msg = MessageManager.getString(
4505               "label.error_when_translating_sequences_submit_bug_report");
4506       final String errorTitle = MessageManager
4507               .getString("label.implementation_error")
4508               + MessageManager.getString("label.translation_failed");
4509       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4510               JvOptionPane.ERROR_MESSAGE);
4511       return;
4512     }
4513     if (al == null || al.getHeight() == 0)
4514     {
4515       final String msg = MessageManager.getString(
4516               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4517       final String errorTitle = MessageManager
4518               .getString("label.translation_failed");
4519       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4520               JvOptionPane.WARNING_MESSAGE);
4521     }
4522     else
4523     {
4524       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4525       af.setFileFormat(this.currentFileFormat);
4526       final String newTitle = MessageManager
4527               .formatMessage("label.translation_of_params", new Object[]
4528               { this.getTitle() });
4529       af.setTitle(newTitle);
4530       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4531       {
4532         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4533         viewport.openSplitFrame(af, new Alignment(seqs));
4534       }
4535       else
4536       {
4537         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4538                 DEFAULT_HEIGHT);
4539       }
4540     }
4541   }
4542
4543   /**
4544    * Set the file format
4545    *
4546    * @param format
4547    */
4548   public void setFileFormat(FileFormatI format)
4549   {
4550     this.currentFileFormat = format;
4551   }
4552
4553   /**
4554    * Try to load a features file onto the alignment.
4555    *
4556    * @param file
4557    *          contents or path to retrieve file
4558    * @param sourceType
4559    *          access mode of file (see jalview.io.AlignFile)
4560    * @return true if features file was parsed correctly.
4561    */
4562   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4563   {
4564     return avc.parseFeaturesFile(file, sourceType,
4565             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4566
4567   }
4568
4569   @Override
4570   public void refreshFeatureUI(boolean enableIfNecessary)
4571   {
4572     // note - currently this is only still here rather than in the controller
4573     // because of the featureSettings hard reference that is yet to be
4574     // abstracted
4575     if (enableIfNecessary)
4576     {
4577       viewport.setShowSequenceFeatures(true);
4578       showSeqFeatures.setSelected(true);
4579     }
4580
4581   }
4582
4583   @Override
4584   public void dragEnter(DropTargetDragEvent evt)
4585   {
4586   }
4587
4588   @Override
4589   public void dragExit(DropTargetEvent evt)
4590   {
4591   }
4592
4593   @Override
4594   public void dragOver(DropTargetDragEvent evt)
4595   {
4596   }
4597
4598   @Override
4599   public void dropActionChanged(DropTargetDragEvent evt)
4600   {
4601   }
4602
4603   @Override
4604   public void drop(DropTargetDropEvent evt)
4605   {
4606     // JAL-1552 - acceptDrop required before getTransferable call for
4607     // Java's Transferable for native dnd
4608     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4609     Transferable t = evt.getTransferable();
4610     final AlignFrame thisaf = this;
4611     final List<String> files = new ArrayList<>();
4612     List<DataSourceType> protocols = new ArrayList<>();
4613
4614     try
4615     {
4616       Desktop.transferFromDropTarget(files, protocols, evt, t);
4617     } catch (Exception e)
4618     {
4619       e.printStackTrace();
4620     }
4621     if (files != null)
4622     {
4623       new Thread(new Runnable()
4624       {
4625         @Override
4626         public void run()
4627         {
4628           try
4629           {
4630             // check to see if any of these files have names matching sequences
4631             // in
4632             // the alignment
4633             SequenceIdMatcher idm = new SequenceIdMatcher(
4634                     viewport.getAlignment().getSequencesArray());
4635             /**
4636              * Object[] { String,SequenceI}
4637              */
4638             ArrayList<Object[]> filesmatched = new ArrayList<>();
4639             ArrayList<String> filesnotmatched = new ArrayList<>();
4640             for (int i = 0; i < files.size(); i++)
4641             {
4642               String file = files.get(i).toString();
4643               String pdbfn = "";
4644               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4645               if (protocol == DataSourceType.FILE)
4646               {
4647                 File fl = new File(file);
4648                 pdbfn = fl.getName();
4649               }
4650               else if (protocol == DataSourceType.URL)
4651               {
4652                 URL url = new URL(file);
4653                 pdbfn = url.getFile();
4654               }
4655               if (pdbfn.length() > 0)
4656               {
4657                 // attempt to find a match in the alignment
4658                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4659                 int l = 0, c = pdbfn.indexOf(".");
4660                 while (mtch == null && c != -1)
4661                 {
4662                   do
4663                   {
4664                     l = c;
4665                   } while ((c = pdbfn.indexOf(".", l)) > l);
4666                   if (l > -1)
4667                   {
4668                     pdbfn = pdbfn.substring(0, l);
4669                   }
4670                   mtch = idm.findAllIdMatches(pdbfn);
4671                 }
4672                 if (mtch != null)
4673                 {
4674                   FileFormatI type = null;
4675                   try
4676                   {
4677                     type = new IdentifyFile().identify(file, protocol);
4678                   } catch (Exception ex)
4679                   {
4680                     type = null;
4681                   }
4682                   if (type != null && type.isStructureFile())
4683                   {
4684                     filesmatched.add(new Object[] { file, protocol, mtch });
4685                     continue;
4686                   }
4687                 }
4688                 // File wasn't named like one of the sequences or wasn't a PDB
4689                 // file.
4690                 filesnotmatched.add(file);
4691               }
4692             }
4693             int assocfiles = 0;
4694             if (filesmatched.size() > 0)
4695             {
4696               if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4697                       || JvOptionPane.showConfirmDialog(thisaf,
4698                               MessageManager.formatMessage(
4699                                       "label.automatically_associate_structure_files_with_sequences_same_name",
4700                                       new Object[]
4701                                       { Integer.valueOf(filesmatched.size())
4702                                               .toString() }),
4703                               MessageManager.getString(
4704                                       "label.automatically_associate_structure_files_by_name"),
4705                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4706
4707               {
4708                 for (Object[] fm : filesmatched)
4709                 {
4710                   // try and associate
4711                   // TODO: may want to set a standard ID naming formalism for
4712                   // associating PDB files which have no IDs.
4713                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4714                   {
4715                     PDBEntry pe = new AssociatePdbFileWithSeq()
4716                             .associatePdbWithSeq((String) fm[0],
4717                                     (DataSourceType) fm[1], toassoc, false,
4718                                     Desktop.instance);
4719                     if (pe != null)
4720                     {
4721                       System.err.println("Associated file : "
4722                               + ((String) fm[0]) + " with "
4723                               + toassoc.getDisplayId(true));
4724                       assocfiles++;
4725                     }
4726                   }
4727                   // TODO: do we need to update overview ? only if features are
4728                   // shown I guess
4729                   alignPanel.paintAlignment(true, false);
4730                 }
4731               }
4732             }
4733             if (filesnotmatched.size() > 0)
4734             {
4735               if (assocfiles > 0 && (Cache.getDefault(
4736                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4737                       || JvOptionPane.showConfirmDialog(thisaf,
4738                               "<html>" + MessageManager.formatMessage(
4739                                       "label.ignore_unmatched_dropped_files_info",
4740                                       new Object[]
4741                                       { Integer.valueOf(
4742                                               filesnotmatched.size())
4743                                               .toString() })
4744                                       + "</html>",
4745                               MessageManager.getString(
4746                                       "label.ignore_unmatched_dropped_files"),
4747                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4748               {
4749                 return;
4750               }
4751               for (String fn : filesnotmatched)
4752               {
4753                 loadJalviewDataFile(fn, null, null, null);
4754               }
4755
4756             }
4757           } catch (Exception ex)
4758           {
4759             ex.printStackTrace();
4760           }
4761         }
4762       }).start();
4763     }
4764   }
4765
4766   /**
4767    * Attempt to load a "dropped" file or URL string, by testing in turn for
4768    * <ul>
4769    * <li>an Annotation file</li>
4770    * <li>a JNet file</li>
4771    * <li>a features file</li>
4772    * <li>else try to interpret as an alignment file</li>
4773    * </ul>
4774    *
4775    * @param file
4776    *          either a filename or a URL string.
4777    * @throws InterruptedException
4778    * @throws IOException
4779    */
4780   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4781           FileFormatI format, SequenceI assocSeq)
4782   {
4783     try
4784     {
4785       if (sourceType == null)
4786       {
4787         sourceType = FormatAdapter.checkProtocol(file);
4788       }
4789       // if the file isn't identified, or not positively identified as some
4790       // other filetype (PFAM is default unidentified alignment file type) then
4791       // try to parse as annotation.
4792       boolean isAnnotation = (format == null
4793               || FileFormat.Pfam.equals(format))
4794                       ? new AnnotationFile().annotateAlignmentView(viewport,
4795                               file, sourceType)
4796                       : false;
4797
4798       if (!isAnnotation)
4799       {
4800         // first see if its a T-COFFEE score file
4801         TCoffeeScoreFile tcf = null;
4802         try
4803         {
4804           tcf = new TCoffeeScoreFile(file, sourceType);
4805           if (tcf.isValid())
4806           {
4807             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4808             {
4809               buildColourMenu();
4810               changeColour(
4811                       new TCoffeeColourScheme(viewport.getAlignment()));
4812               isAnnotation = true;
4813               statusBar.setText(MessageManager.getString(
4814                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4815             }
4816             else
4817             {
4818               // some problem - if no warning its probable that the ID matching
4819               // process didn't work
4820               JvOptionPane.showMessageDialog(Desktop.desktop,
4821                       tcf.getWarningMessage() == null
4822                               ? MessageManager.getString(
4823                                       "label.check_file_matches_sequence_ids_alignment")
4824                               : tcf.getWarningMessage(),
4825                       MessageManager.getString(
4826                               "label.problem_reading_tcoffee_score_file"),
4827                       JvOptionPane.WARNING_MESSAGE);
4828             }
4829           }
4830           else
4831           {
4832             tcf = null;
4833           }
4834         } catch (Exception x)
4835         {
4836           Cache.log.debug(
4837                   "Exception when processing data source as T-COFFEE score file",
4838                   x);
4839           tcf = null;
4840         }
4841         if (tcf == null)
4842         {
4843           // try to see if its a JNet 'concise' style annotation file *before*
4844           // we
4845           // try to parse it as a features file
4846           if (format == null)
4847           {
4848             format = new IdentifyFile().identify(file, sourceType);
4849           }
4850           if (FileFormat.ScoreMatrix == format)
4851           {
4852             ScoreMatrixFile sm = new ScoreMatrixFile(
4853                     new FileParse(file, sourceType));
4854             sm.parse();
4855             // todo: i18n this message
4856             statusBar.setText(MessageManager.formatMessage(
4857                     "label.successfully_loaded_matrix",
4858                     sm.getMatrixName()));
4859           }
4860           else if (FileFormat.Jnet.equals(format))
4861           {
4862             JPredFile predictions = new JPredFile(file, sourceType);
4863             new JnetAnnotationMaker();
4864             JnetAnnotationMaker.add_annotation(predictions,
4865                     viewport.getAlignment(), 0, false);
4866             viewport.getAlignment().setupJPredAlignment();
4867             isAnnotation = true;
4868           }
4869           // else if (IdentifyFile.FeaturesFile.equals(format))
4870           else if (FileFormat.Features.equals(format))
4871           {
4872             if (parseFeaturesFile(file, sourceType))
4873             {
4874               alignPanel.paintAlignment(true, true);
4875             }
4876           }
4877           else
4878           {
4879             new FileLoader().LoadFile(viewport, file, sourceType, format);
4880           }
4881         }
4882       }
4883       if (isAnnotation)
4884       {
4885         alignPanel.adjustAnnotationHeight();
4886         viewport.updateSequenceIdColours();
4887         buildSortByAnnotationScoresMenu();
4888         alignPanel.paintAlignment(true, true);
4889       }
4890     } catch (Exception ex)
4891     {
4892       ex.printStackTrace();
4893     } catch (OutOfMemoryError oom)
4894     {
4895       try
4896       {
4897         System.gc();
4898       } catch (Exception x)
4899       {
4900       }
4901       new OOMWarning(
4902               "loading data "
4903                       + (sourceType != null
4904                               ? (sourceType == DataSourceType.PASTE
4905                                       ? "from clipboard."
4906                                       : "using " + sourceType + " from "
4907                                               + file)
4908                               : ".")
4909                       + (format != null
4910                               ? "(parsing as '" + format + "' file)"
4911                               : ""),
4912               oom, Desktop.desktop);
4913     }
4914   }
4915
4916   /**
4917    * Method invoked by the ChangeListener on the tabbed pane, in other words
4918    * when a different tabbed pane is selected by the user or programmatically.
4919    */
4920   @Override
4921   public void tabSelectionChanged(int index)
4922   {
4923     if (index > -1)
4924     {
4925       alignPanel = alignPanels.get(index);
4926       viewport = alignPanel.av;
4927       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4928       setMenusFromViewport(viewport);
4929     }
4930
4931     /*
4932      * 'focus' any colour slider that is open to the selected viewport
4933      */
4934     if (viewport.getConservationSelected())
4935     {
4936       SliderPanel.setConservationSlider(alignPanel,
4937               viewport.getResidueShading(), alignPanel.getViewName());
4938     }
4939     else
4940     {
4941       SliderPanel.hideConservationSlider();
4942     }
4943     if (viewport.getAbovePIDThreshold())
4944     {
4945       SliderPanel.setPIDSliderSource(alignPanel,
4946               viewport.getResidueShading(), alignPanel.getViewName());
4947     }
4948     else
4949     {
4950       SliderPanel.hidePIDSlider();
4951     }
4952
4953     /*
4954      * If there is a frame linked to this one in a SplitPane, switch it to the
4955      * same view tab index. No infinite recursion of calls should happen, since
4956      * tabSelectionChanged() should not get invoked on setting the selected
4957      * index to an unchanged value. Guard against setting an invalid index
4958      * before the new view peer tab has been created.
4959      */
4960     final AlignViewportI peer = viewport.getCodingComplement();
4961     if (peer != null)
4962     {
4963       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4964               .getAlignPanel().alignFrame;
4965       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4966       {
4967         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4968       }
4969     }
4970   }
4971
4972   /**
4973    * On right mouse click on view tab, prompt for and set new view name.
4974    */
4975   @Override
4976   public void tabbedPane_mousePressed(MouseEvent e)
4977   {
4978     if (e.isPopupTrigger())
4979     {
4980       String msg = MessageManager.getString("label.enter_view_name");
4981       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4982               JvOptionPane.QUESTION_MESSAGE);
4983
4984       if (reply != null)
4985       {
4986         viewport.viewName = reply;
4987         // TODO warn if reply is in getExistingViewNames()?
4988         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4989       }
4990     }
4991   }
4992
4993   public AlignViewport getCurrentView()
4994   {
4995     return viewport;
4996   }
4997
4998   /**
4999    * Open the dialog for regex description parsing.
5000    */
5001   @Override
5002   protected void extractScores_actionPerformed(ActionEvent e)
5003   {
5004     ParseProperties pp = new jalview.analysis.ParseProperties(
5005             viewport.getAlignment());
5006     // TODO: verify regex and introduce GUI dialog for version 2.5
5007     // if (pp.getScoresFromDescription("col", "score column ",
5008     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5009     // true)>0)
5010     if (pp.getScoresFromDescription("description column",
5011             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5012     {
5013       buildSortByAnnotationScoresMenu();
5014     }
5015   }
5016
5017   /*
5018    * (non-Javadoc)
5019    *
5020    * @see
5021    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5022    * )
5023    */
5024   @Override
5025   protected void showDbRefs_actionPerformed(ActionEvent e)
5026   {
5027     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5028   }
5029
5030   /*
5031    * (non-Javadoc)
5032    *
5033    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5034    * ActionEvent)
5035    */
5036   @Override
5037   protected void showNpFeats_actionPerformed(ActionEvent e)
5038   {
5039     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5040   }
5041
5042   /**
5043    * find the viewport amongst the tabs in this alignment frame and close that
5044    * tab
5045    *
5046    * @param av
5047    */
5048   public boolean closeView(AlignViewportI av)
5049   {
5050     if (viewport == av)
5051     {
5052       this.closeMenuItem_actionPerformed(false);
5053       return true;
5054     }
5055     Component[] comp = tabbedPane.getComponents();
5056     for (int i = 0; comp != null && i < comp.length; i++)
5057     {
5058       if (comp[i] instanceof AlignmentPanel)
5059       {
5060         if (((AlignmentPanel) comp[i]).av == av)
5061         {
5062           // close the view.
5063           closeView((AlignmentPanel) comp[i]);
5064           return true;
5065         }
5066       }
5067     }
5068     return false;
5069   }
5070
5071   protected void build_fetchdbmenu(JMenu webService)
5072   {
5073     // Temporary hack - DBRef Fetcher always top level ws entry.
5074     // TODO We probably want to store a sequence database checklist in
5075     // preferences and have checkboxes.. rather than individual sources selected
5076     // here
5077     final JMenu rfetch = new JMenu(
5078             MessageManager.getString("action.fetch_db_references"));
5079     rfetch.setToolTipText(MessageManager.getString(
5080             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5081     webService.add(rfetch);
5082
5083     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5084             MessageManager.getString("option.trim_retrieved_seqs"));
5085     trimrs.setToolTipText(
5086             MessageManager.getString("label.trim_retrieved_sequences"));
5087     trimrs.setSelected(
5088             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5089     trimrs.addActionListener(new ActionListener()
5090     {
5091       @Override
5092       public void actionPerformed(ActionEvent e)
5093       {
5094         trimrs.setSelected(trimrs.isSelected());
5095         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5096                 Boolean.valueOf(trimrs.isSelected()).toString());
5097       };
5098     });
5099     rfetch.add(trimrs);
5100     JMenuItem fetchr = new JMenuItem(
5101             MessageManager.getString("label.standard_databases"));
5102     fetchr.setToolTipText(
5103             MessageManager.getString("label.fetch_embl_uniprot"));
5104     fetchr.addActionListener(new ActionListener()
5105     {
5106
5107       @Override
5108       public void actionPerformed(ActionEvent e)
5109       {
5110         new Thread(new Runnable()
5111         {
5112           @Override
5113           public void run()
5114           {
5115             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5116                     .getAlignment().isNucleotide();
5117             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5118                     alignPanel.av.getSequenceSelection(),
5119                     alignPanel.alignFrame, null,
5120                     alignPanel.alignFrame.featureSettings, isNucleotide);
5121             dbRefFetcher.addListener(new FetchFinishedListenerI()
5122             {
5123               @Override
5124               public void finished()
5125               {
5126                 AlignFrame.this.setMenusForViewport();
5127               }
5128             });
5129             dbRefFetcher.fetchDBRefs(false);
5130           }
5131         }).start();
5132
5133       }
5134
5135     });
5136     rfetch.add(fetchr);
5137     final AlignFrame me = this;
5138     new Thread(new Runnable()
5139     {
5140       @Override
5141       public void run()
5142       {
5143         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5144                 .getSequenceFetcherSingleton(me);
5145         javax.swing.SwingUtilities.invokeLater(new Runnable()
5146         {
5147           @Override
5148           public void run()
5149           {
5150             String[] dbclasses = sf.getOrderedSupportedSources();
5151             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5152             // jalview.util.QuickSort.sort(otherdb, otherdb);
5153             List<DbSourceProxy> otherdb;
5154             JMenu dfetch = new JMenu();
5155             JMenu ifetch = new JMenu();
5156             JMenuItem fetchr = null;
5157             int comp = 0, icomp = 0, mcomp = 15;
5158             String mname = null;
5159             int dbi = 0;
5160             for (String dbclass : dbclasses)
5161             {
5162               otherdb = sf.getSourceProxy(dbclass);
5163               // add a single entry for this class, or submenu allowing 'fetch
5164               // all' or pick one
5165               if (otherdb == null || otherdb.size() < 1)
5166               {
5167                 continue;
5168               }
5169               // List<DbSourceProxy> dbs=otherdb;
5170               // otherdb=new ArrayList<DbSourceProxy>();
5171               // for (DbSourceProxy db:dbs)
5172               // {
5173               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5174               // }
5175               if (mname == null)
5176               {
5177                 mname = "From " + dbclass;
5178               }
5179               if (otherdb.size() == 1)
5180               {
5181                 final DbSourceProxy[] dassource = otherdb
5182                         .toArray(new DbSourceProxy[0]);
5183                 DbSourceProxy src = otherdb.get(0);
5184                 fetchr = new JMenuItem(src.getDbSource());
5185                 fetchr.addActionListener(new ActionListener()
5186                 {
5187
5188                   @Override
5189                   public void actionPerformed(ActionEvent e)
5190                   {
5191                     new Thread(new Runnable()
5192                     {
5193
5194                       @Override
5195                       public void run()
5196                       {
5197                         boolean isNucleotide = alignPanel.alignFrame
5198                                 .getViewport().getAlignment()
5199                                 .isNucleotide();
5200                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5201                                 alignPanel.av.getSequenceSelection(),
5202                                 alignPanel.alignFrame, dassource,
5203                                 alignPanel.alignFrame.featureSettings,
5204                                 isNucleotide);
5205                         dbRefFetcher
5206                                 .addListener(new FetchFinishedListenerI()
5207                                 {
5208                                   @Override
5209                                   public void finished()
5210                                   {
5211                                     AlignFrame.this.setMenusForViewport();
5212                                   }
5213                                 });
5214                         dbRefFetcher.fetchDBRefs(false);
5215                       }
5216                     }).start();
5217                   }
5218
5219                 });
5220                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5221                         MessageManager.formatMessage(
5222                                 "label.fetch_retrieve_from", new Object[]
5223                                 { src.getDbName() })));
5224                 dfetch.add(fetchr);
5225                 comp++;
5226               }
5227               else
5228               {
5229                 final DbSourceProxy[] dassource = otherdb
5230                         .toArray(new DbSourceProxy[0]);
5231                 // fetch all entry
5232                 DbSourceProxy src = otherdb.get(0);
5233                 fetchr = new JMenuItem(MessageManager
5234                         .formatMessage("label.fetch_all_param", new Object[]
5235                         { src.getDbSource() }));
5236                 fetchr.addActionListener(new ActionListener()
5237                 {
5238                   @Override
5239                   public void actionPerformed(ActionEvent e)
5240                   {
5241                     new Thread(new Runnable()
5242                     {
5243
5244                       @Override
5245                       public void run()
5246                       {
5247                         boolean isNucleotide = alignPanel.alignFrame
5248                                 .getViewport().getAlignment()
5249                                 .isNucleotide();
5250                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5251                                 alignPanel.av.getSequenceSelection(),
5252                                 alignPanel.alignFrame, dassource,
5253                                 alignPanel.alignFrame.featureSettings,
5254                                 isNucleotide);
5255                         dbRefFetcher
5256                                 .addListener(new FetchFinishedListenerI()
5257                                 {
5258                                   @Override
5259                                   public void finished()
5260                                   {
5261                                     AlignFrame.this.setMenusForViewport();
5262                                   }
5263                                 });
5264                         dbRefFetcher.fetchDBRefs(false);
5265                       }
5266                     }).start();
5267                   }
5268                 });
5269
5270                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5271                         MessageManager.formatMessage(
5272                                 "label.fetch_retrieve_from_all_sources",
5273                                 new Object[]
5274                                 { Integer.valueOf(otherdb.size())
5275                                         .toString(),
5276                                     src.getDbSource(), src.getDbName() })));
5277                 dfetch.add(fetchr);
5278                 comp++;
5279                 // and then build the rest of the individual menus
5280                 ifetch = new JMenu(MessageManager.formatMessage(
5281                         "label.source_from_db_source", new Object[]
5282                         { src.getDbSource() }));
5283                 icomp = 0;
5284                 String imname = null;
5285                 int i = 0;
5286                 for (DbSourceProxy sproxy : otherdb)
5287                 {
5288                   String dbname = sproxy.getDbName();
5289                   String sname = dbname.length() > 5
5290                           ? dbname.substring(0, 5) + "..."
5291                           : dbname;
5292                   String msname = dbname.length() > 10
5293                           ? dbname.substring(0, 10) + "..."
5294                           : dbname;
5295                   if (imname == null)
5296                   {
5297                     imname = MessageManager
5298                             .formatMessage("label.from_msname", new Object[]
5299                             { sname });
5300                   }
5301                   fetchr = new JMenuItem(msname);
5302                   final DbSourceProxy[] dassrc = { sproxy };
5303                   fetchr.addActionListener(new ActionListener()
5304                   {
5305
5306                     @Override
5307                     public void actionPerformed(ActionEvent e)
5308                     {
5309                       new Thread(new Runnable()
5310                       {
5311
5312                         @Override
5313                         public void run()
5314                         {
5315                           boolean isNucleotide = alignPanel.alignFrame
5316                                   .getViewport().getAlignment()
5317                                   .isNucleotide();
5318                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5319                                   alignPanel.av.getSequenceSelection(),
5320                                   alignPanel.alignFrame, dassrc,
5321                                   alignPanel.alignFrame.featureSettings,
5322                                   isNucleotide);
5323                           dbRefFetcher
5324                                   .addListener(new FetchFinishedListenerI()
5325                                   {
5326                                     @Override
5327                                     public void finished()
5328                                     {
5329                                       AlignFrame.this.setMenusForViewport();
5330                                     }
5331                                   });
5332                           dbRefFetcher.fetchDBRefs(false);
5333                         }
5334                       }).start();
5335                     }
5336
5337                   });
5338                   fetchr.setToolTipText(
5339                           "<html>" + MessageManager.formatMessage(
5340                                   "label.fetch_retrieve_from", new Object[]
5341                                   { dbname }));
5342                   ifetch.add(fetchr);
5343                   ++i;
5344                   if (++icomp >= mcomp || i == (otherdb.size()))
5345                   {
5346                     ifetch.setText(MessageManager.formatMessage(
5347                             "label.source_to_target", imname, sname));
5348                     dfetch.add(ifetch);
5349                     ifetch = new JMenu();
5350                     imname = null;
5351                     icomp = 0;
5352                     comp++;
5353                   }
5354                 }
5355               }
5356               ++dbi;
5357               if (comp >= mcomp || dbi >= (dbclasses.length))
5358               {
5359                 dfetch.setText(MessageManager.formatMessage(
5360                         "label.source_to_target", mname, dbclass));
5361                 rfetch.add(dfetch);
5362                 dfetch = new JMenu();
5363                 mname = null;
5364                 comp = 0;
5365               }
5366             }
5367           }
5368         });
5369       }
5370     }).start();
5371
5372   }
5373
5374   /**
5375    * Left justify the whole alignment.
5376    */
5377   @Override
5378   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5379   {
5380     AlignmentI al = viewport.getAlignment();
5381     al.justify(false);
5382     viewport.firePropertyChange("alignment", null, al);
5383   }
5384
5385   /**
5386    * Right justify the whole alignment.
5387    */
5388   @Override
5389   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5390   {
5391     AlignmentI al = viewport.getAlignment();
5392     al.justify(true);
5393     viewport.firePropertyChange("alignment", null, al);
5394   }
5395
5396   @Override
5397   public void setShowSeqFeatures(boolean b)
5398   {
5399     showSeqFeatures.setSelected(b);
5400     viewport.setShowSequenceFeatures(b);
5401   }
5402
5403   /*
5404    * (non-Javadoc)
5405    *
5406    * @see
5407    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5408    * awt.event.ActionEvent)
5409    */
5410   @Override
5411   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5412   {
5413     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5414     alignPanel.paintAlignment(false, false);
5415   }
5416
5417   /*
5418    * (non-Javadoc)
5419    *
5420    * @see
5421    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5422    * .ActionEvent)
5423    */
5424   @Override
5425   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5426   {
5427     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5428     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5429
5430   }
5431
5432   /*
5433    * (non-Javadoc)
5434    *
5435    * @see
5436    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5437    * .event.ActionEvent)
5438    */
5439   @Override
5440   protected void showGroupConservation_actionPerformed(ActionEvent e)
5441   {
5442     viewport.setShowGroupConservation(showGroupConservation.getState());
5443     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5444   }
5445
5446   /*
5447    * (non-Javadoc)
5448    *
5449    * @see
5450    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5451    * .event.ActionEvent)
5452    */
5453   @Override
5454   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5455   {
5456     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5457     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5458   }
5459
5460   /*
5461    * (non-Javadoc)
5462    *
5463    * @see
5464    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5465    * .event.ActionEvent)
5466    */
5467   @Override
5468   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5469   {
5470     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5471     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5472   }
5473
5474   @Override
5475   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5476   {
5477     showSequenceLogo.setState(true);
5478     viewport.setShowSequenceLogo(true);
5479     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5480     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5481   }
5482
5483   @Override
5484   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5485   {
5486     viewport.setShowInformationHistogram(
5487             showInformationHistogram.getState());
5488     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5489   }
5490
5491   @Override
5492   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5493   {
5494     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5495     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5496   }
5497
5498   @Override
5499   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5500   {
5501     showHMMSequenceLogo.setState(true);
5502     viewport.setShowHMMSequenceLogo(true);
5503     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5504     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5505   }
5506
5507   @Override
5508   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5509   {
5510     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5511   }
5512
5513   /*
5514    * (non-Javadoc)
5515    *
5516    * @see
5517    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5518    * .event.ActionEvent)
5519    */
5520   @Override
5521   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5522   {
5523     if (avc.makeGroupsFromSelection())
5524     {
5525       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5526       alignPanel.updateAnnotation();
5527       alignPanel.paintAlignment(true, true);
5528     }
5529   }
5530
5531   public void clearAlignmentSeqRep()
5532   {
5533     // TODO refactor alignmentseqrep to controller
5534     if (viewport.getAlignment().hasSeqrep())
5535     {
5536       viewport.getAlignment().setSeqrep(null);
5537       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5538       alignPanel.updateAnnotation();
5539       alignPanel.paintAlignment(true, true);
5540     }
5541   }
5542
5543   @Override
5544   protected void createGroup_actionPerformed(ActionEvent e)
5545   {
5546     if (avc.createGroup())
5547     {
5548       alignPanel.alignmentChanged();
5549     }
5550   }
5551
5552   @Override
5553   protected void unGroup_actionPerformed(ActionEvent e)
5554   {
5555     if (avc.unGroup())
5556     {
5557       alignPanel.alignmentChanged();
5558     }
5559   }
5560
5561   /**
5562    * make the given alignmentPanel the currently selected tab
5563    *
5564    * @param alignmentPanel
5565    */
5566   public void setDisplayedView(AlignmentPanel alignmentPanel)
5567   {
5568     if (!viewport.getSequenceSetId()
5569             .equals(alignmentPanel.av.getSequenceSetId()))
5570     {
5571       throw new Error(MessageManager.getString(
5572               "error.implementation_error_cannot_show_view_alignment_frame"));
5573     }
5574     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5575             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5576     {
5577       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5578     }
5579   }
5580
5581   /**
5582    * Action on selection of menu options to Show or Hide annotations.
5583    *
5584    * @param visible
5585    * @param forSequences
5586    *          update sequence-related annotations
5587    * @param forAlignment
5588    *          update non-sequence-related annotations
5589    */
5590   @Override
5591   protected void setAnnotationsVisibility(boolean visible,
5592           boolean forSequences, boolean forAlignment)
5593   {
5594     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5595             .getAlignmentAnnotation();
5596     if (anns == null)
5597     {
5598       return;
5599     }
5600     for (AlignmentAnnotation aa : anns)
5601     {
5602       /*
5603        * don't display non-positional annotations on an alignment
5604        */
5605       if (aa.annotations == null)
5606       {
5607         continue;
5608       }
5609       boolean apply = (aa.sequenceRef == null && forAlignment)
5610               || (aa.sequenceRef != null && forSequences);
5611       if (apply)
5612       {
5613         aa.visible = visible;
5614       }
5615     }
5616     alignPanel.validateAnnotationDimensions(true);
5617     alignPanel.alignmentChanged();
5618   }
5619
5620   /**
5621    * Store selected annotation sort order for the view and repaint.
5622    */
5623   @Override
5624   protected void sortAnnotations_actionPerformed()
5625   {
5626     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5627     this.alignPanel.av
5628             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5629     alignPanel.paintAlignment(false, false);
5630   }
5631
5632   /**
5633    *
5634    * @return alignment panels in this alignment frame
5635    */
5636   public List<? extends AlignmentViewPanel> getAlignPanels()
5637   {
5638     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5639   }
5640
5641   /**
5642    * Open a new alignment window, with the cDNA associated with this (protein)
5643    * alignment, aligned as is the protein.
5644    */
5645   protected void viewAsCdna_actionPerformed()
5646   {
5647     // TODO no longer a menu action - refactor as required
5648     final AlignmentI alignment = getViewport().getAlignment();
5649     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5650     if (mappings == null)
5651     {
5652       return;
5653     }
5654     List<SequenceI> cdnaSeqs = new ArrayList<>();
5655     for (SequenceI aaSeq : alignment.getSequences())
5656     {
5657       for (AlignedCodonFrame acf : mappings)
5658       {
5659         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5660         if (dnaSeq != null)
5661         {
5662           /*
5663            * There is a cDNA mapping for this protein sequence - add to new
5664            * alignment. It will share the same dataset sequence as other mapped
5665            * cDNA (no new mappings need to be created).
5666            */
5667           final Sequence newSeq = new Sequence(dnaSeq);
5668           newSeq.setDatasetSequence(dnaSeq);
5669           cdnaSeqs.add(newSeq);
5670         }
5671       }
5672     }
5673     if (cdnaSeqs.size() == 0)
5674     {
5675       // show a warning dialog no mapped cDNA
5676       return;
5677     }
5678     AlignmentI cdna = new Alignment(
5679             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5680     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5681             AlignFrame.DEFAULT_HEIGHT);
5682     cdna.alignAs(alignment);
5683     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5684             + this.title;
5685     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5686             AlignFrame.DEFAULT_HEIGHT);
5687   }
5688
5689   /**
5690    * Set visibility of dna/protein complement view (available when shown in a
5691    * split frame).
5692    *
5693    * @param show
5694    */
5695   @Override
5696   protected void showComplement_actionPerformed(boolean show)
5697   {
5698     SplitContainerI sf = getSplitViewContainer();
5699     if (sf != null)
5700     {
5701       sf.setComplementVisible(this, show);
5702     }
5703   }
5704
5705   /**
5706    * Generate the reverse (optionally complemented) of the selected sequences,
5707    * and add them to the alignment
5708    */
5709   @Override
5710   protected void showReverse_actionPerformed(boolean complement)
5711   {
5712     AlignmentI al = null;
5713     try
5714     {
5715       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5716       al = dna.reverseCdna(complement);
5717       viewport.addAlignment(al, "");
5718       addHistoryItem(new EditCommand(
5719               MessageManager.getString("label.add_sequences"), Action.PASTE,
5720               al.getSequencesArray(), 0, al.getWidth(),
5721               viewport.getAlignment()));
5722     } catch (Exception ex)
5723     {
5724       System.err.println(ex.getMessage());
5725       return;
5726     }
5727   }
5728
5729   /**
5730    * Try to run a script in the Groovy console, having first ensured that this
5731    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5732    * be targeted at this alignment.
5733    */
5734   @Override
5735   protected void runGroovy_actionPerformed()
5736   {
5737     Jalview.setCurrentAlignFrame(this);
5738     groovy.ui.Console console = Desktop.getGroovyConsole();
5739     if (console != null)
5740     {
5741       try
5742       {
5743         console.runScript();
5744       } catch (Exception ex)
5745       {
5746         System.err.println((ex.toString()));
5747         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5748                 MessageManager.getString("label.couldnt_run_groovy_script"),
5749                 MessageManager.getString("label.groovy_support_failed"),
5750                 JvOptionPane.ERROR_MESSAGE);
5751       }
5752     }
5753     else
5754     {
5755       System.err.println("Can't run Groovy script as console not found");
5756     }
5757   }
5758
5759   /**
5760    * Hides columns containing (or not containing) a specified feature, provided
5761    * that would not leave all columns hidden
5762    *
5763    * @param featureType
5764    * @param columnsContaining
5765    * @return
5766    */
5767   public boolean hideFeatureColumns(String featureType,
5768           boolean columnsContaining)
5769   {
5770     boolean notForHiding = avc.markColumnsContainingFeatures(
5771             columnsContaining, false, false, featureType);
5772     if (notForHiding)
5773     {
5774       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5775               false, featureType))
5776       {
5777         getViewport().hideSelectedColumns();
5778         return true;
5779       }
5780     }
5781     return false;
5782   }
5783
5784   @Override
5785   protected void selectHighlightedColumns_actionPerformed(
5786           ActionEvent actionEvent)
5787   {
5788     // include key modifier check in case user selects from menu
5789     avc.markHighlightedColumns(
5790             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5791             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5792                     | ActionEvent.CTRL_MASK)) != 0);
5793   }
5794
5795   /**
5796    * Rebuilds the Colour menu, including any user-defined colours which have
5797    * been loaded either on startup or during the session
5798    */
5799   public void buildColourMenu()
5800   {
5801     colourMenu.removeAll();
5802
5803     colourMenu.add(applyToAllGroups);
5804     colourMenu.add(textColour);
5805     colourMenu.addSeparator();
5806
5807     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5808             false);
5809
5810     colourMenu.addSeparator();
5811     colourMenu.add(conservationMenuItem);
5812     colourMenu.add(modifyConservation);
5813     colourMenu.add(abovePIDThreshold);
5814     colourMenu.add(modifyPID);
5815     colourMenu.add(annotationColour);
5816
5817     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5818     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5819   }
5820
5821   /**
5822    * Open a dialog (if not already open) that allows the user to select and
5823    * calculate PCA or Tree analysis
5824    */
5825   protected void openTreePcaDialog()
5826   {
5827     if (alignPanel.getCalculationDialog() == null)
5828     {
5829       new CalculationChooser(AlignFrame.this);
5830     }
5831   }
5832
5833   /**
5834    * Sets the status of the HMMER menu
5835    */
5836   public void updateHMMERStatus()
5837   {
5838     hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5839   }
5840
5841   /**
5842    * Returns the selected hidden Markov model.
5843    *
5844    * @return
5845    */
5846   public HiddenMarkovModel getSelectedHMM()
5847   {
5848     if (selectedHMMSequence == null)
5849     {
5850       return null;
5851     }
5852     return selectedHMMSequence.getHMM();
5853   }
5854
5855   /**
5856    * Returns the selected hidden Markov model.
5857    *
5858    * @return
5859    */
5860   public SequenceI getSelectedHMMSequence()
5861   {
5862     return selectedHMMSequence;
5863   }
5864
5865   /**
5866    * Sets the selected hidden Markov model
5867    *
5868    * @param selectedHMM
5869    */
5870   public void setSelectedHMMSequence(SequenceI selectedHMM)
5871   {
5872     this.selectedHMMSequence = selectedHMM;
5873     hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5874             + selectedHMM.getHMM().getName());
5875     hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5876             + selectedHMM.getHMM().getName());
5877   }
5878
5879   @Override
5880   public void hmmerMenu_actionPerformed(ActionEvent e)
5881   {
5882     SequenceGroup grp = getViewport().getSelectionGroup();
5883     if (grp != null)
5884     {
5885       hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5886               + grp.getName());
5887     }
5888     else
5889     {
5890       hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5891               + " from Alignment");
5892     }
5893   }
5894
5895   @Override
5896   protected void loadVcf_actionPerformed()
5897   {
5898     JalviewFileChooser chooser = new JalviewFileChooser(
5899             Cache.getProperty("LAST_DIRECTORY"));
5900     chooser.setFileView(new JalviewFileView());
5901     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5902     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5903
5904     int value = chooser.showOpenDialog(null);
5905
5906     if (value == JalviewFileChooser.APPROVE_OPTION)
5907     {
5908       String choice = chooser.getSelectedFile().getPath();
5909       Cache.setProperty("LAST_DIRECTORY", choice);
5910       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5911       new VCFLoader(choice).loadVCF(seqs, this);
5912     }
5913
5914   }
5915 }
5916
5917 class PrintThread extends Thread
5918 {
5919   AlignmentPanel ap;
5920
5921   public PrintThread(AlignmentPanel ap)
5922   {
5923     this.ap = ap;
5924   }
5925
5926   static PageFormat pf;
5927
5928   @Override
5929   public void run()
5930   {
5931     PrinterJob printJob = PrinterJob.getPrinterJob();
5932
5933     if (pf != null)
5934     {
5935       printJob.setPrintable(ap, pf);
5936     }
5937     else
5938     {
5939       printJob.setPrintable(ap);
5940     }
5941
5942     if (printJob.printDialog())
5943     {
5944       try
5945       {
5946         printJob.print();
5947       } catch (Exception PrintException)
5948       {
5949         PrintException.printStackTrace();
5950       }
5951     }
5952   }
5953 }