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.HMMAlignThread;
  67 import jalview.hmmer.HMMBuildThread;
  68 import jalview.hmmer.HMMERParamStore;
  69 import jalview.hmmer.HMMERPreset;
  70 import jalview.hmmer.HMMSearchThread;
  71 import jalview.io.AlignmentProperties;
  72 import jalview.io.AnnotationFile;
  73 import jalview.io.BioJsHTMLOutput;
  74 import jalview.io.DataSourceType;
  75 import jalview.io.FileFormat;
  76 import jalview.io.FileFormatI;
  77 import jalview.io.FileFormats;
  78 import jalview.io.FileLoader;
  79 import jalview.io.FileParse;
  80 import jalview.io.FormatAdapter;
  81 import jalview.io.HtmlSvgOutput;
  82 import jalview.io.IdentifyFile;
  83 import jalview.io.JPredFile;
  84 import jalview.io.JalviewFileChooser;
  85 import jalview.io.JalviewFileView;
  86 import jalview.io.JnetAnnotationMaker;
  87 import jalview.io.NewickFile;
  88 import jalview.io.ScoreMatrixFile;
  89 import jalview.io.TCoffeeScoreFile;
  90 import jalview.jbgui.GAlignFrame;
  91 import jalview.schemes.ColourSchemeI;
  92 import jalview.schemes.ColourSchemes;
  93 import jalview.schemes.ResidueColourScheme;
  94 import jalview.schemes.TCoffeeColourScheme;
  95 import jalview.util.MessageManager;
  96 import jalview.util.StringUtils;
  97 import jalview.viewmodel.AlignmentViewport;
  98 import jalview.viewmodel.ViewportRanges;
  99 import jalview.ws.DBRefFetcher;
 100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 101 import jalview.ws.jws1.Discoverer;
 102 import jalview.ws.jws2.Jws2Discoverer;
 103 import jalview.ws.jws2.jabaws2.Jws2Instance;
 104 import jalview.ws.params.ArgumentI;
 105 import jalview.ws.params.ParamDatastoreI;
 106 import jalview.ws.params.WsParamSetI;
 107 import jalview.ws.seqfetcher.DbSourceProxy;
 108
 109 import java.awt.BorderLayout;
 110 import java.awt.Component;
 111 import java.awt.Rectangle;
 112 import java.awt.Toolkit;
 113 import java.awt.datatransfer.Clipboard;
 114 import java.awt.datatransfer.DataFlavor;
 115 import java.awt.datatransfer.StringSelection;
 116 import java.awt.datatransfer.Transferable;
 117 import java.awt.dnd.DnDConstants;
 118 import java.awt.dnd.DropTargetDragEvent;
 119 import java.awt.dnd.DropTargetDropEvent;
 120 import java.awt.dnd.DropTargetEvent;
 121 import java.awt.dnd.DropTargetListener;
 122 import java.awt.event.ActionEvent;
 123 import java.awt.event.ActionListener;
 124 import java.awt.event.FocusAdapter;
 125 import java.awt.event.FocusEvent;
 126 import java.awt.event.ItemEvent;
 127 import java.awt.event.ItemListener;
 128 import java.awt.event.KeyAdapter;
 129 import java.awt.event.KeyEvent;
 130 import java.awt.event.MouseEvent;
 131 import java.awt.print.PageFormat;
 132 import java.awt.print.PrinterJob;
 133 import java.beans.PropertyChangeEvent;
 134 import java.io.File;
 135 import java.io.FileWriter;
 136 import java.io.IOException;
 137 import java.io.PrintWriter;
 138 import java.net.URL;
 139 import java.util.ArrayList;
 140 import java.util.Arrays;
 141 import java.util.Deque;
 142 import java.util.Enumeration;
 143 import java.util.HashMap;
 144 import java.util.Hashtable;
 145 import java.util.List;
 146 import java.util.Map;
 147 import java.util.Scanner;
 148 import java.util.Vector;
 149
 150 import javax.swing.JCheckBoxMenuItem;
 151 import javax.swing.JEditorPane;
 152 import javax.swing.JFileChooser;
 153 import javax.swing.JFrame;
 154 import javax.swing.JInternalFrame;
 155 import javax.swing.JLayeredPane;
 156 import javax.swing.JMenu;
 157 import javax.swing.JMenuItem;
 158 import javax.swing.JOptionPane;
 159 import javax.swing.JScrollPane;
 160 import javax.swing.SwingUtilities;
 161
 162 /**
 163  * DOCUMENT ME!
 164  *
 165  * @author $author$
 166  * @version $Revision$
 167  */
 168 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 169         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 170 {
 171
 172   Map<String, Float> distribution = new HashMap<>(); // temporary
 173
 174   public static final int DEFAULT_WIDTH = 700;
 175
 176   public static final int DEFAULT_HEIGHT = 500;
 177
 178   /*
 179    * The currently displayed panel (selected tabbed view if more than one)
 180    */
 181   public AlignmentPanel alignPanel;
 182
 183   AlignViewport viewport;
 184
 185   ViewportRanges vpRanges;
 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     vpRanges = viewport.getRanges();
 364     avc = new jalview.controller.AlignViewController(this, viewport,
 365             alignPanel);
 366     if (viewport.getAlignmentConservationAnnotation() == null)
 367     {
 368       // BLOSUM62Colour.setEnabled(false);
 369       conservationMenuItem.setEnabled(false);
 370       modifyConservation.setEnabled(false);
 371       // PIDColour.setEnabled(false);
 372       // abovePIDThreshold.setEnabled(false);
 373       // modifyPID.setEnabled(false);
 374     }
 375
 376     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 377             "No sort");
 378
 379     if (sortby.equals("Id"))
 380     {
 381       sortIDMenuItem_actionPerformed(null);
 382     }
 383     else if (sortby.equals("Pairwise Identity"))
 384     {
 385       sortPairwiseMenuItem_actionPerformed(null);
 386     }
 387
 388     this.alignPanel.av
 389             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 390
 391     setMenusFromViewport(viewport);
 392     buildSortByAnnotationScoresMenu();
 393     calculateTree.addActionListener(new ActionListener()
 394     {
 395
 396       @Override
 397       public void actionPerformed(ActionEvent e)
 398       {
 399         openTreePcaDialog();
 400       }
 401     });
 402     buildColourMenu();
 403     buildHMMERMenu();
 404
 405     if (Desktop.desktop != null)
 406     {
 407       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 408       addServiceListeners();
 409       setGUINucleotide();
 410     }
 411
 412     if (viewport.getWrapAlignment())
 413     {
 414       wrapMenuItem_actionPerformed(null);
 415     }
 416
 417     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 418     {
 419       this.overviewMenuItem_actionPerformed(null);
 420     }
 421
 422     addKeyListener();
 423
 424     final List<AlignmentPanel> selviews = new ArrayList<>();
 425     final List<AlignmentPanel> origview = new ArrayList<>();
 426     final String menuLabel = MessageManager
 427             .getString("label.copy_format_from");
 428     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 429             new ViewSetProvider()
 430             {
 431
 432               @Override
 433               public AlignmentPanel[] getAllAlignmentPanels()
 434               {
 435                 origview.clear();
 436                 origview.add(alignPanel);
 437                 // make an array of all alignment panels except for this one
 438                 List<AlignmentPanel> aps = new ArrayList<>(
 439                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 440                 aps.remove(AlignFrame.this.alignPanel);
 441                 return aps.toArray(new AlignmentPanel[aps.size()]);
 442               }
 443             }, selviews, new ItemListener()
 444             {
 445
 446               @Override
 447               public void itemStateChanged(ItemEvent e)
 448               {
 449                 if (origview.size() > 0)
 450                 {
 451                   final AlignmentPanel ap = origview.get(0);
 452
 453                   /*
 454                    * Copy the ViewStyle of the selected panel to 'this one'.
 455                    * Don't change value of 'scaleProteinAsCdna' unless copying
 456                    * from a SplitFrame.
 457                    */
 458                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 459                           .getViewStyle();
 460                   boolean fromSplitFrame = selviews.get(0)
 461                           .getAlignViewport().getCodingComplement() != null;
 462                   if (!fromSplitFrame)
 463                   {
 464                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 465                             .getViewStyle().isScaleProteinAsCdna());
 466                   }
 467                   ap.getAlignViewport().setViewStyle(vs);
 468
 469                   /*
 470                    * Also rescale ViewStyle of SplitFrame complement if there is
 471                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 472                    * the whole ViewStyle (allow cDNA protein to have different
 473                    * fonts)
 474                    */
 475                   AlignViewportI complement = ap.getAlignViewport()
 476                           .getCodingComplement();
 477                   if (complement != null && vs.isScaleProteinAsCdna())
 478                   {
 479                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 480                     ((SplitFrame) af.getSplitViewContainer())
 481                             .adjustLayout();
 482                     af.setMenusForViewport();
 483                   }
 484
 485                   ap.updateLayout();
 486                   ap.setSelected(true);
 487                   ap.alignFrame.setMenusForViewport();
 488
 489                 }
 490               }
 491             });
 492     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 493             .indexOf("devel") > -1
 494             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 495                     .indexOf("test") > -1)
 496     {
 497       formatMenu.add(vsel);
 498     }
 499     addFocusListener(new FocusAdapter()
 500     {
 501       @Override
 502       public void focusGained(FocusEvent e)
 503       {
 504         Jalview.setCurrentAlignFrame(AlignFrame.this);
 505       }
 506     });
 507
 508   }
 509
 510   /**
 511    * Adds all menu items to the HMMER menu
 512    */
 513   private void buildHMMERMenu()
 514   {
 515     hmmerMenu.removeAll();
 516
 517     hmmerMenu.add(hmmAlign);
 518     hmmerMenu.add(hmmBuild);
 519     hmmerMenu.add(hmmSearch);
 520   }
 521
 522   /**
 523    * Change the filename and format for the alignment, and enable the 'reload'
 524    * button functionality.
 525    *
 526    * @param file
 527    *          valid filename
 528    * @param format
 529    *          format of file
 530    */
 531   public void setFileName(String file, FileFormatI format)
 532   {
 533     fileName = file;
 534     setFileFormat(format);
 535     reload.setEnabled(true);
 536   }
 537
 538   /**
 539    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 540    * events
 541    */
 542   void addKeyListener()
 543   {
 544     addKeyListener(new KeyAdapter()
 545     {
 546       @Override
 547       public void keyPressed(KeyEvent evt)
 548       {
 549         if (viewport.cursorMode
 550                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 551                         && evt.getKeyCode() <= KeyEvent.VK_9)
 552                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 553                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 554                 && Character.isDigit(evt.getKeyChar()))
 555         {
 556           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 557         }
 558
 559         switch (evt.getKeyCode())
 560         {
 561
 562         case 27: // escape key
 563           deselectAllSequenceMenuItem_actionPerformed(null);
 564
 565           break;
 566
 567         case KeyEvent.VK_DOWN:
 568           if (evt.isAltDown() || !viewport.cursorMode)
 569           {
 570             moveSelectedSequences(false);
 571           }
 572           if (viewport.cursorMode)
 573           {
 574             alignPanel.getSeqPanel().moveCursor(0, 1);
 575           }
 576           break;
 577
 578         case KeyEvent.VK_UP:
 579           if (evt.isAltDown() || !viewport.cursorMode)
 580           {
 581             moveSelectedSequences(true);
 582           }
 583           if (viewport.cursorMode)
 584           {
 585             alignPanel.getSeqPanel().moveCursor(0, -1);
 586           }
 587
 588           break;
 589
 590         case KeyEvent.VK_LEFT:
 591           if (evt.isAltDown() || !viewport.cursorMode)
 592           {
 593             slideSequences(false,
 594                     alignPanel.getSeqPanel().getKeyboardNo1());
 595           }
 596           else
 597           {
 598             alignPanel.getSeqPanel().moveCursor(-1, 0);
 599           }
 600
 601           break;
 602
 603         case KeyEvent.VK_RIGHT:
 604           if (evt.isAltDown() || !viewport.cursorMode)
 605           {
 606             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 607           }
 608           else
 609           {
 610             alignPanel.getSeqPanel().moveCursor(1, 0);
 611           }
 612           break;
 613
 614         case KeyEvent.VK_SPACE:
 615           if (viewport.cursorMode)
 616           {
 617             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 618                     || evt.isShiftDown() || evt.isAltDown());
 619           }
 620           break;
 621
 622         // case KeyEvent.VK_A:
 623         // if (viewport.cursorMode)
 624         // {
 625         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 626         // //System.out.println("A");
 627         // }
 628         // break;
 629         /*
 630          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 631          * System.out.println("closing bracket"); } break;
 632          */
 633         case KeyEvent.VK_DELETE:
 634         case KeyEvent.VK_BACK_SPACE:
 635           if (!viewport.cursorMode)
 636           {
 637             cut_actionPerformed(null);
 638           }
 639           else
 640           {
 641             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 642                     || evt.isShiftDown() || evt.isAltDown());
 643           }
 644
 645           break;
 646
 647         case KeyEvent.VK_S:
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().setCursorRow();
 651           }
 652           break;
 653         case KeyEvent.VK_C:
 654           if (viewport.cursorMode && !evt.isControlDown())
 655           {
 656             alignPanel.getSeqPanel().setCursorColumn();
 657           }
 658           break;
 659         case KeyEvent.VK_P:
 660           if (viewport.cursorMode)
 661           {
 662             alignPanel.getSeqPanel().setCursorPosition();
 663           }
 664           break;
 665
 666         case KeyEvent.VK_ENTER:
 667         case KeyEvent.VK_COMMA:
 668           if (viewport.cursorMode)
 669           {
 670             alignPanel.getSeqPanel().setCursorRowAndColumn();
 671           }
 672           break;
 673
 674         case KeyEvent.VK_Q:
 675           if (viewport.cursorMode)
 676           {
 677             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 678           }
 679           break;
 680         case KeyEvent.VK_M:
 681           if (viewport.cursorMode)
 682           {
 683             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 684           }
 685           break;
 686
 687         case KeyEvent.VK_F2:
 688           viewport.cursorMode = !viewport.cursorMode;
 689           statusBar.setText(MessageManager
 690                   .formatMessage("label.keyboard_editing_mode", new String[]
 691                   { (viewport.cursorMode ? "on" : "off") }));
 692           if (viewport.cursorMode)
 693           {
 694             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 695                     .getStartRes();
 696             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 697                     .getStartSeq();
 698           }
 699           alignPanel.getSeqPanel().seqCanvas.repaint();
 700           break;
 701
 702         case KeyEvent.VK_F1:
 703           try
 704           {
 705             Help.showHelpWindow();
 706           } catch (Exception ex)
 707           {
 708             ex.printStackTrace();
 709           }
 710           break;
 711         case KeyEvent.VK_H:
 712         {
 713           boolean toggleSeqs = !evt.isControlDown();
 714           boolean toggleCols = !evt.isShiftDown();
 715           toggleHiddenRegions(toggleSeqs, toggleCols);
 716           break;
 717         }
 718         case KeyEvent.VK_B:
 719         {
 720           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 721           boolean modifyExisting = true; // always modify, don't clear
 722                                          // evt.isShiftDown();
 723           boolean invertHighlighted = evt.isAltDown();
 724           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 725                   toggleSel);
 726           break;
 727         }
 728         case KeyEvent.VK_PAGE_UP:
 729           vpRanges.pageUp();
 730           break;
 731         case KeyEvent.VK_PAGE_DOWN:
 732           vpRanges.pageDown();
 733           break;
 734         }
 735       }
 736
 737       @Override
 738       public void keyReleased(KeyEvent evt)
 739       {
 740         switch (evt.getKeyCode())
 741         {
 742         case KeyEvent.VK_LEFT:
 743           if (evt.isAltDown() || !viewport.cursorMode)
 744           {
 745             viewport.firePropertyChange("alignment", null,
 746                     viewport.getAlignment().getSequences());
 747           }
 748           break;
 749
 750         case KeyEvent.VK_RIGHT:
 751           if (evt.isAltDown() || !viewport.cursorMode)
 752           {
 753             viewport.firePropertyChange("alignment", null,
 754                     viewport.getAlignment().getSequences());
 755           }
 756           break;
 757         }
 758       }
 759     });
 760   }
 761
 762   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 763   {
 764     ap.alignFrame = this;
 765     avc = new jalview.controller.AlignViewController(this, viewport,
 766             alignPanel);
 767
 768     alignPanels.add(ap);
 769
 770     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 771
 772     int aSize = alignPanels.size();
 773
 774     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 775
 776     if (aSize == 1 && ap.av.viewName == null)
 777     {
 778       this.getContentPane().add(ap, BorderLayout.CENTER);
 779     }
 780     else
 781     {
 782       if (aSize == 2)
 783       {
 784         setInitialTabVisible();
 785       }
 786
 787       expandViews.setEnabled(true);
 788       gatherViews.setEnabled(true);
 789       tabbedPane.addTab(ap.av.viewName, ap);
 790
 791       ap.setVisible(false);
 792     }
 793
 794     if (newPanel)
 795     {
 796       if (ap.av.isPadGaps())
 797       {
 798         ap.av.getAlignment().padGaps();
 799       }
 800       ap.av.updateConservation(ap);
 801       ap.av.updateConsensus(ap);
 802       ap.av.updateStrucConsensus(ap);
 803       ap.av.updateInformation(ap);
 804     }
 805   }
 806
 807   public void setInitialTabVisible()
 808   {
 809     expandViews.setEnabled(true);
 810     gatherViews.setEnabled(true);
 811     tabbedPane.setVisible(true);
 812     AlignmentPanel first = alignPanels.get(0);
 813     tabbedPane.addTab(first.av.viewName, first);
 814     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 815   }
 816
 817   public AlignViewport getViewport()
 818   {
 819     return viewport;
 820   }
 821
 822   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 823   private void addServiceListeners()
 824   {
 825     final java.beans.PropertyChangeListener thisListener;
 826     Desktop.instance.addJalviewPropertyChangeListener("services",
 827             thisListener = new java.beans.PropertyChangeListener()
 828             {
 829               @Override
 830               public void propertyChange(PropertyChangeEvent evt)
 831               {
 832                 // // System.out.println("Discoverer property change.");
 833                 // if (evt.getPropertyName().equals("services"))
 834                 {
 835                   SwingUtilities.invokeLater(new Runnable()
 836                   {
 837
 838                     @Override
 839                     public void run()
 840                     {
 841                       System.err.println(
 842                               "Rebuild WS Menu for service change");
 843                       BuildWebServiceMenu();
 844                     }
 845
 846                   });
 847                 }
 848               }
 849             });
 850     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 851     {
 852       @Override
 853       public void internalFrameClosed(
 854               javax.swing.event.InternalFrameEvent evt)
 855       {
 856         // System.out.println("deregistering discoverer listener");
 857         Desktop.instance.removeJalviewPropertyChangeListener("services",
 858                 thisListener);
 859         closeMenuItem_actionPerformed(true);
 860       };
 861     });
 862     // Finally, build the menu once to get current service state
 863     new Thread(new Runnable()
 864     {
 865       @Override
 866       public void run()
 867       {
 868         BuildWebServiceMenu();
 869       }
 870     }).start();
 871   }
 872
 873   /**
 874    * Configure menu items that vary according to whether the alignment is
 875    * nucleotide or protein
 876    */
 877   public void setGUINucleotide()
 878   {
 879     AlignmentI al = getViewport().getAlignment();
 880     boolean nucleotide = al.isNucleotide();
 881
 882     showTranslation.setVisible(nucleotide);
 883     showReverse.setVisible(nucleotide);
 884     showReverseComplement.setVisible(nucleotide);
 885     conservationMenuItem.setEnabled(!nucleotide);
 886     modifyConservation
 887             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 888     showGroupConservation.setEnabled(!nucleotide);
 889
 890     showComplementMenuItem
 891             .setText(nucleotide ? MessageManager.getString("label.protein")
 892                     : MessageManager.getString("label.nucleotide"));
 893   }
 894
 895   /**
 896    * set up menus for the current viewport. This may be called after any
 897    * operation that affects the data in the current view (selection changed,
 898    * etc) to update the menus to reflect the new state.
 899    */
 900   @Override
 901   public void setMenusForViewport()
 902   {
 903     setMenusFromViewport(viewport);
 904   }
 905
 906   /**
 907    * Need to call this method when tabs are selected for multiple views, or when
 908    * loading from Jalview2XML.java
 909    *
 910    * @param av
 911    *          AlignViewport
 912    */
 913   void setMenusFromViewport(AlignViewport av)
 914   {
 915     padGapsMenuitem.setSelected(av.isPadGaps());
 916     colourTextMenuItem.setSelected(av.isShowColourText());
 917     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 918     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 919     conservationMenuItem.setSelected(av.getConservationSelected());
 920     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 921     seqLimits.setSelected(av.getShowJVSuffix());
 922     idRightAlign.setSelected(av.isRightAlignIds());
 923     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 924     renderGapsMenuItem.setSelected(av.isRenderGaps());
 925     wrapMenuItem.setSelected(av.getWrapAlignment());
 926     scaleAbove.setVisible(av.getWrapAlignment());
 927     scaleLeft.setVisible(av.getWrapAlignment());
 928     scaleRight.setVisible(av.getWrapAlignment());
 929     annotationPanelMenuItem.setState(av.isShowAnnotation());
 930     /*
 931      * Show/hide annotations only enabled if annotation panel is shown
 932      */
 933     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 934     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 935     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 936     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 937     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 938     viewTextMenuItem.setSelected(av.getShowText());
 939     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 940     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 941     showGroupConservation.setSelected(av.isShowGroupConservation());
 942     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 943     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 944     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 945     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 946     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 947     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 948
 949     ColourMenuHelper.setColourSelected(colourMenu,
 950             av.getGlobalColourScheme());
 951
 952     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 953     hiddenMarkers.setState(av.getShowHiddenMarkers());
 954     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 955     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 956     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 957     autoCalculate.setSelected(av.autoCalculateConsensus);
 958     sortByTree.setSelected(av.sortByTree);
 959     listenToViewSelections.setSelected(av.followSelection);
 960
 961     showProducts.setEnabled(canShowProducts());
 962     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 963
 964     updateEditMenuBar();
 965   }
 966
 967   /**
 968    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 969    *
 970    * @param b
 971    */
 972   public void setGroovyEnabled(boolean b)
 973   {
 974     runGroovy.setEnabled(b);
 975   }
 976
 977   private IProgressIndicator progressBar;
 978
 979   /*
 980    * (non-Javadoc)
 981    *
 982    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 983    */
 984   @Override
 985   public void setProgressBar(String message, long id)
 986   {
 987     progressBar.setProgressBar(message, id);
 988   }
 989
 990   @Override
 991   public void registerHandler(final long id,
 992           final IProgressIndicatorHandler handler)
 993   {
 994     progressBar.registerHandler(id, handler);
 995   }
 996
 997   /**
 998    *
 999    * @return true if any progress bars are still active
1000    */
1001   @Override
1002   public boolean operationInProgress()
1003   {
1004     return progressBar.operationInProgress();
1005   }
1006
1007   @Override
1008   public void setStatus(String text)
1009   {
1010     statusBar.setText(text);
1011   }
1012
1013   /*
1014    * Added so Castor Mapping file can obtain Jalview Version
1015    */
1016   public String getVersion()
1017   {
1018     return jalview.bin.Cache.getProperty("VERSION");
1019   }
1020
1021   public FeatureRenderer getFeatureRenderer()
1022   {
1023     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1024   }
1025
1026   @Override
1027   public void fetchSequence_actionPerformed(ActionEvent e)
1028   {
1029     new jalview.gui.SequenceFetcher(this);
1030   }
1031
1032   @Override
1033   public void addFromFile_actionPerformed(ActionEvent e)
1034   {
1035     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1036   }
1037
1038   @Override
1039   public void hmmBuildSettings_actionPerformed(ActionEvent e)
1040           throws IOException, InterruptedException
1041   {
1042     if (!(alignmentIsSufficient(1)))
1043     {
1044       return;
1045     }
1046     WsParamSetI set = new HMMERPreset();
1047     List<ArgumentI> args = new ArrayList<>();
1048     ParamDatastoreI store = new HMMERParamStore("hmmbuild");
1049     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1050             args);
1051     if (params.showRunDialog())
1052     {
1053       new Thread(new HMMBuildThread(this, params.getJobParams())).start();
1054     }
1055     alignPanel.repaint();
1056
1057   }
1058
1059   @Override
1060   public void hmmAlignSettings_actionPerformed(ActionEvent e)
1061           throws IOException, InterruptedException
1062   {
1063     if (!(checkForHMM() && alignmentIsSufficient(2)))
1064     {
1065       return;
1066     }
1067     WsParamSetI set = new HMMERPreset();
1068     List<ArgumentI> args = new ArrayList<>();
1069     ParamDatastoreI store = new HMMERParamStore("hmmalign");
1070     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1071             args);
1072     if (params.showRunDialog())
1073     {
1074       new Thread(new HMMAlignThread(this, true, params.getJobParams()))
1075             .start();
1076     }
1077     alignPanel.repaint();
1078   }
1079
1080   @Override
1081   public void hmmSearchSettings_actionPerformed(ActionEvent e)
1082   {
1083     if (!checkForHMM())
1084     {
1085       return;
1086     }
1087     WsParamSetI set = new HMMERPreset();
1088     List<ArgumentI> args = new ArrayList<>();
1089     ParamDatastoreI store = new HMMERParamStore("hmmsearch");
1090     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1091             args);
1092     if (params.showRunDialog())
1093     {
1094       new Thread(new HMMSearchThread(this, true, params.getJobParams()))
1095             .start();
1096     }
1097     alignPanel.repaint();
1098   }
1099
1100   @Override
1101   public void hmmBuildRun_actionPerformed(ActionEvent e)
1102           throws IOException, InterruptedException
1103   {
1104     if (!alignmentIsSufficient(1))
1105     {
1106       return;
1107     }
1108     new Thread(new HMMBuildThread(this, null)).start();
1109     alignPanel.repaint();
1110
1111   }
1112
1113   @Override
1114   public void hmmAlignRun_actionPerformed(ActionEvent e)
1115           throws IOException, InterruptedException
1116   {
1117     if (!(checkForHMM() && alignmentIsSufficient(2)))
1118     {
1119       return;
1120     }
1121     new Thread(new HMMAlignThread(this, true, null))
1122             .start();
1123     alignPanel.repaint();
1124   }
1125
1126   @Override
1127   public void hmmSearchRun_actionPerformed(ActionEvent e)
1128   {
1129     if (!checkForHMM())
1130     {
1131       return;
1132     }
1133     new Thread(new HMMSearchThread(this, true, null))
1134             .start();
1135     alignPanel.repaint();
1136   }
1137
1138   /**
1139    * Checks if the frame has a selected hidden Markov model
1140    *
1141    * @return
1142    */
1143   private boolean checkForHMM()
1144   {
1145     if (getSelectedHMM() == null)
1146     {
1147       JOptionPane.showMessageDialog(this,
1148               MessageManager.getString("warn.no_selected_hmm"));
1149       return false;
1150     }
1151     return true;
1152   }
1153
1154   /**
1155    * Checks if the alignment contains the required number of sequences.
1156    *
1157    * @param required
1158    * @return
1159    */
1160   public boolean alignmentIsSufficient(int required)
1161   {
1162     if (getViewport().getAlignment().getSequences().size() < required)
1163     {
1164       JOptionPane.showMessageDialog(this,
1165               MessageManager.getString("warn.not_enough_sequences"));
1166       return false;
1167     }
1168     return true;
1169   }
1170
1171   @Override
1172   public void addDatabase_actionPerformed(ActionEvent e) throws IOException
1173   {
1174     if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
1175     {
1176       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1177       Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
1178     }
1179
1180     String path = openFileChooser(false);
1181     if (new File(path).exists())
1182     {
1183       IdentifyFile identifier = new IdentifyFile();
1184       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1185       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1186               || format == FileFormat.Pfam)
1187       {
1188         String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
1189         String currentDbPaths = Cache
1190                 .getProperty(Preferences.HMMSEARCH_DB_PATHS);
1191         currentDbPaths += " " + path;
1192
1193         String fileName = StringUtils.getLastToken(path, new String("/"));
1194         Scanner scanner = new Scanner(fileName).useDelimiter(".");
1195         String name = scanner.next();
1196         scanner.close();
1197         currentDbs += " " + path; // TODO remove path from file name
1198         scanner.close();
1199
1200         Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
1201         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1202       }
1203       else
1204       {
1205         JOptionPane.showMessageDialog(this,
1206                 MessageManager.getString("warn.invalid_format"));
1207       }
1208     }
1209     else
1210     {
1211       JOptionPane.showMessageDialog(this,
1212               MessageManager.getString("warn.not_enough_sequences"));
1213     }
1214   }
1215
1216   /**
1217    * Opens a file chooser
1218    *
1219    * @param forFolder
1220    * @return
1221    */
1222   protected String openFileChooser(boolean forFolder)
1223   {
1224     String choice = null;
1225     JFileChooser chooser = new JFileChooser();
1226     if (forFolder)
1227     {
1228       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1229     }
1230     chooser.setDialogTitle(
1231             MessageManager.getString("label.open_local_file"));
1232     chooser.setToolTipText(MessageManager.getString("action.open"));
1233
1234     int value = chooser.showOpenDialog(this);
1235
1236     if (value == JFileChooser.APPROVE_OPTION)
1237     {
1238       choice = chooser.getSelectedFile().getPath();
1239     }
1240     return choice;
1241   }
1242
1243   @Override
1244   public void reload_actionPerformed(ActionEvent e)
1245   {
1246     if (fileName != null)
1247     {
1248       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1249       // originating file's format
1250       // TODO: work out how to recover feature settings for correct view(s) when
1251       // file is reloaded.
1252       if (FileFormat.Jalview.equals(currentFileFormat))
1253       {
1254         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1255         for (int i = 0; i < frames.length; i++)
1256         {
1257           if (frames[i] instanceof AlignFrame && frames[i] != this
1258                   && ((AlignFrame) frames[i]).fileName != null
1259                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1260           {
1261             try
1262             {
1263               frames[i].setSelected(true);
1264               Desktop.instance.closeAssociatedWindows();
1265             } catch (java.beans.PropertyVetoException ex)
1266             {
1267             }
1268           }
1269
1270         }
1271         Desktop.instance.closeAssociatedWindows();
1272
1273         FileLoader loader = new FileLoader();
1274         DataSourceType protocol = fileName.startsWith("http:")
1275                 ? DataSourceType.URL
1276                 : DataSourceType.FILE;
1277         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1278       }
1279       else
1280       {
1281         Rectangle bounds = this.getBounds();
1282
1283         FileLoader loader = new FileLoader();
1284         DataSourceType protocol = fileName.startsWith("http:")
1285                 ? DataSourceType.URL
1286                 : DataSourceType.FILE;
1287         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1288                 protocol, currentFileFormat);
1289
1290         newframe.setBounds(bounds);
1291         if (featureSettings != null && featureSettings.isShowing())
1292         {
1293           final Rectangle fspos = featureSettings.frame.getBounds();
1294           // TODO: need a 'show feature settings' function that takes bounds -
1295           // need to refactor Desktop.addFrame
1296           newframe.featureSettings_actionPerformed(null);
1297           final FeatureSettings nfs = newframe.featureSettings;
1298           SwingUtilities.invokeLater(new Runnable()
1299           {
1300             @Override
1301             public void run()
1302             {
1303               nfs.frame.setBounds(fspos);
1304             }
1305           });
1306           this.featureSettings.close();
1307           this.featureSettings = null;
1308         }
1309         this.closeMenuItem_actionPerformed(true);
1310       }
1311     }
1312   }
1313
1314   @Override
1315   public void addFromText_actionPerformed(ActionEvent e)
1316   {
1317     Desktop.instance
1318             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1319   }
1320
1321   @Override
1322   public void addFromURL_actionPerformed(ActionEvent e)
1323   {
1324     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1325   }
1326
1327   @Override
1328   public void save_actionPerformed(ActionEvent e)
1329   {
1330     if (fileName == null || (currentFileFormat == null)
1331             || fileName.startsWith("http"))
1332     {
1333       saveAs_actionPerformed(null);
1334     }
1335     else
1336     {
1337       saveAlignment(fileName, currentFileFormat);
1338     }
1339   }
1340
1341   /**
1342    * DOCUMENT ME!
1343    *
1344    * @param e
1345    *          DOCUMENT ME!
1346    */
1347   @Override
1348   public void saveAs_actionPerformed(ActionEvent e)
1349   {
1350     String format = currentFileFormat == null ? null
1351             : currentFileFormat.getName();
1352     JalviewFileChooser chooser = JalviewFileChooser
1353             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1354
1355     chooser.setFileView(new JalviewFileView());
1356     chooser.setDialogTitle(
1357             MessageManager.getString("label.save_alignment_to_file"));
1358     chooser.setToolTipText(MessageManager.getString("action.save"));
1359
1360     int value = chooser.showSaveDialog(this);
1361
1362     if (value == JalviewFileChooser.APPROVE_OPTION)
1363     {
1364       currentFileFormat = chooser.getSelectedFormat();
1365       while (currentFileFormat == null)
1366       {
1367         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1368                 MessageManager.getString(
1369                         "label.select_file_format_before_saving"),
1370                 MessageManager.getString("label.file_format_not_specified"),
1371                 JvOptionPane.WARNING_MESSAGE);
1372         currentFileFormat = chooser.getSelectedFormat();
1373         value = chooser.showSaveDialog(this);
1374         if (value != JalviewFileChooser.APPROVE_OPTION)
1375         {
1376           return;
1377         }
1378       }
1379
1380       fileName = chooser.getSelectedFile().getPath();
1381
1382       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1383
1384       Cache.setProperty("LAST_DIRECTORY", fileName);
1385       saveAlignment(fileName, currentFileFormat);
1386     }
1387   }
1388
1389   public boolean saveAlignment(String file, FileFormatI format)
1390   {
1391     boolean success = true;
1392
1393     if (FileFormat.Jalview.equals(format))
1394     {
1395       String shortName = title;
1396
1397       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1398       {
1399         shortName = shortName.substring(
1400                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1401       }
1402
1403       success = new Jalview2XML().saveAlignment(this, file, shortName);
1404
1405       statusBar.setText(MessageManager.formatMessage(
1406               "label.successfully_saved_to_file_in_format", new Object[]
1407               { fileName, format }));
1408
1409     }
1410     else
1411     {
1412       AlignmentExportData exportData = getAlignmentForExport(format,
1413               viewport, null);
1414       if (exportData.getSettings().isCancelled())
1415       {
1416         return false;
1417       }
1418       FormatAdapter f = new FormatAdapter(alignPanel,
1419               exportData.getSettings());
1420       String output = f.formatSequences(format, exportData.getAlignment(), // class
1421                                                                            // cast
1422                                                                            // exceptions
1423                                                                            // will
1424               // occur in the distant future
1425               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1426               f.getCacheSuffixDefault(format),
1427               viewport.getAlignment().getHiddenColumns());
1428
1429       if (output == null)
1430       {
1431         success = false;
1432       }
1433       else
1434       {
1435         try
1436         {
1437           PrintWriter out = new PrintWriter(new FileWriter(file));
1438
1439           out.print(output);
1440           out.close();
1441           this.setTitle(file);
1442           statusBar.setText(MessageManager.formatMessage(
1443                   "label.successfully_saved_to_file_in_format", new Object[]
1444                   { fileName, format.getName() }));
1445         } catch (Exception ex)
1446         {
1447           success = false;
1448           ex.printStackTrace();
1449         }
1450       }
1451     }
1452
1453     if (!success)
1454     {
1455       JvOptionPane.showInternalMessageDialog(this, MessageManager
1456               .formatMessage("label.couldnt_save_file", new Object[]
1457               { fileName }),
1458               MessageManager.getString("label.error_saving_file"),
1459               JvOptionPane.WARNING_MESSAGE);
1460     }
1461
1462     return success;
1463   }
1464
1465   private void warningMessage(String warning, String title)
1466   {
1467     if (new jalview.util.Platform().isHeadless())
1468     {
1469       System.err.println("Warning: " + title + "\nWarning: " + warning);
1470
1471     }
1472     else
1473     {
1474       JvOptionPane.showInternalMessageDialog(this, warning, title,
1475               JvOptionPane.WARNING_MESSAGE);
1476     }
1477     return;
1478   }
1479
1480   /**
1481    * DOCUMENT ME!
1482    *
1483    * @param e
1484    *          DOCUMENT ME!
1485    */
1486   @Override
1487   protected void outputText_actionPerformed(ActionEvent e)
1488   {
1489     FileFormatI fileFormat = FileFormats.getInstance()
1490             .forName(e.getActionCommand());
1491     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1492             viewport, null);
1493     if (exportData.getSettings().isCancelled())
1494     {
1495       return;
1496     }
1497     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1498     cap.setForInput(null);
1499     try
1500     {
1501       FileFormatI format = fileFormat;
1502       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1503               .formatSequences(format, exportData.getAlignment(),
1504                       exportData.getOmitHidden(),
1505                       exportData.getStartEndPostions(),
1506                       viewport.getAlignment().getHiddenColumns()));
1507       Desktop.addInternalFrame(cap, MessageManager
1508               .formatMessage("label.alignment_output_command", new Object[]
1509               { e.getActionCommand() }), 600, 500);
1510     } catch (OutOfMemoryError oom)
1511     {
1512       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1513               oom);
1514       cap.dispose();
1515     }
1516
1517   }
1518
1519   public static AlignmentExportData getAlignmentForExport(
1520           FileFormatI format, AlignViewportI viewport,
1521           AlignExportSettingI exportSettings)
1522   {
1523     AlignmentI alignmentToExport = null;
1524     AlignExportSettingI settings = exportSettings;
1525     String[] omitHidden = null;
1526
1527     HiddenSequences hiddenSeqs = viewport.getAlignment()
1528             .getHiddenSequences();
1529
1530     alignmentToExport = viewport.getAlignment();
1531
1532     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1533     if (settings == null)
1534     {
1535       settings = new AlignExportSettings(hasHiddenSeqs,
1536               viewport.hasHiddenColumns(), format);
1537     }
1538     // settings.isExportAnnotations();
1539
1540     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1541     {
1542       omitHidden = viewport.getViewAsString(false,
1543               settings.isExportHiddenSequences());
1544     }
1545
1546     int[] alignmentStartEnd = new int[2];
1547     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1548     {
1549       alignmentToExport = hiddenSeqs.getFullAlignment();
1550     }
1551     else
1552     {
1553       alignmentToExport = viewport.getAlignment();
1554     }
1555     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1556             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1557     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1558             omitHidden, alignmentStartEnd, settings);
1559     return ed;
1560   }
1561
1562   /**
1563    * DOCUMENT ME!
1564    *
1565    * @param e
1566    *          DOCUMENT ME!
1567    */
1568   @Override
1569   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1570   {
1571     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1572     htmlSVG.exportHTML(null);
1573   }
1574
1575   @Override
1576   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1577   {
1578     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1579     bjs.exportHTML(null);
1580   }
1581
1582   public void createImageMap(File file, String image)
1583   {
1584     alignPanel.makePNGImageMap(file, image);
1585   }
1586
1587   /**
1588    * DOCUMENT ME!
1589    *
1590    * @param e
1591    *          DOCUMENT ME!
1592    */
1593   @Override
1594   public void createPNG(File f)
1595   {
1596     alignPanel.makePNG(f);
1597   }
1598
1599   /**
1600    * DOCUMENT ME!
1601    *
1602    * @param e
1603    *          DOCUMENT ME!
1604    */
1605   @Override
1606   public void createEPS(File f)
1607   {
1608     alignPanel.makeEPS(f);
1609   }
1610
1611   @Override
1612   public void createSVG(File f)
1613   {
1614     alignPanel.makeSVG(f);
1615   }
1616
1617   @Override
1618   public void pageSetup_actionPerformed(ActionEvent e)
1619   {
1620     PrinterJob printJob = PrinterJob.getPrinterJob();
1621     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1622   }
1623
1624   /**
1625    * DOCUMENT ME!
1626    *
1627    * @param e
1628    *          DOCUMENT ME!
1629    */
1630   @Override
1631   public void printMenuItem_actionPerformed(ActionEvent e)
1632   {
1633     // Putting in a thread avoids Swing painting problems
1634     PrintThread thread = new PrintThread(alignPanel);
1635     thread.start();
1636   }
1637
1638   @Override
1639   public void exportFeatures_actionPerformed(ActionEvent e)
1640   {
1641     new AnnotationExporter().exportFeatures(alignPanel);
1642   }
1643
1644   @Override
1645   public void exportAnnotations_actionPerformed(ActionEvent e)
1646   {
1647     new AnnotationExporter().exportAnnotations(alignPanel);
1648   }
1649
1650   @Override
1651   public void associatedData_actionPerformed(ActionEvent e)
1652           throws IOException, InterruptedException
1653   {
1654     // Pick the tree file
1655     JalviewFileChooser chooser = new JalviewFileChooser(
1656             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1657     chooser.setFileView(new JalviewFileView());
1658     chooser.setDialogTitle(
1659             MessageManager.getString("label.load_jalview_annotations"));
1660     chooser.setToolTipText(
1661             MessageManager.getString("label.load_jalview_annotations"));
1662
1663     int value = chooser.showOpenDialog(null);
1664
1665     if (value == JalviewFileChooser.APPROVE_OPTION)
1666     {
1667       String choice = chooser.getSelectedFile().getPath();
1668       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1669       loadJalviewDataFile(choice, null, null, null);
1670     }
1671
1672   }
1673
1674   /**
1675    * Close the current view or all views in the alignment frame. If the frame
1676    * only contains one view then the alignment will be removed from memory.
1677    *
1678    * @param closeAllTabs
1679    */
1680   @Override
1681   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1682   {
1683     if (alignPanels != null && alignPanels.size() < 2)
1684     {
1685       closeAllTabs = true;
1686     }
1687
1688     try
1689     {
1690       if (alignPanels != null)
1691       {
1692         if (closeAllTabs)
1693         {
1694           if (this.isClosed())
1695           {
1696             // really close all the windows - otherwise wait till
1697             // setClosed(true) is called
1698             for (int i = 0; i < alignPanels.size(); i++)
1699             {
1700               AlignmentPanel ap = alignPanels.get(i);
1701               ap.closePanel();
1702             }
1703           }
1704         }
1705         else
1706         {
1707           closeView(alignPanel);
1708         }
1709       }
1710
1711       if (closeAllTabs)
1712       {
1713         /*
1714          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1715          * be called recursively, with the frame now in 'closed' state
1716          */
1717         this.setClosed(true);
1718       }
1719     } catch (Exception ex)
1720     {
1721       ex.printStackTrace();
1722     }
1723   }
1724
1725   /**
1726    * Close the specified panel and close up tabs appropriately.
1727    *
1728    * @param panelToClose
1729    */
1730   public void closeView(AlignmentPanel panelToClose)
1731   {
1732     int index = tabbedPane.getSelectedIndex();
1733     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1734     alignPanels.remove(panelToClose);
1735     panelToClose.closePanel();
1736     panelToClose = null;
1737
1738     tabbedPane.removeTabAt(closedindex);
1739     tabbedPane.validate();
1740
1741     if (index > closedindex || index == tabbedPane.getTabCount())
1742     {
1743       // modify currently selected tab index if necessary.
1744       index--;
1745     }
1746
1747     this.tabSelectionChanged(index);
1748   }
1749
1750   /**
1751    * DOCUMENT ME!
1752    */
1753   void updateEditMenuBar()
1754   {
1755
1756     if (viewport.getHistoryList().size() > 0)
1757     {
1758       undoMenuItem.setEnabled(true);
1759       CommandI command = viewport.getHistoryList().peek();
1760       undoMenuItem.setText(MessageManager
1761               .formatMessage("label.undo_command", new Object[]
1762               { command.getDescription() }));
1763     }
1764     else
1765     {
1766       undoMenuItem.setEnabled(false);
1767       undoMenuItem.setText(MessageManager.getString("action.undo"));
1768     }
1769
1770     if (viewport.getRedoList().size() > 0)
1771     {
1772       redoMenuItem.setEnabled(true);
1773
1774       CommandI command = viewport.getRedoList().peek();
1775       redoMenuItem.setText(MessageManager
1776               .formatMessage("label.redo_command", new Object[]
1777               { command.getDescription() }));
1778     }
1779     else
1780     {
1781       redoMenuItem.setEnabled(false);
1782       redoMenuItem.setText(MessageManager.getString("action.redo"));
1783     }
1784   }
1785
1786   @Override
1787   public void addHistoryItem(CommandI command)
1788   {
1789     if (command.getSize() > 0)
1790     {
1791       viewport.addToHistoryList(command);
1792       viewport.clearRedoList();
1793       updateEditMenuBar();
1794       viewport.updateHiddenColumns();
1795       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1796       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1797       // viewport.getColumnSelection()
1798       // .getHiddenColumns().size() > 0);
1799     }
1800   }
1801
1802   /**
1803    *
1804    * @return alignment objects for all views
1805    */
1806   AlignmentI[] getViewAlignments()
1807   {
1808     if (alignPanels != null)
1809     {
1810       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1811       int i = 0;
1812       for (AlignmentPanel ap : alignPanels)
1813       {
1814         als[i++] = ap.av.getAlignment();
1815       }
1816       return als;
1817     }
1818     if (viewport != null)
1819     {
1820       return new AlignmentI[] { viewport.getAlignment() };
1821     }
1822     return null;
1823   }
1824
1825   /**
1826    * DOCUMENT ME!
1827    *
1828    * @param e
1829    *          DOCUMENT ME!
1830    */
1831   @Override
1832   protected void undoMenuItem_actionPerformed(ActionEvent e)
1833   {
1834     if (viewport.getHistoryList().isEmpty())
1835     {
1836       return;
1837     }
1838     CommandI command = viewport.getHistoryList().pop();
1839     viewport.addToRedoList(command);
1840     command.undoCommand(getViewAlignments());
1841
1842     AlignmentViewport originalSource = getOriginatingSource(command);
1843     updateEditMenuBar();
1844
1845     if (originalSource != null)
1846     {
1847       if (originalSource != viewport)
1848       {
1849         Cache.log.warn(
1850                 "Implementation worry: mismatch of viewport origin for undo");
1851       }
1852       originalSource.updateHiddenColumns();
1853       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1854       // null
1855       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1856       // viewport.getColumnSelection()
1857       // .getHiddenColumns().size() > 0);
1858       originalSource.firePropertyChange("alignment", null,
1859               originalSource.getAlignment().getSequences());
1860     }
1861   }
1862
1863   /**
1864    * DOCUMENT ME!
1865    *
1866    * @param e
1867    *          DOCUMENT ME!
1868    */
1869   @Override
1870   protected void redoMenuItem_actionPerformed(ActionEvent e)
1871   {
1872     if (viewport.getRedoList().size() < 1)
1873     {
1874       return;
1875     }
1876
1877     CommandI command = viewport.getRedoList().pop();
1878     viewport.addToHistoryList(command);
1879     command.doCommand(getViewAlignments());
1880
1881     AlignmentViewport originalSource = getOriginatingSource(command);
1882     updateEditMenuBar();
1883
1884     if (originalSource != null)
1885     {
1886
1887       if (originalSource != viewport)
1888       {
1889         Cache.log.warn(
1890                 "Implementation worry: mismatch of viewport origin for redo");
1891       }
1892       originalSource.updateHiddenColumns();
1893       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1894       // null
1895       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1896       // viewport.getColumnSelection()
1897       // .getHiddenColumns().size() > 0);
1898       originalSource.firePropertyChange("alignment", null,
1899               originalSource.getAlignment().getSequences());
1900     }
1901   }
1902
1903   AlignmentViewport getOriginatingSource(CommandI command)
1904   {
1905     AlignmentViewport originalSource = null;
1906     // For sequence removal and addition, we need to fire
1907     // the property change event FROM the viewport where the
1908     // original alignment was altered
1909     AlignmentI al = null;
1910     if (command instanceof EditCommand)
1911     {
1912       EditCommand editCommand = (EditCommand) command;
1913       al = editCommand.getAlignment();
1914       List<Component> comps = PaintRefresher.components
1915               .get(viewport.getSequenceSetId());
1916
1917       for (Component comp : comps)
1918       {
1919         if (comp instanceof AlignmentPanel)
1920         {
1921           if (al == ((AlignmentPanel) comp).av.getAlignment())
1922           {
1923             originalSource = ((AlignmentPanel) comp).av;
1924             break;
1925           }
1926         }
1927       }
1928     }
1929
1930     if (originalSource == null)
1931     {
1932       // The original view is closed, we must validate
1933       // the current view against the closed view first
1934       if (al != null)
1935       {
1936         PaintRefresher.validateSequences(al, viewport.getAlignment());
1937       }
1938
1939       originalSource = viewport;
1940     }
1941
1942     return originalSource;
1943   }
1944
1945   /**
1946    * DOCUMENT ME!
1947    *
1948    * @param up
1949    *          DOCUMENT ME!
1950    */
1951   public void moveSelectedSequences(boolean up)
1952   {
1953     SequenceGroup sg = viewport.getSelectionGroup();
1954
1955     if (sg == null)
1956     {
1957       return;
1958     }
1959     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1960             viewport.getHiddenRepSequences(), up);
1961     alignPanel.paintAlignment(true);
1962   }
1963
1964   synchronized void slideSequences(boolean right, int size)
1965   {
1966     List<SequenceI> sg = new ArrayList<>();
1967     if (viewport.cursorMode)
1968     {
1969       sg.add(viewport.getAlignment()
1970               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1971     }
1972     else if (viewport.getSelectionGroup() != null
1973             && viewport.getSelectionGroup().getSize() != viewport
1974                     .getAlignment().getHeight())
1975     {
1976       sg = viewport.getSelectionGroup()
1977               .getSequences(viewport.getHiddenRepSequences());
1978     }
1979
1980     if (sg.size() < 1)
1981     {
1982       return;
1983     }
1984
1985     List<SequenceI> invertGroup = new ArrayList<>();
1986
1987     for (SequenceI seq : viewport.getAlignment().getSequences())
1988     {
1989       if (!sg.contains(seq))
1990       {
1991         invertGroup.add(seq);
1992       }
1993     }
1994
1995     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1996
1997     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1998     for (int i = 0; i < invertGroup.size(); i++)
1999     {
2000       seqs2[i] = invertGroup.get(i);
2001     }
2002
2003     SlideSequencesCommand ssc;
2004     if (right)
2005     {
2006       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2007               viewport.getGapCharacter());
2008     }
2009     else
2010     {
2011       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2012               viewport.getGapCharacter());
2013     }
2014
2015     int groupAdjustment = 0;
2016     if (ssc.getGapsInsertedBegin() && right)
2017     {
2018       if (viewport.cursorMode)
2019       {
2020         alignPanel.getSeqPanel().moveCursor(size, 0);
2021       }
2022       else
2023       {
2024         groupAdjustment = size;
2025       }
2026     }
2027     else if (!ssc.getGapsInsertedBegin() && !right)
2028     {
2029       if (viewport.cursorMode)
2030       {
2031         alignPanel.getSeqPanel().moveCursor(-size, 0);
2032       }
2033       else
2034       {
2035         groupAdjustment = -size;
2036       }
2037     }
2038
2039     if (groupAdjustment != 0)
2040     {
2041       viewport.getSelectionGroup().setStartRes(
2042               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2043       viewport.getSelectionGroup().setEndRes(
2044               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2045     }
2046
2047     /*
2048      * just extend the last slide command if compatible; but not if in
2049      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2050      */
2051     boolean appendHistoryItem = false;
2052     Deque<CommandI> historyList = viewport.getHistoryList();
2053     boolean inSplitFrame = getSplitViewContainer() != null;
2054     if (!inSplitFrame && historyList != null && historyList.size() > 0
2055             && historyList.peek() instanceof SlideSequencesCommand)
2056     {
2057       appendHistoryItem = ssc.appendSlideCommand(
2058               (SlideSequencesCommand) historyList.peek());
2059     }
2060
2061     if (!appendHistoryItem)
2062     {
2063       addHistoryItem(ssc);
2064     }
2065
2066     repaint();
2067   }
2068
2069   /**
2070    * DOCUMENT ME!
2071    *
2072    * @param e
2073    *          DOCUMENT ME!
2074    */
2075   @Override
2076   protected void copy_actionPerformed(ActionEvent e)
2077   {
2078     System.gc();
2079     if (viewport.getSelectionGroup() == null)
2080     {
2081       return;
2082     }
2083     // TODO: preserve the ordering of displayed alignment annotation in any
2084     // internal paste (particularly sequence associated annotation)
2085     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2086     String[] omitHidden = null;
2087
2088     if (viewport.hasHiddenColumns())
2089     {
2090       omitHidden = viewport.getViewAsString(true);
2091     }
2092
2093     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2094             seqs, omitHidden, null);
2095
2096     StringSelection ss = new StringSelection(output);
2097
2098     try
2099     {
2100       jalview.gui.Desktop.internalCopy = true;
2101       // Its really worth setting the clipboard contents
2102       // to empty before setting the large StringSelection!!
2103       Toolkit.getDefaultToolkit().getSystemClipboard()
2104               .setContents(new StringSelection(""), null);
2105
2106       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2107               Desktop.instance);
2108     } catch (OutOfMemoryError er)
2109     {
2110       new OOMWarning("copying region", er);
2111       return;
2112     }
2113
2114     ArrayList<int[]> hiddenColumns = null;
2115     if (viewport.hasHiddenColumns())
2116     {
2117       hiddenColumns = new ArrayList<>();
2118
2119       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2120       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2121       ArrayList<int[]> hiddenRegions = viewport.getAlignment()
2122               .getHiddenColumns().getHiddenColumnsCopy();
2123       for (int[] region : hiddenRegions)
2124
2125       {
2126         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
2127         {
2128           hiddenColumns
2129                   .add(new int[]
2130                   { region[0] - hiddenOffset, region[1] - hiddenOffset });
2131         }
2132       }
2133     }
2134
2135     Desktop.jalviewClipboard = new Object[] { seqs,
2136         viewport.getAlignment().getDataset(), hiddenColumns };
2137     statusBar.setText(MessageManager.formatMessage(
2138             "label.copied_sequences_to_clipboard", new Object[]
2139             { Integer.valueOf(seqs.length).toString() }));
2140   }
2141
2142   /**
2143    * DOCUMENT ME!
2144    *
2145    * @param e
2146    *          DOCUMENT ME!
2147    * @throws InterruptedException
2148    * @throws IOException
2149    */
2150   @Override
2151   protected void pasteNew_actionPerformed(ActionEvent e)
2152           throws IOException, InterruptedException
2153   {
2154     paste(true);
2155   }
2156
2157   /**
2158    * DOCUMENT ME!
2159    *
2160    * @param e
2161    *          DOCUMENT ME!
2162    * @throws InterruptedException
2163    * @throws IOException
2164    */
2165   @Override
2166   protected void pasteThis_actionPerformed(ActionEvent e)
2167           throws IOException, InterruptedException
2168   {
2169     paste(false);
2170   }
2171
2172   /**
2173    * Paste contents of Jalview clipboard
2174    *
2175    * @param newAlignment
2176    *          true to paste to a new alignment, otherwise add to this.
2177    * @throws InterruptedException
2178    * @throws IOException
2179    */
2180   void paste(boolean newAlignment) throws IOException, InterruptedException
2181   {
2182     boolean externalPaste = true;
2183     try
2184     {
2185       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2186       Transferable contents = c.getContents(this);
2187
2188       if (contents == null)
2189       {
2190         return;
2191       }
2192
2193       String str;
2194       FileFormatI format;
2195       try
2196       {
2197         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2198         if (str.length() < 1)
2199         {
2200           return;
2201         }
2202
2203         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2204
2205       } catch (OutOfMemoryError er)
2206       {
2207         new OOMWarning("Out of memory pasting sequences!!", er);
2208         return;
2209       }
2210
2211       SequenceI[] sequences;
2212       boolean annotationAdded = false;
2213       AlignmentI alignment = null;
2214
2215       if (Desktop.jalviewClipboard != null)
2216       {
2217         // The clipboard was filled from within Jalview, we must use the
2218         // sequences
2219         // And dataset from the copied alignment
2220         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2221         // be doubly sure that we create *new* sequence objects.
2222         sequences = new SequenceI[newseq.length];
2223         for (int i = 0; i < newseq.length; i++)
2224         {
2225           sequences[i] = new Sequence(newseq[i]);
2226         }
2227         alignment = new Alignment(sequences);
2228         externalPaste = false;
2229       }
2230       else
2231       {
2232         // parse the clipboard as an alignment.
2233         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2234                 format);
2235         sequences = alignment.getSequencesArray();
2236       }
2237
2238       int alwidth = 0;
2239       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2240       int fgroup = -1;
2241
2242       if (newAlignment)
2243       {
2244
2245         if (Desktop.jalviewClipboard != null)
2246         {
2247           // dataset is inherited
2248           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2249         }
2250         else
2251         {
2252           // new dataset is constructed
2253           alignment.setDataset(null);
2254         }
2255         alwidth = alignment.getWidth() + 1;
2256       }
2257       else
2258       {
2259         AlignmentI pastedal = alignment; // preserve pasted alignment object
2260         // Add pasted sequences and dataset into existing alignment.
2261         alignment = viewport.getAlignment();
2262         alwidth = alignment.getWidth() + 1;
2263         // decide if we need to import sequences from an existing dataset
2264         boolean importDs = Desktop.jalviewClipboard != null
2265                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2266         // importDs==true instructs us to copy over new dataset sequences from
2267         // an existing alignment
2268         Vector newDs = (importDs) ? new Vector() : null; // used to create
2269         // minimum dataset set
2270
2271         for (int i = 0; i < sequences.length; i++)
2272         {
2273           if (importDs)
2274           {
2275             newDs.addElement(null);
2276           }
2277           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2278           // paste
2279           if (importDs && ds != null)
2280           {
2281             if (!newDs.contains(ds))
2282             {
2283               newDs.setElementAt(ds, i);
2284               ds = new Sequence(ds);
2285               // update with new dataset sequence
2286               sequences[i].setDatasetSequence(ds);
2287             }
2288             else
2289             {
2290               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2291             }
2292           }
2293           else
2294           {
2295             // copy and derive new dataset sequence
2296             sequences[i] = sequences[i].deriveSequence();
2297             alignment.getDataset()
2298                     .addSequence(sequences[i].getDatasetSequence());
2299             // TODO: avoid creation of duplicate dataset sequences with a
2300             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2301           }
2302           alignment.addSequence(sequences[i]); // merges dataset
2303         }
2304         if (newDs != null)
2305         {
2306           newDs.clear(); // tidy up
2307         }
2308         if (alignment.getAlignmentAnnotation() != null)
2309         {
2310           for (AlignmentAnnotation alan : alignment
2311                   .getAlignmentAnnotation())
2312           {
2313             if (alan.graphGroup > fgroup)
2314             {
2315               fgroup = alan.graphGroup;
2316             }
2317           }
2318         }
2319         if (pastedal.getAlignmentAnnotation() != null)
2320         {
2321           // Add any annotation attached to alignment.
2322           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2323           for (int i = 0; i < alann.length; i++)
2324           {
2325             annotationAdded = true;
2326             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2327             {
2328               AlignmentAnnotation newann = new AlignmentAnnotation(
2329                       alann[i]);
2330               if (newann.graphGroup > -1)
2331               {
2332                 if (newGraphGroups.size() <= newann.graphGroup
2333                         || newGraphGroups.get(newann.graphGroup) == null)
2334                 {
2335                   for (int q = newGraphGroups
2336                           .size(); q <= newann.graphGroup; q++)
2337                   {
2338                     newGraphGroups.add(q, null);
2339                   }
2340                   newGraphGroups.set(newann.graphGroup,
2341                           new Integer(++fgroup));
2342                 }
2343                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2344                         .intValue();
2345               }
2346
2347               newann.padAnnotation(alwidth);
2348               alignment.addAnnotation(newann);
2349             }
2350           }
2351         }
2352       }
2353       if (!newAlignment)
2354       {
2355         // /////
2356         // ADD HISTORY ITEM
2357         //
2358         addHistoryItem(new EditCommand(
2359                 MessageManager.getString("label.add_sequences"),
2360                 Action.PASTE, sequences, 0, alignment.getWidth(),
2361                 alignment));
2362       }
2363       // Add any annotations attached to sequences
2364       for (int i = 0; i < sequences.length; i++)
2365       {
2366         if (sequences[i].getAnnotation() != null)
2367         {
2368           AlignmentAnnotation newann;
2369           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2370           {
2371             annotationAdded = true;
2372             newann = sequences[i].getAnnotation()[a];
2373             newann.adjustForAlignment();
2374             newann.padAnnotation(alwidth);
2375             if (newann.graphGroup > -1)
2376             {
2377               if (newann.graphGroup > -1)
2378               {
2379                 if (newGraphGroups.size() <= newann.graphGroup
2380                         || newGraphGroups.get(newann.graphGroup) == null)
2381                 {
2382                   for (int q = newGraphGroups
2383                           .size(); q <= newann.graphGroup; q++)
2384                   {
2385                     newGraphGroups.add(q, null);
2386                   }
2387                   newGraphGroups.set(newann.graphGroup,
2388                           new Integer(++fgroup));
2389                 }
2390                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2391                         .intValue();
2392               }
2393             }
2394             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2395             // was
2396             // duplicated
2397             // earlier
2398             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2399                     a);
2400           }
2401         }
2402       }
2403       if (!newAlignment)
2404       {
2405
2406         // propagate alignment changed.
2407         vpRanges.setEndSeq(alignment.getHeight());
2408         if (annotationAdded)
2409         {
2410           // Duplicate sequence annotation in all views.
2411           AlignmentI[] alview = this.getViewAlignments();
2412           for (int i = 0; i < sequences.length; i++)
2413           {
2414             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2415             if (sann == null)
2416             {
2417               continue;
2418             }
2419             for (int avnum = 0; avnum < alview.length; avnum++)
2420             {
2421               if (alview[avnum] != alignment)
2422               {
2423                 // duplicate in a view other than the one with input focus
2424                 int avwidth = alview[avnum].getWidth() + 1;
2425                 // this relies on sann being preserved after we
2426                 // modify the sequence's annotation array for each duplication
2427                 for (int a = 0; a < sann.length; a++)
2428                 {
2429                   AlignmentAnnotation newann = new AlignmentAnnotation(
2430                           sann[a]);
2431                   sequences[i].addAlignmentAnnotation(newann);
2432                   newann.padAnnotation(avwidth);
2433                   alview[avnum].addAnnotation(newann); // annotation was
2434                   // duplicated earlier
2435                   // TODO JAL-1145 graphGroups are not updated for sequence
2436                   // annotation added to several views. This may cause
2437                   // strangeness
2438                   alview[avnum].setAnnotationIndex(newann, a);
2439                 }
2440               }
2441             }
2442           }
2443           buildSortByAnnotationScoresMenu();
2444         }
2445         viewport.firePropertyChange("alignment", null,
2446                 alignment.getSequences());
2447         if (alignPanels != null)
2448         {
2449           for (AlignmentPanel ap : alignPanels)
2450           {
2451             ap.validateAnnotationDimensions(false);
2452           }
2453         }
2454         else
2455         {
2456           alignPanel.validateAnnotationDimensions(false);
2457         }
2458
2459       }
2460       else
2461       {
2462         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2463                 DEFAULT_HEIGHT);
2464         String newtitle = new String("Copied sequences");
2465
2466         if (Desktop.jalviewClipboard != null
2467                 && Desktop.jalviewClipboard[2] != null)
2468         {
2469           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2470           for (int[] region : hc)
2471           {
2472             af.viewport.hideColumns(region[0], region[1]);
2473           }
2474         }
2475
2476         // >>>This is a fix for the moment, until a better solution is
2477         // found!!<<<
2478         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2479                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2480                         .getFeatureRenderer());
2481
2482         // TODO: maintain provenance of an alignment, rather than just make the
2483         // title a concatenation of operations.
2484         if (!externalPaste)
2485         {
2486           if (title.startsWith("Copied sequences"))
2487           {
2488             newtitle = title;
2489           }
2490           else
2491           {
2492             newtitle = newtitle.concat("- from " + title);
2493           }
2494         }
2495         else
2496         {
2497           newtitle = new String("Pasted sequences");
2498         }
2499
2500         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2501                 DEFAULT_HEIGHT);
2502
2503       }
2504
2505     } catch (Exception ex)
2506     {
2507       ex.printStackTrace();
2508       System.out.println("Exception whilst pasting: " + ex);
2509       // could be anything being pasted in here
2510     }
2511   }
2512
2513   @Override
2514   protected void expand_newalign(ActionEvent e)
2515   {
2516     try
2517     {
2518       AlignmentI alignment = AlignmentUtils
2519               .expandContext(getViewport().getAlignment(), -1);
2520       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2521               DEFAULT_HEIGHT);
2522       String newtitle = new String("Flanking alignment");
2523
2524       if (Desktop.jalviewClipboard != null
2525               && Desktop.jalviewClipboard[2] != null)
2526       {
2527         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2528         for (int region[] : hc)
2529         {
2530           af.viewport.hideColumns(region[0], region[1]);
2531         }
2532       }
2533
2534       // >>>This is a fix for the moment, until a better solution is
2535       // found!!<<<
2536       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2537               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2538                       .getFeatureRenderer());
2539
2540       // TODO: maintain provenance of an alignment, rather than just make the
2541       // title a concatenation of operations.
2542       {
2543         if (title.startsWith("Copied sequences"))
2544         {
2545           newtitle = title;
2546         }
2547         else
2548         {
2549           newtitle = newtitle.concat("- from " + title);
2550         }
2551       }
2552
2553       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2554
2555     } catch (Exception ex)
2556     {
2557       ex.printStackTrace();
2558       System.out.println("Exception whilst pasting: " + ex);
2559       // could be anything being pasted in here
2560     } catch (OutOfMemoryError oom)
2561     {
2562       new OOMWarning("Viewing flanking region of alignment", oom);
2563     }
2564   }
2565
2566   /**
2567    * DOCUMENT ME!
2568    *
2569    * @param e
2570    *          DOCUMENT ME!
2571    */
2572   @Override
2573   protected void cut_actionPerformed(ActionEvent e)
2574   {
2575     copy_actionPerformed(null);
2576     delete_actionPerformed(null);
2577   }
2578
2579   /**
2580    * DOCUMENT ME!
2581    *
2582    * @param e
2583    *          DOCUMENT ME!
2584    */
2585   @Override
2586   protected void delete_actionPerformed(ActionEvent evt)
2587   {
2588
2589     SequenceGroup sg = viewport.getSelectionGroup();
2590     if (sg == null)
2591     {
2592       return;
2593     }
2594
2595     /*
2596      * If the cut affects all sequences, warn, remove highlighted columns
2597      */
2598     if (sg.getSize() == viewport.getAlignment().getHeight())
2599     {
2600       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2601               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2602       if (isEntireAlignWidth)
2603       {
2604         int confirm = JvOptionPane.showConfirmDialog(this,
2605                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2606                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2607                 JvOptionPane.OK_CANCEL_OPTION);
2608
2609         if (confirm == JvOptionPane.CANCEL_OPTION
2610                 || confirm == JvOptionPane.CLOSED_OPTION)
2611         {
2612           return;
2613         }
2614       }
2615       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2616               sg.getEndRes() + 1);
2617     }
2618     SequenceI[] cut = sg.getSequences()
2619             .toArray(new SequenceI[sg.getSize()]);
2620
2621     addHistoryItem(new EditCommand(
2622             MessageManager.getString("label.cut_sequences"), Action.CUT,
2623             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2624             viewport.getAlignment()));
2625
2626     viewport.setSelectionGroup(null);
2627     viewport.sendSelection();
2628     viewport.getAlignment().deleteGroup(sg);
2629
2630     viewport.firePropertyChange("alignment", null,
2631             viewport.getAlignment().getSequences());
2632     if (viewport.getAlignment().getHeight() < 1)
2633     {
2634       try
2635       {
2636         this.setClosed(true);
2637       } catch (Exception ex)
2638       {
2639       }
2640     }
2641   }
2642
2643   /**
2644    * DOCUMENT ME!
2645    *
2646    * @param e
2647    *          DOCUMENT ME!
2648    */
2649   @Override
2650   protected void deleteGroups_actionPerformed(ActionEvent e)
2651   {
2652     if (avc.deleteGroups())
2653     {
2654       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2655       alignPanel.updateAnnotation();
2656       alignPanel.paintAlignment(true);
2657     }
2658   }
2659
2660   /**
2661    * DOCUMENT ME!
2662    *
2663    * @param e
2664    *          DOCUMENT ME!
2665    */
2666   @Override
2667   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2668   {
2669     SequenceGroup sg = new SequenceGroup();
2670
2671     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2672     {
2673       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2674     }
2675
2676     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2677     viewport.setSelectionGroup(sg);
2678     viewport.sendSelection();
2679     // JAL-2034 - should delegate to
2680     // alignPanel to decide if overview needs
2681     // updating.
2682     alignPanel.paintAlignment(false);
2683     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2684   }
2685
2686   /**
2687    * DOCUMENT ME!
2688    *
2689    * @param e
2690    *          DOCUMENT ME!
2691    */
2692   @Override
2693   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2694   {
2695     if (viewport.cursorMode)
2696     {
2697       alignPanel.getSeqPanel().keyboardNo1 = null;
2698       alignPanel.getSeqPanel().keyboardNo2 = null;
2699     }
2700     viewport.setSelectionGroup(null);
2701     viewport.getColumnSelection().clear();
2702     viewport.setSelectionGroup(null);
2703     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2704     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2705     // JAL-2034 - should delegate to
2706     // alignPanel to decide if overview needs
2707     // updating.
2708     alignPanel.paintAlignment(false);
2709     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2710     viewport.sendSelection();
2711   }
2712
2713   /**
2714    * DOCUMENT ME!
2715    *
2716    * @param e
2717    *          DOCUMENT ME!
2718    */
2719   @Override
2720   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2721   {
2722     SequenceGroup sg = viewport.getSelectionGroup();
2723
2724     if (sg == null)
2725     {
2726       selectAllSequenceMenuItem_actionPerformed(null);
2727
2728       return;
2729     }
2730
2731     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2732     {
2733       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2734     }
2735     // JAL-2034 - should delegate to
2736     // alignPanel to decide if overview needs
2737     // updating.
2738
2739     alignPanel.paintAlignment(true);
2740     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2741     viewport.sendSelection();
2742   }
2743
2744   @Override
2745   public void invertColSel_actionPerformed(ActionEvent e)
2746   {
2747     viewport.invertColumnSelection();
2748     alignPanel.paintAlignment(true);
2749     viewport.sendSelection();
2750   }
2751
2752   /**
2753    * DOCUMENT ME!
2754    *
2755    * @param e
2756    *          DOCUMENT ME!
2757    */
2758   @Override
2759   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2760   {
2761     trimAlignment(true);
2762   }
2763
2764   /**
2765    * DOCUMENT ME!
2766    *
2767    * @param e
2768    *          DOCUMENT ME!
2769    */
2770   @Override
2771   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2772   {
2773     trimAlignment(false);
2774   }
2775
2776   void trimAlignment(boolean trimLeft)
2777   {
2778     ColumnSelection colSel = viewport.getColumnSelection();
2779     int column;
2780
2781     if (!colSel.isEmpty())
2782     {
2783       if (trimLeft)
2784       {
2785         column = colSel.getMin();
2786       }
2787       else
2788       {
2789         column = colSel.getMax();
2790       }
2791
2792       SequenceI[] seqs;
2793       if (viewport.getSelectionGroup() != null)
2794       {
2795         seqs = viewport.getSelectionGroup()
2796                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2797       }
2798       else
2799       {
2800         seqs = viewport.getAlignment().getSequencesArray();
2801       }
2802
2803       TrimRegionCommand trimRegion;
2804       if (trimLeft)
2805       {
2806         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2807                 column, viewport.getAlignment());
2808         vpRanges.setStartRes(0);
2809       }
2810       else
2811       {
2812         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2813                 column, viewport.getAlignment());
2814       }
2815
2816       statusBar.setText(MessageManager
2817               .formatMessage("label.removed_columns", new String[]
2818               { Integer.valueOf(trimRegion.getSize()).toString() }));
2819
2820       addHistoryItem(trimRegion);
2821
2822       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2823       {
2824         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2825                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2826         {
2827           viewport.getAlignment().deleteGroup(sg);
2828         }
2829       }
2830
2831       viewport.firePropertyChange("alignment", null,
2832               viewport.getAlignment().getSequences());
2833     }
2834   }
2835
2836   /**
2837    * DOCUMENT ME!
2838    *
2839    * @param e
2840    *          DOCUMENT ME!
2841    */
2842   @Override
2843   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2844   {
2845     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2846
2847     SequenceI[] seqs;
2848     if (viewport.getSelectionGroup() != null)
2849     {
2850       seqs = viewport.getSelectionGroup()
2851               .getSequencesAsArray(viewport.getHiddenRepSequences());
2852       start = viewport.getSelectionGroup().getStartRes();
2853       end = viewport.getSelectionGroup().getEndRes();
2854     }
2855     else
2856     {
2857       seqs = viewport.getAlignment().getSequencesArray();
2858     }
2859
2860     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2861             "Remove Gapped Columns", seqs, start, end,
2862             viewport.getAlignment());
2863
2864     addHistoryItem(removeGapCols);
2865
2866     statusBar.setText(MessageManager
2867             .formatMessage("label.removed_empty_columns", new Object[]
2868             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2869
2870     // This is to maintain viewport position on first residue
2871     // of first sequence
2872     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2873     int startRes = seq.findPosition(vpRanges.getStartRes());
2874     // ShiftList shifts;
2875     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2876     // edit.alColumnChanges=shifts.getInverse();
2877     // if (viewport.hasHiddenColumns)
2878     // viewport.getColumnSelection().compensateForEdits(shifts);
2879     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2880     viewport.firePropertyChange("alignment", null,
2881             viewport.getAlignment().getSequences());
2882
2883   }
2884
2885   /**
2886    * DOCUMENT ME!
2887    *
2888    * @param e
2889    *          DOCUMENT ME!
2890    */
2891   @Override
2892   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2893   {
2894     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2895
2896     SequenceI[] seqs;
2897     if (viewport.getSelectionGroup() != null)
2898     {
2899       seqs = viewport.getSelectionGroup()
2900               .getSequencesAsArray(viewport.getHiddenRepSequences());
2901       start = viewport.getSelectionGroup().getStartRes();
2902       end = viewport.getSelectionGroup().getEndRes();
2903     }
2904     else
2905     {
2906       seqs = viewport.getAlignment().getSequencesArray();
2907     }
2908
2909     // This is to maintain viewport position on first residue
2910     // of first sequence
2911     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2912     int startRes = seq.findPosition(vpRanges.getStartRes());
2913
2914     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2915             viewport.getAlignment()));
2916
2917     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2918
2919     viewport.firePropertyChange("alignment", null,
2920             viewport.getAlignment().getSequences());
2921
2922   }
2923
2924   /**
2925    * DOCUMENT ME!
2926    *
2927    * @param e
2928    *          DOCUMENT ME!
2929    */
2930   @Override
2931   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2932   {
2933     viewport.setPadGaps(padGapsMenuitem.isSelected());
2934     viewport.firePropertyChange("alignment", null,
2935             viewport.getAlignment().getSequences());
2936   }
2937
2938   /**
2939    * DOCUMENT ME!
2940    *
2941    * @param e
2942    *          DOCUMENT ME!
2943    */
2944   @Override
2945   public void findMenuItem_actionPerformed(ActionEvent e)
2946   {
2947     new Finder();
2948   }
2949
2950   /**
2951    * Create a new view of the current alignment.
2952    */
2953   @Override
2954   public void newView_actionPerformed(ActionEvent e)
2955   {
2956     newView(null, true);
2957   }
2958
2959   /**
2960    * Creates and shows a new view of the current alignment.
2961    *
2962    * @param viewTitle
2963    *          title of newly created view; if null, one will be generated
2964    * @param copyAnnotation
2965    *          if true then duplicate all annnotation, groups and settings
2966    * @return new alignment panel, already displayed.
2967    */
2968   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2969   {
2970     /*
2971      * Create a new AlignmentPanel (with its own, new Viewport)
2972      */
2973     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2974             true);
2975     if (!copyAnnotation)
2976     {
2977       /*
2978        * remove all groups and annotation except for the automatic stuff
2979        */
2980       newap.av.getAlignment().deleteAllGroups();
2981       newap.av.getAlignment().deleteAllAnnotations(false);
2982     }
2983
2984     newap.av.setGatherViewsHere(false);
2985
2986     if (viewport.viewName == null)
2987     {
2988       viewport.viewName = MessageManager
2989               .getString("label.view_name_original");
2990     }
2991
2992     /*
2993      * Views share the same edits undo and redo stacks
2994      */
2995     newap.av.setHistoryList(viewport.getHistoryList());
2996     newap.av.setRedoList(viewport.getRedoList());
2997
2998     /*
2999      * Views share the same mappings; need to deregister any new mappings
3000      * created by copyAlignPanel, and register the new reference to the shared
3001      * mappings
3002      */
3003     newap.av.replaceMappings(viewport.getAlignment());
3004
3005     /*
3006      * start up cDNA consensus (if applicable) now mappings are in place
3007      */
3008     if (newap.av.initComplementConsensus())
3009     {
3010       newap.refresh(true); // adjust layout of annotations
3011     }
3012
3013     newap.av.viewName = getNewViewName(viewTitle);
3014
3015     addAlignmentPanel(newap, true);
3016     newap.alignmentChanged();
3017
3018     if (alignPanels.size() == 2)
3019     {
3020       viewport.setGatherViewsHere(true);
3021     }
3022     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3023     return newap;
3024   }
3025
3026   /**
3027    * Make a new name for the view, ensuring it is unique within the current
3028    * sequenceSetId. (This used to be essential for Jalview Project archives, but
3029    * these now use viewId. Unique view names are still desirable for usability.)
3030    *
3031    * @param viewTitle
3032    * @return
3033    */
3034   protected String getNewViewName(String viewTitle)
3035   {
3036     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3037     boolean addFirstIndex = false;
3038     if (viewTitle == null || viewTitle.trim().length() == 0)
3039     {
3040       viewTitle = MessageManager.getString("action.view");
3041       addFirstIndex = true;
3042     }
3043     else
3044     {
3045       index = 1;// we count from 1 if given a specific name
3046     }
3047     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3048
3049     List<Component> comps = PaintRefresher.components
3050             .get(viewport.getSequenceSetId());
3051
3052     List<String> existingNames = getExistingViewNames(comps);
3053
3054     while (existingNames.contains(newViewName))
3055     {
3056       newViewName = viewTitle + " " + (++index);
3057     }
3058     return newViewName;
3059   }
3060
3061   /**
3062    * Returns a list of distinct view names found in the given list of
3063    * components. View names are held on the viewport of an AlignmentPanel.
3064    *
3065    * @param comps
3066    * @return
3067    */
3068   protected List<String> getExistingViewNames(List<Component> comps)
3069   {
3070     List<String> existingNames = new ArrayList<>();
3071     for (Component comp : comps)
3072     {
3073       if (comp instanceof AlignmentPanel)
3074       {
3075         AlignmentPanel ap = (AlignmentPanel) comp;
3076         if (!existingNames.contains(ap.av.viewName))
3077         {
3078           existingNames.add(ap.av.viewName);
3079         }
3080       }
3081     }
3082     return existingNames;
3083   }
3084
3085   /**
3086    * Explode tabbed views into separate windows.
3087    */
3088   @Override
3089   public void expandViews_actionPerformed(ActionEvent e)
3090   {
3091     Desktop.explodeViews(this);
3092   }
3093
3094   /**
3095    * Gather views in separate windows back into a tabbed presentation.
3096    */
3097   @Override
3098   public void gatherViews_actionPerformed(ActionEvent e)
3099   {
3100     Desktop.instance.gatherViews(this);
3101   }
3102
3103   /**
3104    * DOCUMENT ME!
3105    *
3106    * @param e
3107    *          DOCUMENT ME!
3108    */
3109   @Override
3110   public void font_actionPerformed(ActionEvent e)
3111   {
3112     new FontChooser(alignPanel);
3113   }
3114
3115   /**
3116    * DOCUMENT ME!
3117    *
3118    * @param e
3119    *          DOCUMENT ME!
3120    */
3121   @Override
3122   protected void seqLimit_actionPerformed(ActionEvent e)
3123   {
3124     viewport.setShowJVSuffix(seqLimits.isSelected());
3125
3126     alignPanel.getIdPanel().getIdCanvas()
3127             .setPreferredSize(alignPanel.calculateIdWidth());
3128     alignPanel.paintAlignment(true);
3129   }
3130
3131   @Override
3132   public void idRightAlign_actionPerformed(ActionEvent e)
3133   {
3134     viewport.setRightAlignIds(idRightAlign.isSelected());
3135     alignPanel.paintAlignment(true);
3136   }
3137
3138   @Override
3139   public void centreColumnLabels_actionPerformed(ActionEvent e)
3140   {
3141     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3142     alignPanel.paintAlignment(true);
3143   }
3144
3145   /*
3146    * (non-Javadoc)
3147    *
3148    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3149    */
3150   @Override
3151   protected void followHighlight_actionPerformed()
3152   {
3153     /*
3154      * Set the 'follow' flag on the Viewport (and scroll to position if now
3155      * true).
3156      */
3157     final boolean state = this.followHighlightMenuItem.getState();
3158     viewport.setFollowHighlight(state);
3159     if (state)
3160     {
3161       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3162     }
3163   }
3164
3165   /**
3166    * DOCUMENT ME!
3167    *
3168    * @param e
3169    *          DOCUMENT ME!
3170    */
3171   @Override
3172   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3173   {
3174     viewport.setColourText(colourTextMenuItem.isSelected());
3175     alignPanel.paintAlignment(true);
3176   }
3177
3178   /**
3179    * DOCUMENT ME!
3180    *
3181    * @param e
3182    *          DOCUMENT ME!
3183    */
3184   @Override
3185   public void wrapMenuItem_actionPerformed(ActionEvent e)
3186   {
3187     scaleAbove.setVisible(wrapMenuItem.isSelected());
3188     scaleLeft.setVisible(wrapMenuItem.isSelected());
3189     scaleRight.setVisible(wrapMenuItem.isSelected());
3190     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3191     alignPanel.updateLayout();
3192   }
3193
3194   @Override
3195   public void showAllSeqs_actionPerformed(ActionEvent e)
3196   {
3197     viewport.showAllHiddenSeqs();
3198   }
3199
3200   @Override
3201   public void showAllColumns_actionPerformed(ActionEvent e)
3202   {
3203     viewport.showAllHiddenColumns();
3204     alignPanel.paintAlignment(true);
3205     viewport.sendSelection();
3206   }
3207
3208   @Override
3209   public void hideSelSequences_actionPerformed(ActionEvent e)
3210   {
3211     viewport.hideAllSelectedSeqs();
3212   }
3213
3214   /**
3215    * called by key handler and the hide all/show all menu items
3216    *
3217    * @param toggleSeqs
3218    * @param toggleCols
3219    */
3220   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3221   {
3222
3223     boolean hide = false;
3224     SequenceGroup sg = viewport.getSelectionGroup();
3225     if (!toggleSeqs && !toggleCols)
3226     {
3227       // Hide everything by the current selection - this is a hack - we do the
3228       // invert and then hide
3229       // first check that there will be visible columns after the invert.
3230       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3231               && sg.getStartRes() <= sg.getEndRes()))
3232       {
3233         // now invert the sequence set, if required - empty selection implies
3234         // that no hiding is required.
3235         if (sg != null)
3236         {
3237           invertSequenceMenuItem_actionPerformed(null);
3238           sg = viewport.getSelectionGroup();
3239           toggleSeqs = true;
3240
3241         }
3242         viewport.expandColSelection(sg, true);
3243         // finally invert the column selection and get the new sequence
3244         // selection.
3245         invertColSel_actionPerformed(null);
3246         toggleCols = true;
3247       }
3248     }
3249
3250     if (toggleSeqs)
3251     {
3252       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3253       {
3254         hideSelSequences_actionPerformed(null);
3255         hide = true;
3256       }
3257       else if (!(toggleCols && viewport.hasSelectedColumns()))
3258       {
3259         showAllSeqs_actionPerformed(null);
3260       }
3261     }
3262
3263     if (toggleCols)
3264     {
3265       if (viewport.hasSelectedColumns())
3266       {
3267         hideSelColumns_actionPerformed(null);
3268         if (!toggleSeqs)
3269         {
3270           viewport.setSelectionGroup(sg);
3271         }
3272       }
3273       else if (!hide)
3274       {
3275         showAllColumns_actionPerformed(null);
3276       }
3277     }
3278   }
3279
3280   /*
3281    * (non-Javadoc)
3282    *
3283    * @see
3284    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3285    * event.ActionEvent)
3286    */
3287   @Override
3288   public void hideAllButSelection_actionPerformed(ActionEvent e)
3289   {
3290     toggleHiddenRegions(false, false);
3291     viewport.sendSelection();
3292   }
3293
3294   /*
3295    * (non-Javadoc)
3296    *
3297    * @see
3298    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3299    * .ActionEvent)
3300    */
3301   @Override
3302   public void hideAllSelection_actionPerformed(ActionEvent e)
3303   {
3304     SequenceGroup sg = viewport.getSelectionGroup();
3305     viewport.expandColSelection(sg, false);
3306     viewport.hideAllSelectedSeqs();
3307     viewport.hideSelectedColumns();
3308     alignPanel.paintAlignment(true);
3309     viewport.sendSelection();
3310   }
3311
3312   /*
3313    * (non-Javadoc)
3314    *
3315    * @see
3316    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3317    * ActionEvent)
3318    */
3319   @Override
3320   public void showAllhidden_actionPerformed(ActionEvent e)
3321   {
3322     viewport.showAllHiddenColumns();
3323     viewport.showAllHiddenSeqs();
3324     alignPanel.paintAlignment(true);
3325     viewport.sendSelection();
3326   }
3327
3328   @Override
3329   public void hideSelColumns_actionPerformed(ActionEvent e)
3330   {
3331     viewport.hideSelectedColumns();
3332     alignPanel.paintAlignment(true);
3333     viewport.sendSelection();
3334   }
3335
3336   @Override
3337   public void hiddenMarkers_actionPerformed(ActionEvent e)
3338   {
3339     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3340     repaint();
3341   }
3342
3343   /**
3344    * DOCUMENT ME!
3345    *
3346    * @param e
3347    *          DOCUMENT ME!
3348    */
3349   @Override
3350   protected void scaleAbove_actionPerformed(ActionEvent e)
3351   {
3352     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3353     alignPanel.paintAlignment(true);
3354   }
3355
3356   /**
3357    * DOCUMENT ME!
3358    *
3359    * @param e
3360    *          DOCUMENT ME!
3361    */
3362   @Override
3363   protected void scaleLeft_actionPerformed(ActionEvent e)
3364   {
3365     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3366     alignPanel.paintAlignment(true);
3367   }
3368
3369   /**
3370    * DOCUMENT ME!
3371    *
3372    * @param e
3373    *          DOCUMENT ME!
3374    */
3375   @Override
3376   protected void scaleRight_actionPerformed(ActionEvent e)
3377   {
3378     viewport.setScaleRightWrapped(scaleRight.isSelected());
3379     alignPanel.paintAlignment(true);
3380   }
3381
3382   /**
3383    * DOCUMENT ME!
3384    *
3385    * @param e
3386    *          DOCUMENT ME!
3387    */
3388   @Override
3389   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3390   {
3391     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3392     alignPanel.paintAlignment(true);
3393   }
3394
3395   /**
3396    * DOCUMENT ME!
3397    *
3398    * @param e
3399    *          DOCUMENT ME!
3400    */
3401   @Override
3402   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3403   {
3404     viewport.setShowText(viewTextMenuItem.isSelected());
3405     alignPanel.paintAlignment(true);
3406   }
3407
3408   /**
3409    * DOCUMENT ME!
3410    *
3411    * @param e
3412    *          DOCUMENT ME!
3413    */
3414   @Override
3415   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3416   {
3417     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3418     alignPanel.paintAlignment(true);
3419   }
3420
3421   public FeatureSettings featureSettings;
3422
3423   @Override
3424   public FeatureSettingsControllerI getFeatureSettingsUI()
3425   {
3426     return featureSettings;
3427   }
3428
3429   @Override
3430   public void featureSettings_actionPerformed(ActionEvent e)
3431   {
3432     if (featureSettings != null)
3433     {
3434       featureSettings.close();
3435       featureSettings = null;
3436     }
3437     if (!showSeqFeatures.isSelected())
3438     {
3439       // make sure features are actually displayed
3440       showSeqFeatures.setSelected(true);
3441       showSeqFeatures_actionPerformed(null);
3442     }
3443     featureSettings = new FeatureSettings(this);
3444   }
3445
3446   /**
3447    * Set or clear 'Show Sequence Features'
3448    *
3449    * @param evt
3450    *          DOCUMENT ME!
3451    */
3452   @Override
3453   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3454   {
3455     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3456     alignPanel.paintAlignment(true);
3457   }
3458
3459   /**
3460    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3461    * the annotations panel as a whole.
3462    *
3463    * The options to show/hide all annotations should be enabled when the panel
3464    * is shown, and disabled when the panel is hidden.
3465    *
3466    * @param e
3467    */
3468   @Override
3469   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3470   {
3471     final boolean setVisible = annotationPanelMenuItem.isSelected();
3472     viewport.setShowAnnotation(setVisible);
3473     this.showAllSeqAnnotations.setEnabled(setVisible);
3474     this.hideAllSeqAnnotations.setEnabled(setVisible);
3475     this.showAllAlAnnotations.setEnabled(setVisible);
3476     this.hideAllAlAnnotations.setEnabled(setVisible);
3477     alignPanel.updateLayout();
3478   }
3479
3480   @Override
3481   public void alignmentProperties()
3482   {
3483     JEditorPane editPane = new JEditorPane("text/html", "");
3484     editPane.setEditable(false);
3485     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3486             .formatAsHtml();
3487     editPane.setText(
3488             MessageManager.formatMessage("label.html_content", new Object[]
3489             { contents.toString() }));
3490     JInternalFrame frame = new JInternalFrame();
3491     frame.getContentPane().add(new JScrollPane(editPane));
3492
3493     Desktop.addInternalFrame(frame, MessageManager
3494             .formatMessage("label.alignment_properties", new Object[]
3495             { getTitle() }), 500, 400);
3496   }
3497
3498   /**
3499    * DOCUMENT ME!
3500    *
3501    * @param e
3502    *          DOCUMENT ME!
3503    */
3504   @Override
3505   public void overviewMenuItem_actionPerformed(ActionEvent e)
3506   {
3507     if (alignPanel.overviewPanel != null)
3508     {
3509       return;
3510     }
3511
3512     JInternalFrame frame = new JInternalFrame();
3513     final OverviewPanel overview = new OverviewPanel(alignPanel);
3514     frame.setContentPane(overview);
3515     Desktop.addInternalFrame(frame, MessageManager
3516             .formatMessage("label.overview_params", new Object[]
3517             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3518             true, true);
3519     frame.pack();
3520     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3521     frame.addInternalFrameListener(
3522             new javax.swing.event.InternalFrameAdapter()
3523             {
3524               @Override
3525               public void internalFrameClosed(
3526                       javax.swing.event.InternalFrameEvent evt)
3527               {
3528                 overview.dispose();
3529                 alignPanel.setOverviewPanel(null);
3530               };
3531             });
3532
3533     alignPanel.setOverviewPanel(overview);
3534   }
3535
3536   @Override
3537   public void textColour_actionPerformed()
3538   {
3539     new TextColourChooser().chooseColour(alignPanel, null);
3540   }
3541
3542   /*
3543    * public void covariationColour_actionPerformed() {
3544    * changeColour(new
3545    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3546    * ()[0])); }
3547    */
3548   @Override
3549   public void annotationColour_actionPerformed()
3550   {
3551     new AnnotationColourChooser(viewport, alignPanel);
3552   }
3553
3554   @Override
3555   public void annotationColumn_actionPerformed(ActionEvent e)
3556   {
3557     new AnnotationColumnChooser(viewport, alignPanel);
3558   }
3559
3560   /**
3561    * Action on the user checking or unchecking the option to apply the selected
3562    * colour scheme to all groups. If unchecked, groups may have their own
3563    * independent colour schemes.
3564    *
3565    * @param selected
3566    */
3567   @Override
3568   public void applyToAllGroups_actionPerformed(boolean selected)
3569   {
3570     viewport.setColourAppliesToAllGroups(selected);
3571   }
3572
3573   /**
3574    * Action on user selecting a colour from the colour menu
3575    *
3576    * @param name
3577    *          the name (not the menu item label!) of the colour scheme
3578    */
3579   @Override
3580   public void changeColour_actionPerformed(String name)
3581   {
3582     /*
3583      * 'User Defined' opens a panel to configure or load a
3584      * user-defined colour scheme
3585      */
3586     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3587     {
3588       new UserDefinedColours(alignPanel);
3589       return;
3590     }
3591
3592     /*
3593      * otherwise set the chosen colour scheme (or null for 'None')
3594      */
3595     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3596             viewport.getAlignment(), viewport.getHiddenRepSequences());
3597     changeColour(cs);
3598   }
3599
3600   /**
3601    * Actions on setting or changing the alignment colour scheme
3602    *
3603    * @param cs
3604    */
3605   @Override
3606   public void changeColour(ColourSchemeI cs)
3607   {
3608     // TODO: pull up to controller method
3609     ColourMenuHelper.setColourSelected(colourMenu, cs);
3610
3611     viewport.setGlobalColourScheme(cs);
3612
3613     alignPanel.paintAlignment(true);
3614   }
3615
3616   /**
3617    * Show the PID threshold slider panel
3618    */
3619   @Override
3620   protected void modifyPID_actionPerformed()
3621   {
3622     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3623             alignPanel.getViewName());
3624     SliderPanel.showPIDSlider();
3625   }
3626
3627   /**
3628    * Show the Conservation slider panel
3629    */
3630   @Override
3631   protected void modifyConservation_actionPerformed()
3632   {
3633     SliderPanel.setConservationSlider(alignPanel,
3634             viewport.getResidueShading(), alignPanel.getViewName());
3635     SliderPanel.showConservationSlider();
3636   }
3637
3638   /**
3639    * Action on selecting or deselecting (Colour) By Conservation
3640    */
3641   @Override
3642   public void conservationMenuItem_actionPerformed(boolean selected)
3643   {
3644     modifyConservation.setEnabled(selected);
3645     viewport.setConservationSelected(selected);
3646     viewport.getResidueShading().setConservationApplied(selected);
3647
3648     changeColour(viewport.getGlobalColourScheme());
3649     if (selected)
3650     {
3651       modifyConservation_actionPerformed();
3652     }
3653     else
3654     {
3655       SliderPanel.hideConservationSlider();
3656     }
3657   }
3658
3659   /**
3660    * Action on selecting or deselecting (Colour) Above PID Threshold
3661    */
3662   @Override
3663   public void abovePIDThreshold_actionPerformed(boolean selected)
3664   {
3665     modifyPID.setEnabled(selected);
3666     viewport.setAbovePIDThreshold(selected);
3667     if (!selected)
3668     {
3669       viewport.getResidueShading().setThreshold(0,
3670               viewport.isIgnoreGapsConsensus());
3671     }
3672
3673     changeColour(viewport.getGlobalColourScheme());
3674     if (selected)
3675     {
3676       modifyPID_actionPerformed();
3677     }
3678     else
3679     {
3680       SliderPanel.hidePIDSlider();
3681     }
3682   }
3683
3684   /**
3685    * DOCUMENT ME!
3686    *
3687    * @param e
3688    *          DOCUMENT ME!
3689    */
3690   @Override
3691   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3692   {
3693     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3694     AlignmentSorter.sortByPID(viewport.getAlignment(),
3695             viewport.getAlignment().getSequenceAt(0));
3696     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3697             viewport.getAlignment()));
3698     alignPanel.paintAlignment(true);
3699   }
3700
3701   /**
3702    * DOCUMENT ME!
3703    *
3704    * @param e
3705    *          DOCUMENT ME!
3706    */
3707   @Override
3708   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3709   {
3710     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3711     AlignmentSorter.sortByID(viewport.getAlignment());
3712     addHistoryItem(
3713             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3714     alignPanel.paintAlignment(true);
3715   }
3716
3717   /**
3718    * DOCUMENT ME!
3719    *
3720    * @param e
3721    *          DOCUMENT ME!
3722    */
3723   @Override
3724   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3725   {
3726     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3727     AlignmentSorter.sortByLength(viewport.getAlignment());
3728     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3729             viewport.getAlignment()));
3730     alignPanel.paintAlignment(true);
3731   }
3732
3733   /**
3734    * DOCUMENT ME!
3735    *
3736    * @param e
3737    *          DOCUMENT ME!
3738    */
3739   @Override
3740   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3741   {
3742     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3743     AlignmentSorter.sortByGroup(viewport.getAlignment());
3744     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3745             viewport.getAlignment()));
3746
3747     alignPanel.paintAlignment(true);
3748   }
3749
3750   /**
3751    * DOCUMENT ME!
3752    *
3753    * @param e
3754    *          DOCUMENT ME!
3755    */
3756   @Override
3757   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3758   {
3759     new RedundancyPanel(alignPanel, this);
3760   }
3761
3762   /**
3763    * DOCUMENT ME!
3764    *
3765    * @param e
3766    *          DOCUMENT ME!
3767    */
3768   @Override
3769   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3770   {
3771     if ((viewport.getSelectionGroup() == null)
3772             || (viewport.getSelectionGroup().getSize() < 2))
3773     {
3774       JvOptionPane.showInternalMessageDialog(this,
3775               MessageManager.getString(
3776                       "label.you_must_select_least_two_sequences"),
3777               MessageManager.getString("label.invalid_selection"),
3778               JvOptionPane.WARNING_MESSAGE);
3779     }
3780     else
3781     {
3782       JInternalFrame frame = new JInternalFrame();
3783       frame.setContentPane(new PairwiseAlignPanel(viewport));
3784       Desktop.addInternalFrame(frame,
3785               MessageManager.getString("action.pairwise_alignment"), 600,
3786               500);
3787     }
3788   }
3789
3790   @Override
3791   public void autoCalculate_actionPerformed(ActionEvent e)
3792   {
3793     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3794     if (viewport.autoCalculateConsensus)
3795     {
3796       viewport.firePropertyChange("alignment", null,
3797               viewport.getAlignment().getSequences());
3798     }
3799   }
3800
3801   @Override
3802   public void sortByTreeOption_actionPerformed(ActionEvent e)
3803   {
3804     viewport.sortByTree = sortByTree.isSelected();
3805   }
3806
3807   @Override
3808   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3809   {
3810     viewport.followSelection = listenToViewSelections.isSelected();
3811   }
3812
3813   /**
3814    * Constructs a tree panel and adds it to the desktop
3815    *
3816    * @param type
3817    *          tree type (NJ or AV)
3818    * @param modelName
3819    *          name of score model used to compute the tree
3820    * @param options
3821    *          parameters for the distance or similarity calculation
3822    */
3823   void newTreePanel(String type, String modelName,
3824           SimilarityParamsI options)
3825   {
3826     String frameTitle = "";
3827     TreePanel tp;
3828
3829     boolean onSelection = false;
3830     if (viewport.getSelectionGroup() != null
3831             && viewport.getSelectionGroup().getSize() > 0)
3832     {
3833       SequenceGroup sg = viewport.getSelectionGroup();
3834
3835       /* Decide if the selection is a column region */
3836       for (SequenceI _s : sg.getSequences())
3837       {
3838         if (_s.getLength() < sg.getEndRes())
3839         {
3840           JvOptionPane.showMessageDialog(Desktop.desktop,
3841                   MessageManager.getString(
3842                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3843                   MessageManager.getString(
3844                           "label.sequences_selection_not_aligned"),
3845                   JvOptionPane.WARNING_MESSAGE);
3846
3847           return;
3848         }
3849       }
3850       onSelection = true;
3851     }
3852     else
3853     {
3854       if (viewport.getAlignment().getHeight() < 2)
3855       {
3856         return;
3857       }
3858     }
3859
3860     tp = new TreePanel(alignPanel, type, modelName, options);
3861     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3862
3863     frameTitle += " from ";
3864
3865     if (viewport.viewName != null)
3866     {
3867       frameTitle += viewport.viewName + " of ";
3868     }
3869
3870     frameTitle += this.title;
3871
3872     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3873   }
3874
3875   /**
3876    * DOCUMENT ME!
3877    *
3878    * @param title
3879    *          DOCUMENT ME!
3880    * @param order
3881    *          DOCUMENT ME!
3882    */
3883   public void addSortByOrderMenuItem(String title,
3884           final AlignmentOrder order)
3885   {
3886     final JMenuItem item = new JMenuItem(MessageManager
3887             .formatMessage("action.by_title_param", new Object[]
3888             { title }));
3889     sort.add(item);
3890     item.addActionListener(new java.awt.event.ActionListener()
3891     {
3892       @Override
3893       public void actionPerformed(ActionEvent e)
3894       {
3895         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3896
3897         // TODO: JBPNote - have to map order entries to curent SequenceI
3898         // pointers
3899         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3900
3901         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3902                 viewport.getAlignment()));
3903
3904         alignPanel.paintAlignment(true);
3905       }
3906     });
3907   }
3908
3909   /**
3910    * Add a new sort by annotation score menu item
3911    *
3912    * @param sort
3913    *          the menu to add the option to
3914    * @param scoreLabel
3915    *          the label used to retrieve scores for each sequence on the
3916    *          alignment
3917    */
3918   public void addSortByAnnotScoreMenuItem(JMenu sort,
3919           final String scoreLabel)
3920   {
3921     final JMenuItem item = new JMenuItem(scoreLabel);
3922     sort.add(item);
3923     item.addActionListener(new java.awt.event.ActionListener()
3924     {
3925       @Override
3926       public void actionPerformed(ActionEvent e)
3927       {
3928         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3929         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3930                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3931         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3932                 viewport.getAlignment()));
3933         alignPanel.paintAlignment(true);
3934       }
3935     });
3936   }
3937
3938   /**
3939    * last hash for alignment's annotation array - used to minimise cost of
3940    * rebuild.
3941    */
3942   protected int _annotationScoreVectorHash;
3943
3944   /**
3945    * search the alignment and rebuild the sort by annotation score submenu the
3946    * last alignment annotation vector hash is stored to minimize cost of
3947    * rebuilding in subsequence calls.
3948    *
3949    */
3950   @Override
3951   public void buildSortByAnnotationScoresMenu()
3952   {
3953     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3954     {
3955       return;
3956     }
3957
3958     if (viewport.getAlignment().getAlignmentAnnotation()
3959             .hashCode() != _annotationScoreVectorHash)
3960     {
3961       sortByAnnotScore.removeAll();
3962       // almost certainly a quicker way to do this - but we keep it simple
3963       Hashtable scoreSorts = new Hashtable();
3964       AlignmentAnnotation aann[];
3965       for (SequenceI sqa : viewport.getAlignment().getSequences())
3966       {
3967         aann = sqa.getAnnotation();
3968         for (int i = 0; aann != null && i < aann.length; i++)
3969         {
3970           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3971           {
3972             scoreSorts.put(aann[i].label, aann[i].label);
3973           }
3974         }
3975       }
3976       Enumeration labels = scoreSorts.keys();
3977       while (labels.hasMoreElements())
3978       {
3979         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3980                 (String) labels.nextElement());
3981       }
3982       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3983       scoreSorts.clear();
3984
3985       _annotationScoreVectorHash = viewport.getAlignment()
3986               .getAlignmentAnnotation().hashCode();
3987     }
3988   }
3989
3990   /**
3991    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3992    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3993    * call. Listeners are added to remove the menu item when the treePanel is
3994    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3995    * modified.
3996    */
3997   @Override
3998   public void buildTreeSortMenu()
3999   {
4000     sortByTreeMenu.removeAll();
4001
4002     List<Component> comps = PaintRefresher.components
4003             .get(viewport.getSequenceSetId());
4004     List<TreePanel> treePanels = new ArrayList<>();
4005     for (Component comp : comps)
4006     {
4007       if (comp instanceof TreePanel)
4008       {
4009         treePanels.add((TreePanel) comp);
4010       }
4011     }
4012
4013     if (treePanels.size() < 1)
4014     {
4015       sortByTreeMenu.setVisible(false);
4016       return;
4017     }
4018
4019     sortByTreeMenu.setVisible(true);
4020
4021     for (final TreePanel tp : treePanels)
4022     {
4023       final JMenuItem item = new JMenuItem(tp.getTitle());
4024       item.addActionListener(new java.awt.event.ActionListener()
4025       {
4026         @Override
4027         public void actionPerformed(ActionEvent e)
4028         {
4029           tp.sortByTree_actionPerformed();
4030           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4031
4032         }
4033       });
4034
4035       sortByTreeMenu.add(item);
4036     }
4037   }
4038
4039   public boolean sortBy(AlignmentOrder alorder, String undoname)
4040   {
4041     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4042     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4043     if (undoname != null)
4044     {
4045       addHistoryItem(new OrderCommand(undoname, oldOrder,
4046               viewport.getAlignment()));
4047     }
4048     alignPanel.paintAlignment(true);
4049     return true;
4050   }
4051
4052   /**
4053    * Work out whether the whole set of sequences or just the selected set will
4054    * be submitted for multiple alignment.
4055    *
4056    */
4057   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4058   {
4059     // Now, check we have enough sequences
4060     AlignmentView msa = null;
4061
4062     if ((viewport.getSelectionGroup() != null)
4063             && (viewport.getSelectionGroup().getSize() > 1))
4064     {
4065       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4066       // some common interface!
4067       /*
4068        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4069        * SequenceI[sz = seqs.getSize(false)];
4070        *
4071        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4072        * seqs.getSequenceAt(i); }
4073        */
4074       msa = viewport.getAlignmentView(true);
4075     }
4076     else if (viewport.getSelectionGroup() != null
4077             && viewport.getSelectionGroup().getSize() == 1)
4078     {
4079       int option = JvOptionPane.showConfirmDialog(this,
4080               MessageManager.getString("warn.oneseq_msainput_selection"),
4081               MessageManager.getString("label.invalid_selection"),
4082               JvOptionPane.OK_CANCEL_OPTION);
4083       if (option == JvOptionPane.OK_OPTION)
4084       {
4085         msa = viewport.getAlignmentView(false);
4086       }
4087     }
4088     else
4089     {
4090       msa = viewport.getAlignmentView(false);
4091     }
4092     return msa;
4093   }
4094
4095   /**
4096    * Decides what is submitted to a secondary structure prediction service: the
4097    * first sequence in the alignment, or in the current selection, or, if the
4098    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4099    * region or the whole alignment. (where the first sequence in the set is the
4100    * one that the prediction will be for).
4101    */
4102   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4103   {
4104     AlignmentView seqs = null;
4105
4106     if ((viewport.getSelectionGroup() != null)
4107             && (viewport.getSelectionGroup().getSize() > 0))
4108     {
4109       seqs = viewport.getAlignmentView(true);
4110     }
4111     else
4112     {
4113       seqs = viewport.getAlignmentView(false);
4114     }
4115     // limit sequences - JBPNote in future - could spawn multiple prediction
4116     // jobs
4117     // TODO: viewport.getAlignment().isAligned is a global state - the local
4118     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4119     if (!viewport.getAlignment().isAligned(false))
4120     {
4121       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4122       // TODO: if seqs.getSequences().length>1 then should really have warned
4123       // user!
4124
4125     }
4126     return seqs;
4127   }
4128
4129   /**
4130    * DOCUMENT ME!
4131    *
4132    * @param e
4133    *          DOCUMENT ME!
4134    */
4135   @Override
4136   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4137   {
4138     // Pick the tree file
4139     JalviewFileChooser chooser = new JalviewFileChooser(
4140             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4141     chooser.setFileView(new JalviewFileView());
4142     chooser.setDialogTitle(
4143             MessageManager.getString("label.select_newick_like_tree_file"));
4144     chooser.setToolTipText(
4145             MessageManager.getString("label.load_tree_file"));
4146
4147     int value = chooser.showOpenDialog(null);
4148
4149     if (value == JalviewFileChooser.APPROVE_OPTION)
4150     {
4151       String filePath = chooser.getSelectedFile().getPath();
4152       Cache.setProperty("LAST_DIRECTORY", filePath);
4153       NewickFile fin = null;
4154       try
4155       {
4156         fin = new NewickFile(filePath, DataSourceType.FILE);
4157         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4158       } catch (Exception ex)
4159       {
4160         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4161                 MessageManager.getString("label.problem_reading_tree_file"),
4162                 JvOptionPane.WARNING_MESSAGE);
4163         ex.printStackTrace();
4164       }
4165       if (fin != null && fin.hasWarningMessage())
4166       {
4167         JvOptionPane.showMessageDialog(Desktop.desktop,
4168                 fin.getWarningMessage(),
4169                 MessageManager
4170                         .getString("label.possible_problem_with_tree_file"),
4171                 JvOptionPane.WARNING_MESSAGE);
4172       }
4173     }
4174   }
4175
4176   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4177   {
4178     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4179   }
4180
4181   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4182           int h, int x, int y)
4183   {
4184     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4185   }
4186
4187   /**
4188    * Add a treeviewer for the tree extracted from a Newick file object to the
4189    * current alignment view
4190    *
4191    * @param nf
4192    *          the tree
4193    * @param title
4194    *          tree viewer title
4195    * @param input
4196    *          Associated alignment input data (or null)
4197    * @param w
4198    *          width
4199    * @param h
4200    *          height
4201    * @param x
4202    *          position
4203    * @param y
4204    *          position
4205    * @return TreePanel handle
4206    */
4207   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4208           AlignmentView input, int w, int h, int x, int y)
4209   {
4210     TreePanel tp = null;
4211
4212     try
4213     {
4214       nf.parse();
4215
4216       if (nf.getTree() != null)
4217       {
4218         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4219
4220         tp.setSize(w, h);
4221
4222         if (x > 0 && y > 0)
4223         {
4224           tp.setLocation(x, y);
4225         }
4226
4227         Desktop.addInternalFrame(tp, treeTitle, w, h);
4228       }
4229     } catch (Exception ex)
4230     {
4231       ex.printStackTrace();
4232     }
4233
4234     return tp;
4235   }
4236
4237   private boolean buildingMenu = false;
4238
4239   /**
4240    * Generates menu items and listener event actions for web service clients
4241    *
4242    */
4243   public void BuildWebServiceMenu()
4244   {
4245     while (buildingMenu)
4246     {
4247       try
4248       {
4249         System.err.println("Waiting for building menu to finish.");
4250         Thread.sleep(10);
4251       } catch (Exception e)
4252       {
4253       }
4254     }
4255     final AlignFrame me = this;
4256     buildingMenu = true;
4257     new Thread(new Runnable()
4258     {
4259       @Override
4260       public void run()
4261       {
4262         final List<JMenuItem> legacyItems = new ArrayList<>();
4263         try
4264         {
4265           // System.err.println("Building ws menu again "
4266           // + Thread.currentThread());
4267           // TODO: add support for context dependent disabling of services based
4268           // on
4269           // alignment and current selection
4270           // TODO: add additional serviceHandle parameter to specify abstract
4271           // handler
4272           // class independently of AbstractName
4273           // TODO: add in rediscovery GUI function to restart discoverer
4274           // TODO: group services by location as well as function and/or
4275           // introduce
4276           // object broker mechanism.
4277           final Vector<JMenu> wsmenu = new Vector<>();
4278           final IProgressIndicator af = me;
4279
4280           /*
4281            * do not i18n these strings - they are hard-coded in class
4282            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4283            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4284            */
4285           final JMenu msawsmenu = new JMenu("Alignment");
4286           final JMenu secstrmenu = new JMenu(
4287                   "Secondary Structure Prediction");
4288           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4289           final JMenu analymenu = new JMenu("Analysis");
4290           final JMenu dismenu = new JMenu("Protein Disorder");
4291           // JAL-940 - only show secondary structure prediction services from
4292           // the legacy server
4293           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4294               // &&
4295           Discoverer.services != null && (Discoverer.services.size() > 0))
4296           {
4297             // TODO: refactor to allow list of AbstractName/Handler bindings to
4298             // be
4299             // stored or retrieved from elsewhere
4300             // No MSAWS used any more:
4301             // Vector msaws = null; // (Vector)
4302             // Discoverer.services.get("MsaWS");
4303             Vector secstrpr = (Vector) Discoverer.services
4304                     .get("SecStrPred");
4305             if (secstrpr != null)
4306             {
4307               // Add any secondary structure prediction services
4308               for (int i = 0, j = secstrpr.size(); i < j; i++)
4309               {
4310                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4311                         .get(i);
4312                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4313                         .getServiceClient(sh);
4314                 int p = secstrmenu.getItemCount();
4315                 impl.attachWSMenuEntry(secstrmenu, me);
4316                 int q = secstrmenu.getItemCount();
4317                 for (int litm = p; litm < q; litm++)
4318                 {
4319                   legacyItems.add(secstrmenu.getItem(litm));
4320                 }
4321               }
4322             }
4323           }
4324
4325           // Add all submenus in the order they should appear on the web
4326           // services menu
4327           wsmenu.add(msawsmenu);
4328           wsmenu.add(secstrmenu);
4329           wsmenu.add(dismenu);
4330           wsmenu.add(analymenu);
4331           // No search services yet
4332           // wsmenu.add(seqsrchmenu);
4333
4334           javax.swing.SwingUtilities.invokeLater(new Runnable()
4335           {
4336             @Override
4337             public void run()
4338             {
4339               try
4340               {
4341                 webService.removeAll();
4342                 // first, add discovered services onto the webservices menu
4343                 if (wsmenu.size() > 0)
4344                 {
4345                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4346                   {
4347                     webService.add(wsmenu.get(i));
4348                   }
4349                 }
4350                 else
4351                 {
4352                   webService.add(me.webServiceNoServices);
4353                 }
4354                 // TODO: move into separate menu builder class.
4355                 boolean new_sspred = false;
4356                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4357                 {
4358                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4359                   if (jws2servs != null)
4360                   {
4361                     if (jws2servs.hasServices())
4362                     {
4363                       jws2servs.attachWSMenuEntry(webService, me);
4364                       for (Jws2Instance sv : jws2servs.getServices())
4365                       {
4366                         if (sv.description.toLowerCase().contains("jpred"))
4367                         {
4368                           for (JMenuItem jmi : legacyItems)
4369                           {
4370                             jmi.setVisible(false);
4371                           }
4372                         }
4373                       }
4374
4375                     }
4376                     if (jws2servs.isRunning())
4377                     {
4378                       JMenuItem tm = new JMenuItem(
4379                               "Still discovering JABA Services");
4380                       tm.setEnabled(false);
4381                       webService.add(tm);
4382                     }
4383                   }
4384                 }
4385                 build_urlServiceMenu(me.webService);
4386                 build_fetchdbmenu(webService);
4387                 for (JMenu item : wsmenu)
4388                 {
4389                   if (item.getItemCount() == 0)
4390                   {
4391                     item.setEnabled(false);
4392                   }
4393                   else
4394                   {
4395                     item.setEnabled(true);
4396                   }
4397                 }
4398               } catch (Exception e)
4399               {
4400                 Cache.log.debug(
4401                         "Exception during web service menu building process.",
4402                         e);
4403               }
4404             }
4405           });
4406         } catch (Exception e)
4407         {
4408         }
4409         buildingMenu = false;
4410       }
4411     }).start();
4412
4413   }
4414
4415   /**
4416    * construct any groupURL type service menu entries.
4417    *
4418    * @param webService
4419    */
4420   private void build_urlServiceMenu(JMenu webService)
4421   {
4422     // TODO: remove this code when 2.7 is released
4423     // DEBUG - alignmentView
4424     /*
4425      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4426      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4427      *
4428      * @Override public void actionPerformed(ActionEvent e) {
4429      * jalview.datamodel.AlignmentView
4430      * .testSelectionViews(af.viewport.getAlignment(),
4431      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4432      *
4433      * }); webService.add(testAlView);
4434      */
4435     // TODO: refactor to RestClient discoverer and merge menu entries for
4436     // rest-style services with other types of analysis/calculation service
4437     // SHmmr test client - still being implemented.
4438     // DEBUG - alignmentView
4439
4440     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4441             .getRestClients())
4442     {
4443       client.attachWSMenuEntry(
4444               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4445               this);
4446     }
4447   }
4448
4449   /**
4450    * Searches the alignment sequences for xRefs and builds the Show
4451    * Cross-References menu (formerly called Show Products), with database
4452    * sources for which cross-references are found (protein sources for a
4453    * nucleotide alignment and vice versa)
4454    *
4455    * @return true if Show Cross-references menu should be enabled
4456    */
4457   public boolean canShowProducts()
4458   {
4459     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4460     AlignmentI dataset = viewport.getAlignment().getDataset();
4461
4462     showProducts.removeAll();
4463     final boolean dna = viewport.getAlignment().isNucleotide();
4464
4465     if (seqs == null || seqs.length == 0)
4466     {
4467       // nothing to see here.
4468       return false;
4469     }
4470
4471     boolean showp = false;
4472     try
4473     {
4474       List<String> ptypes = new CrossRef(seqs, dataset)
4475               .findXrefSourcesForSequences(dna);
4476
4477       for (final String source : ptypes)
4478       {
4479         showp = true;
4480         final AlignFrame af = this;
4481         JMenuItem xtype = new JMenuItem(source);
4482         xtype.addActionListener(new ActionListener()
4483         {
4484           @Override
4485           public void actionPerformed(ActionEvent e)
4486           {
4487             showProductsFor(af.viewport.getSequenceSelection(), dna,
4488                     source);
4489           }
4490         });
4491         showProducts.add(xtype);
4492       }
4493       showProducts.setVisible(showp);
4494       showProducts.setEnabled(showp);
4495     } catch (Exception e)
4496     {
4497       Cache.log.warn(
4498               "canShowProducts threw an exception - please report to help@jalview.org",
4499               e);
4500       return false;
4501     }
4502     return showp;
4503   }
4504
4505   /**
4506    * Finds and displays cross-references for the selected sequences (protein
4507    * products for nucleotide sequences, dna coding sequences for peptides).
4508    *
4509    * @param sel
4510    *          the sequences to show cross-references for
4511    * @param dna
4512    *          true if from a nucleotide alignment (so showing proteins)
4513    * @param source
4514    *          the database to show cross-references for
4515    */
4516   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4517           final String source)
4518   {
4519     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4520             .start();
4521   }
4522
4523   /**
4524    * Construct and display a new frame containing the translation of this
4525    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4526    */
4527   @Override
4528   public void showTranslation_actionPerformed(ActionEvent e)
4529   {
4530     AlignmentI al = null;
4531     try
4532     {
4533       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4534
4535       al = dna.translateCdna();
4536     } catch (Exception ex)
4537     {
4538       jalview.bin.Cache.log.error(
4539               "Exception during translation. Please report this !", ex);
4540       final String msg = MessageManager.getString(
4541               "label.error_when_translating_sequences_submit_bug_report");
4542       final String errorTitle = MessageManager
4543               .getString("label.implementation_error")
4544               + MessageManager.getString("label.translation_failed");
4545       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4546               JvOptionPane.ERROR_MESSAGE);
4547       return;
4548     }
4549     if (al == null || al.getHeight() == 0)
4550     {
4551       final String msg = MessageManager.getString(
4552               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4553       final String errorTitle = MessageManager
4554               .getString("label.translation_failed");
4555       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4556               JvOptionPane.WARNING_MESSAGE);
4557     }
4558     else
4559     {
4560       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4561       af.setFileFormat(this.currentFileFormat);
4562       final String newTitle = MessageManager
4563               .formatMessage("label.translation_of_params", new Object[]
4564               { this.getTitle() });
4565       af.setTitle(newTitle);
4566       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4567       {
4568         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4569         viewport.openSplitFrame(af, new Alignment(seqs));
4570       }
4571       else
4572       {
4573         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4574                 DEFAULT_HEIGHT);
4575       }
4576     }
4577   }
4578
4579   /**
4580    * Set the file format
4581    *
4582    * @param format
4583    */
4584   public void setFileFormat(FileFormatI format)
4585   {
4586     this.currentFileFormat = format;
4587   }
4588
4589   /**
4590    * Try to load a features file onto the alignment.
4591    *
4592    * @param file
4593    *          contents or path to retrieve file
4594    * @param sourceType
4595    *          access mode of file (see jalview.io.AlignFile)
4596    * @return true if features file was parsed correctly.
4597    */
4598   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4599   {
4600     return avc.parseFeaturesFile(file, sourceType,
4601             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4602
4603   }
4604
4605   @Override
4606   public void refreshFeatureUI(boolean enableIfNecessary)
4607   {
4608     // note - currently this is only still here rather than in the controller
4609     // because of the featureSettings hard reference that is yet to be
4610     // abstracted
4611     if (enableIfNecessary)
4612     {
4613       viewport.setShowSequenceFeatures(true);
4614       showSeqFeatures.setSelected(true);
4615     }
4616
4617   }
4618
4619   @Override
4620   public void dragEnter(DropTargetDragEvent evt)
4621   {
4622   }
4623
4624   @Override
4625   public void dragExit(DropTargetEvent evt)
4626   {
4627   }
4628
4629   @Override
4630   public void dragOver(DropTargetDragEvent evt)
4631   {
4632   }
4633
4634   @Override
4635   public void dropActionChanged(DropTargetDragEvent evt)
4636   {
4637   }
4638
4639   @Override
4640   public void drop(DropTargetDropEvent evt)
4641   {
4642     // JAL-1552 - acceptDrop required before getTransferable call for
4643     // Java's Transferable for native dnd
4644     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4645     Transferable t = evt.getTransferable();
4646     List<String> files = new ArrayList<>();
4647     List<DataSourceType> protocols = new ArrayList<>();
4648
4649     try
4650     {
4651       Desktop.transferFromDropTarget(files, protocols, evt, t);
4652     } catch (Exception e)
4653     {
4654       e.printStackTrace();
4655     }
4656     if (files != null)
4657     {
4658       try
4659       {
4660         // check to see if any of these files have names matching sequences in
4661         // the alignment
4662         SequenceIdMatcher idm = new SequenceIdMatcher(
4663                 viewport.getAlignment().getSequencesArray());
4664         /**
4665          * Object[] { String,SequenceI}
4666          */
4667         ArrayList<Object[]> filesmatched = new ArrayList<>();
4668         ArrayList<String> filesnotmatched = new ArrayList<>();
4669         for (int i = 0; i < files.size(); i++)
4670         {
4671           String file = files.get(i).toString();
4672           String pdbfn = "";
4673           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4674           if (protocol == DataSourceType.FILE)
4675           {
4676             File fl = new File(file);
4677             pdbfn = fl.getName();
4678           }
4679           else if (protocol == DataSourceType.URL)
4680           {
4681             URL url = new URL(file);
4682             pdbfn = url.getFile();
4683           }
4684           if (pdbfn.length() > 0)
4685           {
4686             // attempt to find a match in the alignment
4687             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4688             int l = 0, c = pdbfn.indexOf(".");
4689             while (mtch == null && c != -1)
4690             {
4691               do
4692               {
4693                 l = c;
4694               } while ((c = pdbfn.indexOf(".", l)) > l);
4695               if (l > -1)
4696               {
4697                 pdbfn = pdbfn.substring(0, l);
4698               }
4699               mtch = idm.findAllIdMatches(pdbfn);
4700             }
4701             if (mtch != null)
4702             {
4703               FileFormatI type = null;
4704               try
4705               {
4706                 type = new IdentifyFile().identify(file, protocol);
4707               } catch (Exception ex)
4708               {
4709                 type = null;
4710               }
4711               if (type != null && type.isStructureFile())
4712               {
4713                 filesmatched.add(new Object[] { file, protocol, mtch });
4714                 continue;
4715               }
4716             }
4717             // File wasn't named like one of the sequences or wasn't a PDB file.
4718             filesnotmatched.add(file);
4719           }
4720         }
4721         int assocfiles = 0;
4722         if (filesmatched.size() > 0)
4723         {
4724           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4725                   || JvOptionPane.showConfirmDialog(this,
4726                           MessageManager.formatMessage(
4727                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4728                                   new Object[]
4729                                   { Integer.valueOf(filesmatched.size())
4730                                           .toString() }),
4731                           MessageManager.getString(
4732                                   "label.automatically_associate_structure_files_by_name"),
4733                           JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4734
4735           {
4736             for (Object[] fm : filesmatched)
4737             {
4738               // try and associate
4739               // TODO: may want to set a standard ID naming formalism for
4740               // associating PDB files which have no IDs.
4741               for (SequenceI toassoc : (SequenceI[]) fm[2])
4742               {
4743                 PDBEntry pe = new AssociatePdbFileWithSeq()
4744                         .associatePdbWithSeq((String) fm[0],
4745                                 (DataSourceType) fm[1], toassoc, false,
4746                                 Desktop.instance);
4747                 if (pe != null)
4748                 {
4749                   System.err.println("Associated file : " + ((String) fm[0])
4750                           + " with " + toassoc.getDisplayId(true));
4751                   assocfiles++;
4752                 }
4753               }
4754               alignPanel.paintAlignment(true);
4755             }
4756           }
4757         }
4758         if (filesnotmatched.size() > 0)
4759         {
4760           if (assocfiles > 0 && (Cache.getDefault(
4761                   "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4762                   || JvOptionPane.showConfirmDialog(this,
4763                           "<html>" + MessageManager.formatMessage(
4764                                   "label.ignore_unmatched_dropped_files_info",
4765                                   new Object[]
4766                                   { Integer.valueOf(filesnotmatched.size())
4767                                           .toString() })
4768                                   + "</html>",
4769                           MessageManager.getString(
4770                                   "label.ignore_unmatched_dropped_files"),
4771                           JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4772           {
4773             return;
4774           }
4775           for (String fn : filesnotmatched)
4776           {
4777             loadJalviewDataFile(fn, null, null, null);
4778           }
4779
4780         }
4781       } catch (Exception ex)
4782       {
4783         ex.printStackTrace();
4784       }
4785     }
4786   }
4787
4788   /**
4789    * Attempt to load a "dropped" file or URL string, by testing in turn for
4790    * <ul>
4791    * <li>an Annotation file</li>
4792    * <li>a JNet file</li>
4793    * <li>a features file</li>
4794    * <li>else try to interpret as an alignment file</li>
4795    * </ul>
4796    *
4797    * @param file
4798    *          either a filename or a URL string.
4799    * @throws InterruptedException
4800    * @throws IOException
4801    */
4802   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4803           FileFormatI format, SequenceI assocSeq)
4804   {
4805     try
4806     {
4807       if (sourceType == null)
4808       {
4809         sourceType = FormatAdapter.checkProtocol(file);
4810       }
4811       // if the file isn't identified, or not positively identified as some
4812       // other filetype (PFAM is default unidentified alignment file type) then
4813       // try to parse as annotation.
4814       boolean isAnnotation = (format == null
4815               || FileFormat.Pfam.equals(format))
4816                       ? new AnnotationFile().annotateAlignmentView(viewport,
4817                               file, sourceType)
4818                       : false;
4819
4820       if (!isAnnotation)
4821       {
4822         // first see if its a T-COFFEE score file
4823         TCoffeeScoreFile tcf = null;
4824         try
4825         {
4826           tcf = new TCoffeeScoreFile(file, sourceType);
4827           if (tcf.isValid())
4828           {
4829             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4830             {
4831               buildColourMenu();
4832               changeColour(
4833                       new TCoffeeColourScheme(viewport.getAlignment()));
4834               isAnnotation = true;
4835               statusBar.setText(MessageManager.getString(
4836                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4837             }
4838             else
4839             {
4840               // some problem - if no warning its probable that the ID matching
4841               // process didn't work
4842               JvOptionPane.showMessageDialog(Desktop.desktop,
4843                       tcf.getWarningMessage() == null
4844                               ? MessageManager.getString(
4845                                       "label.check_file_matches_sequence_ids_alignment")
4846                               : tcf.getWarningMessage(),
4847                       MessageManager.getString(
4848                               "label.problem_reading_tcoffee_score_file"),
4849                       JvOptionPane.WARNING_MESSAGE);
4850             }
4851           }
4852           else
4853           {
4854             tcf = null;
4855           }
4856         } catch (Exception x)
4857         {
4858           Cache.log.debug(
4859                   "Exception when processing data source as T-COFFEE score file",
4860                   x);
4861           tcf = null;
4862         }
4863         if (tcf == null)
4864         {
4865           // try to see if its a JNet 'concise' style annotation file *before*
4866           // we
4867           // try to parse it as a features file
4868           if (format == null)
4869           {
4870             format = new IdentifyFile().identify(file, sourceType);
4871           }
4872           if (FileFormat.ScoreMatrix == format)
4873           {
4874             ScoreMatrixFile sm = new ScoreMatrixFile(
4875                     new FileParse(file, sourceType));
4876             sm.parse();
4877             // todo: i18n this message
4878             statusBar.setText(MessageManager.formatMessage(
4879                     "label.successfully_loaded_matrix",
4880                     sm.getMatrixName()));
4881           }
4882           else if (FileFormat.Jnet.equals(format))
4883           {
4884             JPredFile predictions = new JPredFile(file, sourceType);
4885             new JnetAnnotationMaker();
4886             JnetAnnotationMaker.add_annotation(predictions,
4887                     viewport.getAlignment(), 0, false);
4888             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4889             viewport.getAlignment().setSeqrep(repseq);
4890             HiddenColumns cs = new HiddenColumns();
4891             cs.hideInsertionsFor(repseq);
4892             viewport.getAlignment().setHiddenColumns(cs);
4893             isAnnotation = true;
4894           }
4895           // else if (IdentifyFile.FeaturesFile.equals(format))
4896           else if (FileFormat.Features.equals(format))
4897           {
4898             if (parseFeaturesFile(file, sourceType))
4899             {
4900               alignPanel.paintAlignment(true);
4901             }
4902           }
4903           else
4904           {
4905             new FileLoader().LoadFile(viewport, file, sourceType, format);
4906           }
4907         }
4908       }
4909       if (isAnnotation)
4910       {
4911         alignPanel.adjustAnnotationHeight();
4912         viewport.updateSequenceIdColours();
4913         buildSortByAnnotationScoresMenu();
4914         alignPanel.paintAlignment(true);
4915       }
4916     } catch (Exception ex)
4917     {
4918       ex.printStackTrace();
4919     } catch (OutOfMemoryError oom)
4920     {
4921       try
4922       {
4923         System.gc();
4924       } catch (Exception x)
4925       {
4926       }
4927       new OOMWarning(
4928               "loading data "
4929                       + (sourceType != null
4930                               ? (sourceType == DataSourceType.PASTE
4931                                       ? "from clipboard."
4932                                       : "using " + sourceType + " from "
4933                                               + file)
4934                               : ".")
4935                       + (format != null
4936                               ? "(parsing as '" + format + "' file)"
4937                               : ""),
4938               oom, Desktop.desktop);
4939     }
4940   }
4941
4942   /**
4943    * Method invoked by the ChangeListener on the tabbed pane, in other words
4944    * when a different tabbed pane is selected by the user or programmatically.
4945    */
4946   @Override
4947   public void tabSelectionChanged(int index)
4948   {
4949     if (index > -1)
4950     {
4951       alignPanel = alignPanels.get(index);
4952       viewport = alignPanel.av;
4953       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4954       setMenusFromViewport(viewport);
4955     }
4956
4957     /*
4958      * 'focus' any colour slider that is open to the selected viewport
4959      */
4960     if (viewport.getConservationSelected())
4961     {
4962       SliderPanel.setConservationSlider(alignPanel,
4963               viewport.getResidueShading(), alignPanel.getViewName());
4964     }
4965     else
4966     {
4967       SliderPanel.hideConservationSlider();
4968     }
4969     if (viewport.getAbovePIDThreshold())
4970     {
4971       SliderPanel.setPIDSliderSource(alignPanel,
4972               viewport.getResidueShading(), alignPanel.getViewName());
4973     }
4974     else
4975     {
4976       SliderPanel.hidePIDSlider();
4977     }
4978
4979     /*
4980      * If there is a frame linked to this one in a SplitPane, switch it to the
4981      * same view tab index. No infinite recursion of calls should happen, since
4982      * tabSelectionChanged() should not get invoked on setting the selected
4983      * index to an unchanged value. Guard against setting an invalid index
4984      * before the new view peer tab has been created.
4985      */
4986     final AlignViewportI peer = viewport.getCodingComplement();
4987     if (peer != null)
4988     {
4989       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4990               .getAlignPanel().alignFrame;
4991       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4992       {
4993         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4994       }
4995     }
4996   }
4997
4998   /**
4999    * On right mouse click on view tab, prompt for and set new view name.
5000    */
5001   @Override
5002   public void tabbedPane_mousePressed(MouseEvent e)
5003   {
5004     if (e.isPopupTrigger())
5005     {
5006       String msg = MessageManager.getString("label.enter_view_name");
5007       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5008               JvOptionPane.QUESTION_MESSAGE);
5009
5010       if (reply != null)
5011       {
5012         viewport.viewName = reply;
5013         // TODO warn if reply is in getExistingViewNames()?
5014         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5015       }
5016     }
5017   }
5018
5019   public AlignViewport getCurrentView()
5020   {
5021     return viewport;
5022   }
5023
5024   /**
5025    * Open the dialog for regex description parsing.
5026    */
5027   @Override
5028   protected void extractScores_actionPerformed(ActionEvent e)
5029   {
5030     ParseProperties pp = new jalview.analysis.ParseProperties(
5031             viewport.getAlignment());
5032     // TODO: verify regex and introduce GUI dialog for version 2.5
5033     // if (pp.getScoresFromDescription("col", "score column ",
5034     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5035     // true)>0)
5036     if (pp.getScoresFromDescription("description column",
5037             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5038     {
5039       buildSortByAnnotationScoresMenu();
5040     }
5041   }
5042
5043   /*
5044    * (non-Javadoc)
5045    *
5046    * @see
5047    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5048    * )
5049    */
5050   @Override
5051   protected void showDbRefs_actionPerformed(ActionEvent e)
5052   {
5053     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5054   }
5055
5056   /*
5057    * (non-Javadoc)
5058    *
5059    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5060    * ActionEvent)
5061    */
5062   @Override
5063   protected void showNpFeats_actionPerformed(ActionEvent e)
5064   {
5065     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5066   }
5067
5068   /**
5069    * find the viewport amongst the tabs in this alignment frame and close that
5070    * tab
5071    *
5072    * @param av
5073    */
5074   public boolean closeView(AlignViewportI av)
5075   {
5076     if (viewport == av)
5077     {
5078       this.closeMenuItem_actionPerformed(false);
5079       return true;
5080     }
5081     Component[] comp = tabbedPane.getComponents();
5082     for (int i = 0; comp != null && i < comp.length; i++)
5083     {
5084       if (comp[i] instanceof AlignmentPanel)
5085       {
5086         if (((AlignmentPanel) comp[i]).av == av)
5087         {
5088           // close the view.
5089           closeView((AlignmentPanel) comp[i]);
5090           return true;
5091         }
5092       }
5093     }
5094     return false;
5095   }
5096
5097   protected void build_fetchdbmenu(JMenu webService)
5098   {
5099     // Temporary hack - DBRef Fetcher always top level ws entry.
5100     // TODO We probably want to store a sequence database checklist in
5101     // preferences and have checkboxes.. rather than individual sources selected
5102     // here
5103     final JMenu rfetch = new JMenu(
5104             MessageManager.getString("action.fetch_db_references"));
5105     rfetch.setToolTipText(MessageManager.getString(
5106             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5107     webService.add(rfetch);
5108
5109     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5110             MessageManager.getString("option.trim_retrieved_seqs"));
5111     trimrs.setToolTipText(
5112             MessageManager.getString("label.trim_retrieved_sequences"));
5113     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5114     trimrs.addActionListener(new ActionListener()
5115     {
5116       @Override
5117       public void actionPerformed(ActionEvent e)
5118       {
5119         trimrs.setSelected(trimrs.isSelected());
5120         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5121                 Boolean.valueOf(trimrs.isSelected()).toString());
5122       };
5123     });
5124     rfetch.add(trimrs);
5125     JMenuItem fetchr = new JMenuItem(
5126             MessageManager.getString("label.standard_databases"));
5127     fetchr.setToolTipText(
5128             MessageManager.getString("label.fetch_embl_uniprot"));
5129     fetchr.addActionListener(new ActionListener()
5130     {
5131
5132       @Override
5133       public void actionPerformed(ActionEvent e)
5134       {
5135         new Thread(new Runnable()
5136         {
5137           @Override
5138           public void run()
5139           {
5140             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5141                     .getAlignment().isNucleotide();
5142             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5143                     alignPanel.av.getSequenceSelection(),
5144                     alignPanel.alignFrame, null,
5145                     alignPanel.alignFrame.featureSettings, isNucleotide);
5146             dbRefFetcher.addListener(new FetchFinishedListenerI()
5147             {
5148               @Override
5149               public void finished()
5150               {
5151                 AlignFrame.this.setMenusForViewport();
5152               }
5153             });
5154             dbRefFetcher.fetchDBRefs(false);
5155           }
5156         }).start();
5157
5158       }
5159
5160     });
5161     rfetch.add(fetchr);
5162     final AlignFrame me = this;
5163     new Thread(new Runnable()
5164     {
5165       @Override
5166       public void run()
5167       {
5168         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5169                 .getSequenceFetcherSingleton(me);
5170         javax.swing.SwingUtilities.invokeLater(new Runnable()
5171         {
5172           @Override
5173           public void run()
5174           {
5175             String[] dbclasses = sf.getOrderedSupportedSources();
5176             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5177             // jalview.util.QuickSort.sort(otherdb, otherdb);
5178             List<DbSourceProxy> otherdb;
5179             JMenu dfetch = new JMenu();
5180             JMenu ifetch = new JMenu();
5181             JMenuItem fetchr = null;
5182             int comp = 0, icomp = 0, mcomp = 15;
5183             String mname = null;
5184             int dbi = 0;
5185             for (String dbclass : dbclasses)
5186             {
5187               otherdb = sf.getSourceProxy(dbclass);
5188               // add a single entry for this class, or submenu allowing 'fetch
5189               // all' or pick one
5190               if (otherdb == null || otherdb.size() < 1)
5191               {
5192                 continue;
5193               }
5194               // List<DbSourceProxy> dbs=otherdb;
5195               // otherdb=new ArrayList<DbSourceProxy>();
5196               // for (DbSourceProxy db:dbs)
5197               // {
5198               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5199               // }
5200               if (mname == null)
5201               {
5202                 mname = "From " + dbclass;
5203               }
5204               if (otherdb.size() == 1)
5205               {
5206                 final DbSourceProxy[] dassource = otherdb
5207                         .toArray(new DbSourceProxy[0]);
5208                 DbSourceProxy src = otherdb.get(0);
5209                 fetchr = new JMenuItem(src.getDbSource());
5210                 fetchr.addActionListener(new ActionListener()
5211                 {
5212
5213                   @Override
5214                   public void actionPerformed(ActionEvent e)
5215                   {
5216                     new Thread(new Runnable()
5217                     {
5218
5219                       @Override
5220                       public void run()
5221                       {
5222                         boolean isNucleotide = alignPanel.alignFrame
5223                                 .getViewport().getAlignment()
5224                                 .isNucleotide();
5225                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5226                                 alignPanel.av.getSequenceSelection(),
5227                                 alignPanel.alignFrame, dassource,
5228                                 alignPanel.alignFrame.featureSettings,
5229                                 isNucleotide);
5230                         dbRefFetcher
5231                                 .addListener(new FetchFinishedListenerI()
5232                                 {
5233                                   @Override
5234                                   public void finished()
5235                                   {
5236                                     AlignFrame.this.setMenusForViewport();
5237                                   }
5238                                 });
5239                         dbRefFetcher.fetchDBRefs(false);
5240                       }
5241                     }).start();
5242                   }
5243
5244                 });
5245                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5246                         MessageManager.formatMessage(
5247                                 "label.fetch_retrieve_from", new Object[]
5248                                 { src.getDbName() })));
5249                 dfetch.add(fetchr);
5250                 comp++;
5251               }
5252               else
5253               {
5254                 final DbSourceProxy[] dassource = otherdb
5255                         .toArray(new DbSourceProxy[0]);
5256                 // fetch all entry
5257                 DbSourceProxy src = otherdb.get(0);
5258                 fetchr = new JMenuItem(MessageManager
5259                         .formatMessage("label.fetch_all_param", new Object[]
5260                         { src.getDbSource() }));
5261                 fetchr.addActionListener(new ActionListener()
5262                 {
5263                   @Override
5264                   public void actionPerformed(ActionEvent e)
5265                   {
5266                     new Thread(new Runnable()
5267                     {
5268
5269                       @Override
5270                       public void run()
5271                       {
5272                         boolean isNucleotide = alignPanel.alignFrame
5273                                 .getViewport().getAlignment()
5274                                 .isNucleotide();
5275                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5276                                 alignPanel.av.getSequenceSelection(),
5277                                 alignPanel.alignFrame, dassource,
5278                                 alignPanel.alignFrame.featureSettings,
5279                                 isNucleotide);
5280                         dbRefFetcher
5281                                 .addListener(new FetchFinishedListenerI()
5282                                 {
5283                                   @Override
5284                                   public void finished()
5285                                   {
5286                                     AlignFrame.this.setMenusForViewport();
5287                                   }
5288                                 });
5289                         dbRefFetcher.fetchDBRefs(false);
5290                       }
5291                     }).start();
5292                   }
5293                 });
5294
5295                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5296                         MessageManager.formatMessage(
5297                                 "label.fetch_retrieve_from_all_sources",
5298                                 new Object[]
5299                                 { Integer.valueOf(otherdb.size())
5300                                         .toString(),
5301                                     src.getDbSource(), src.getDbName() })));
5302                 dfetch.add(fetchr);
5303                 comp++;
5304                 // and then build the rest of the individual menus
5305                 ifetch = new JMenu(MessageManager.formatMessage(
5306                         "label.source_from_db_source", new Object[]
5307                         { src.getDbSource() }));
5308                 icomp = 0;
5309                 String imname = null;
5310                 int i = 0;
5311                 for (DbSourceProxy sproxy : otherdb)
5312                 {
5313                   String dbname = sproxy.getDbName();
5314                   String sname = dbname.length() > 5
5315                           ? dbname.substring(0, 5) + "..."
5316                           : dbname;
5317                   String msname = dbname.length() > 10
5318                           ? dbname.substring(0, 10) + "..."
5319                           : dbname;
5320                   if (imname == null)
5321                   {
5322                     imname = MessageManager
5323                             .formatMessage("label.from_msname", new Object[]
5324                             { sname });
5325                   }
5326                   fetchr = new JMenuItem(msname);
5327                   final DbSourceProxy[] dassrc = { sproxy };
5328                   fetchr.addActionListener(new ActionListener()
5329                   {
5330
5331                     @Override
5332                     public void actionPerformed(ActionEvent e)
5333                     {
5334                       new Thread(new Runnable()
5335                       {
5336
5337                         @Override
5338                         public void run()
5339                         {
5340                           boolean isNucleotide = alignPanel.alignFrame
5341                                   .getViewport().getAlignment()
5342                                   .isNucleotide();
5343                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5344                                   alignPanel.av.getSequenceSelection(),
5345                                   alignPanel.alignFrame, dassrc,
5346                                   alignPanel.alignFrame.featureSettings,
5347                                   isNucleotide);
5348                           dbRefFetcher
5349                                   .addListener(new FetchFinishedListenerI()
5350                                   {
5351                                     @Override
5352                                     public void finished()
5353                                     {
5354                                       AlignFrame.this.setMenusForViewport();
5355                                     }
5356                                   });
5357                           dbRefFetcher.fetchDBRefs(false);
5358                         }
5359                       }).start();
5360                     }
5361
5362                   });
5363                   fetchr.setToolTipText(
5364                           "<html>" + MessageManager.formatMessage(
5365                                   "label.fetch_retrieve_from", new Object[]
5366                                   { dbname }));
5367                   ifetch.add(fetchr);
5368                   ++i;
5369                   if (++icomp >= mcomp || i == (otherdb.size()))
5370                   {
5371                     ifetch.setText(MessageManager.formatMessage(
5372                             "label.source_to_target", imname, sname));
5373                     dfetch.add(ifetch);
5374                     ifetch = new JMenu();
5375                     imname = null;
5376                     icomp = 0;
5377                     comp++;
5378                   }
5379                 }
5380               }
5381               ++dbi;
5382               if (comp >= mcomp || dbi >= (dbclasses.length))
5383               {
5384                 dfetch.setText(MessageManager.formatMessage(
5385                         "label.source_to_target", mname, dbclass));
5386                 rfetch.add(dfetch);
5387                 dfetch = new JMenu();
5388                 mname = null;
5389                 comp = 0;
5390               }
5391             }
5392           }
5393         });
5394       }
5395     }).start();
5396
5397   }
5398
5399   /**
5400    * Left justify the whole alignment.
5401    */
5402   @Override
5403   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5404   {
5405     AlignmentI al = viewport.getAlignment();
5406     al.justify(false);
5407     viewport.firePropertyChange("alignment", null, al);
5408   }
5409
5410   /**
5411    * Right justify the whole alignment.
5412    */
5413   @Override
5414   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5415   {
5416     AlignmentI al = viewport.getAlignment();
5417     al.justify(true);
5418     viewport.firePropertyChange("alignment", null, al);
5419   }
5420
5421   @Override
5422   public void setShowSeqFeatures(boolean b)
5423   {
5424     showSeqFeatures.setSelected(b);
5425     viewport.setShowSequenceFeatures(b);
5426   }
5427
5428   /*
5429    * (non-Javadoc)
5430    *
5431    * @see
5432    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5433    * awt.event.ActionEvent)
5434    */
5435   @Override
5436   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5437   {
5438     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5439     alignPanel.paintAlignment(true);
5440   }
5441
5442   /*
5443    * (non-Javadoc)
5444    *
5445    * @see
5446    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5447    * .ActionEvent)
5448    */
5449   @Override
5450   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5451   {
5452     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5453     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5454
5455   }
5456
5457   /*
5458    * (non-Javadoc)
5459    *
5460    * @see
5461    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5462    * .event.ActionEvent)
5463    */
5464   @Override
5465   protected void showGroupConservation_actionPerformed(ActionEvent e)
5466   {
5467     viewport.setShowGroupConservation(showGroupConservation.getState());
5468     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5469   }
5470
5471   /*
5472    * (non-Javadoc)
5473    *
5474    * @see
5475    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5476    * .event.ActionEvent)
5477    */
5478   @Override
5479   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5480   {
5481     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5482     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5483   }
5484
5485   /*
5486    * (non-Javadoc)
5487    *
5488    * @see
5489    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5490    * .event.ActionEvent)
5491    */
5492   @Override
5493   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5494   {
5495     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5496     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5497   }
5498
5499   @Override
5500   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5501   {
5502     showSequenceLogo.setState(true);
5503     viewport.setShowSequenceLogo(true);
5504     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5505     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5506   }
5507
5508   @Override
5509   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5510   {
5511     viewport.setShowInformationHistogram(
5512             showInformationHistogram.getState());
5513     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5514   }
5515
5516   @Override
5517   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5518   {
5519     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5520     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5521   }
5522
5523   @Override
5524   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5525   {
5526     showHMMSequenceLogo.setState(true);
5527     viewport.setShowHMMSequenceLogo(true);
5528     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5529     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5530   }
5531
5532   @Override
5533   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5534   {
5535     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5536   }
5537
5538   /*
5539    * (non-Javadoc)
5540    *
5541    * @see
5542    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5543    * .event.ActionEvent)
5544    */
5545   @Override
5546   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5547   {
5548     if (avc.makeGroupsFromSelection())
5549     {
5550       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5551       alignPanel.updateAnnotation();
5552       alignPanel.paintAlignment(true);
5553     }
5554   }
5555
5556   public void clearAlignmentSeqRep()
5557   {
5558     // TODO refactor alignmentseqrep to controller
5559     if (viewport.getAlignment().hasSeqrep())
5560     {
5561       viewport.getAlignment().setSeqrep(null);
5562       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5563       alignPanel.updateAnnotation();
5564       alignPanel.paintAlignment(true);
5565     }
5566   }
5567
5568   @Override
5569   protected void createGroup_actionPerformed(ActionEvent e)
5570   {
5571     if (avc.createGroup())
5572     {
5573       alignPanel.alignmentChanged();
5574     }
5575   }
5576
5577   @Override
5578   protected void unGroup_actionPerformed(ActionEvent e)
5579   {
5580     if (avc.unGroup())
5581     {
5582       alignPanel.alignmentChanged();
5583     }
5584   }
5585
5586   /**
5587    * make the given alignmentPanel the currently selected tab
5588    *
5589    * @param alignmentPanel
5590    */
5591   public void setDisplayedView(AlignmentPanel alignmentPanel)
5592   {
5593     if (!viewport.getSequenceSetId()
5594             .equals(alignmentPanel.av.getSequenceSetId()))
5595     {
5596       throw new Error(MessageManager.getString(
5597               "error.implementation_error_cannot_show_view_alignment_frame"));
5598     }
5599     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5600             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5601     {
5602       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5603     }
5604   }
5605
5606   /**
5607    * Action on selection of menu options to Show or Hide annotations.
5608    *
5609    * @param visible
5610    * @param forSequences
5611    *          update sequence-related annotations
5612    * @param forAlignment
5613    *          update non-sequence-related annotations
5614    */
5615   @Override
5616   protected void setAnnotationsVisibility(boolean visible,
5617           boolean forSequences, boolean forAlignment)
5618   {
5619     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5620             .getAlignmentAnnotation();
5621     if (anns == null)
5622     {
5623       return;
5624     }
5625     for (AlignmentAnnotation aa : anns)
5626     {
5627       /*
5628        * don't display non-positional annotations on an alignment
5629        */
5630       if (aa.annotations == null)
5631       {
5632         continue;
5633       }
5634       boolean apply = (aa.sequenceRef == null && forAlignment)
5635               || (aa.sequenceRef != null && forSequences);
5636       if (apply)
5637       {
5638         aa.visible = visible;
5639       }
5640     }
5641     alignPanel.validateAnnotationDimensions(true);
5642     alignPanel.alignmentChanged();
5643   }
5644
5645   /**
5646    * Store selected annotation sort order for the view and repaint.
5647    */
5648   @Override
5649   protected void sortAnnotations_actionPerformed()
5650   {
5651     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5652     this.alignPanel.av
5653             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5654     alignPanel.paintAlignment(true);
5655   }
5656
5657   /**
5658    *
5659    * @return alignment panels in this alignment frame
5660    */
5661   public List<? extends AlignmentViewPanel> getAlignPanels()
5662   {
5663     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5664   }
5665
5666   /**
5667    * Open a new alignment window, with the cDNA associated with this (protein)
5668    * alignment, aligned as is the protein.
5669    */
5670   protected void viewAsCdna_actionPerformed()
5671   {
5672     // TODO no longer a menu action - refactor as required
5673     final AlignmentI alignment = getViewport().getAlignment();
5674     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5675     if (mappings == null)
5676     {
5677       return;
5678     }
5679     List<SequenceI> cdnaSeqs = new ArrayList<>();
5680     for (SequenceI aaSeq : alignment.getSequences())
5681     {
5682       for (AlignedCodonFrame acf : mappings)
5683       {
5684         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5685         if (dnaSeq != null)
5686         {
5687           /*
5688            * There is a cDNA mapping for this protein sequence - add to new
5689            * alignment. It will share the same dataset sequence as other mapped
5690            * cDNA (no new mappings need to be created).
5691            */
5692           final Sequence newSeq = new Sequence(dnaSeq);
5693           newSeq.setDatasetSequence(dnaSeq);
5694           cdnaSeqs.add(newSeq);
5695         }
5696       }
5697     }
5698     if (cdnaSeqs.size() == 0)
5699     {
5700       // show a warning dialog no mapped cDNA
5701       return;
5702     }
5703     AlignmentI cdna = new Alignment(
5704             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5705     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5706             AlignFrame.DEFAULT_HEIGHT);
5707     cdna.alignAs(alignment);
5708     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5709             + this.title;
5710     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5711             AlignFrame.DEFAULT_HEIGHT);
5712   }
5713
5714   /**
5715    * Set visibility of dna/protein complement view (available when shown in a
5716    * split frame).
5717    *
5718    * @param show
5719    */
5720   @Override
5721   protected void showComplement_actionPerformed(boolean show)
5722   {
5723     SplitContainerI sf = getSplitViewContainer();
5724     if (sf != null)
5725     {
5726       sf.setComplementVisible(this, show);
5727     }
5728   }
5729
5730   /**
5731    * Generate the reverse (optionally complemented) of the selected sequences,
5732    * and add them to the alignment
5733    */
5734   @Override
5735   protected void showReverse_actionPerformed(boolean complement)
5736   {
5737     AlignmentI al = null;
5738     try
5739     {
5740       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5741       al = dna.reverseCdna(complement);
5742       viewport.addAlignment(al, "");
5743       addHistoryItem(new EditCommand(
5744               MessageManager.getString("label.add_sequences"), Action.PASTE,
5745               al.getSequencesArray(), 0, al.getWidth(),
5746               viewport.getAlignment()));
5747     } catch (Exception ex)
5748     {
5749       System.err.println(ex.getMessage());
5750       return;
5751     }
5752   }
5753
5754   /**
5755    * Try to run a script in the Groovy console, having first ensured that this
5756    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5757    * be targeted at this alignment.
5758    */
5759   @Override
5760   protected void runGroovy_actionPerformed()
5761   {
5762     Jalview.setCurrentAlignFrame(this);
5763     groovy.ui.Console console = Desktop.getGroovyConsole();
5764     if (console != null)
5765     {
5766       try
5767       {
5768         console.runScript();
5769       } catch (Exception ex)
5770       {
5771         System.err.println((ex.toString()));
5772         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5773                 MessageManager.getString("label.couldnt_run_groovy_script"),
5774                 MessageManager.getString("label.groovy_support_failed"),
5775                 JvOptionPane.ERROR_MESSAGE);
5776       }
5777     }
5778     else
5779     {
5780       System.err.println("Can't run Groovy script as console not found");
5781     }
5782   }
5783
5784   /**
5785    * Hides columns containing (or not containing) a specified feature, provided
5786    * that would not leave all columns hidden
5787    *
5788    * @param featureType
5789    * @param columnsContaining
5790    * @return
5791    */
5792   public boolean hideFeatureColumns(String featureType,
5793           boolean columnsContaining)
5794   {
5795     boolean notForHiding = avc.markColumnsContainingFeatures(
5796             columnsContaining, false, false, featureType);
5797     if (notForHiding)
5798     {
5799       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5800               false, featureType))
5801       {
5802         getViewport().hideSelectedColumns();
5803         return true;
5804       }
5805     }
5806     return false;
5807   }
5808
5809   @Override
5810   protected void selectHighlightedColumns_actionPerformed(
5811           ActionEvent actionEvent)
5812   {
5813     // include key modifier check in case user selects from menu
5814     avc.markHighlightedColumns(
5815             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5816             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5817                     | ActionEvent.CTRL_MASK)) != 0);
5818   }
5819
5820   /**
5821    * Rebuilds the Colour menu, including any user-defined colours which have
5822    * been loaded either on startup or during the session
5823    */
5824   public void buildColourMenu()
5825   {
5826     colourMenu.removeAll();
5827
5828     colourMenu.add(applyToAllGroups);
5829     colourMenu.add(textColour);
5830     colourMenu.addSeparator();
5831
5832     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5833             false);
5834
5835     colourMenu.addSeparator();
5836     colourMenu.add(conservationMenuItem);
5837     colourMenu.add(modifyConservation);
5838     colourMenu.add(abovePIDThreshold);
5839     colourMenu.add(modifyPID);
5840     colourMenu.add(annotationColour);
5841
5842     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5843     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5844   }
5845
5846   /**
5847    * Open a dialog (if not already open) that allows the user to select and
5848    * calculate PCA or Tree analysis
5849    */
5850   protected void openTreePcaDialog()
5851   {
5852     if (alignPanel.getCalculationDialog() == null)
5853     {
5854       new CalculationChooser(AlignFrame.this);
5855     }
5856   }
5857
5858   /**
5859    * Sets the status of the HMMER menu
5860    *
5861    * @param status
5862    */
5863   public void updateHMMERStatus(boolean status)
5864   {
5865     hmmerMenu.setEnabled(status);
5866   }
5867
5868   /**
5869    * Returns the selected hidden Markov model.
5870    *
5871    * @return
5872    */
5873   public HiddenMarkovModel getSelectedHMM()
5874   {
5875     if (selectedHMMSequence == null)
5876     {
5877       return null;
5878     }
5879     return selectedHMMSequence.getHMM();
5880   }
5881
5882   /**
5883    * Returns the selected hidden Markov model.
5884    *
5885    * @return
5886    */
5887   public SequenceI getSelectedHMMSequence()
5888   {
5889     return selectedHMMSequence;
5890   }
5891
5892   /**
5893    * Sets the selected hidden Markov model
5894    *
5895    * @param selectedHMM
5896    */
5897   public void setSelectedHMMSequence(SequenceI selectedHMM)
5898   {
5899     this.selectedHMMSequence = selectedHMM;
5900     hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5901             + selectedHMM.getHMM().getName());
5902     hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5903             + selectedHMM.getHMM().getName());
5904   }
5905
5906   @Override
5907   public void hmmerMenu_actionPerformed(ActionEvent e)
5908   {
5909     SequenceGroup grp = getViewport().getSelectionGroup();
5910     if (grp != null)
5911     {
5912       hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5913               + grp.getName());
5914     }
5915     else
5916     {
5917       hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5918               + " from Alignment");
5919     }
5920   }
5921
5922 }
5923
5924 class PrintThread extends Thread
5925 {
5926   AlignmentPanel ap;
5927
5928   public PrintThread(AlignmentPanel ap)
5929   {
5930     this.ap = ap;
5931   }
5932
5933   static PageFormat pf;
5934
5935   @Override
5936   public void run()
5937   {
5938     PrinterJob printJob = PrinterJob.getPrinterJob();
5939
5940     if (pf != null)
5941     {
5942       printJob.setPrintable(ap, pf);
5943     }
5944     else
5945     {
5946       printJob.setPrintable(ap);
5947     }
5948
5949     if (printJob.printDialog())
5950     {
5951       try
5952       {
5953         printJob.print();
5954       } catch (Exception PrintException)
5955       {
5956         PrintException.printStackTrace();
5957       }
5958     }
5959   }
5960 }