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))
1109             .start();
1110     alignPanel.repaint();
1111
1112   }
1113
1114   @Override
1115   public void hmmAlignRun_actionPerformed(ActionEvent e)
1116           throws IOException, InterruptedException
1117   {
1118     if (!(checkForHMM() && alignmentIsSufficient(2)))
1119     {
1120       return;
1121     }
1122     new Thread(new HMMAlignThread(this, true, null))
1123             .start();
1124     alignPanel.repaint();
1125   }
1126
1127   @Override
1128   public void hmmSearchRun_actionPerformed(ActionEvent e)
1129   {
1130     if (!checkForHMM())
1131     {
1132       return;
1133     }
1134     new Thread(new HMMSearchThread(this, true, null))
1135             .start();
1136     alignPanel.repaint();
1137   }
1138
1139   /**
1140    * Checks if the frame has a selected hidden Markov model
1141    *
1142    * @return
1143    */
1144   private boolean checkForHMM()
1145   {
1146     if (getSelectedHMM() == null)
1147     {
1148       JOptionPane.showMessageDialog(this,
1149               MessageManager.getString("warn.no_selected_hmm"));
1150       return false;
1151     }
1152     return true;
1153   }
1154
1155   /**
1156    * Checks if the alignment contains the required number of sequences.
1157    *
1158    * @param required
1159    * @return
1160    */
1161   public boolean alignmentIsSufficient(int required)
1162   {
1163     if (getViewport().getAlignment().getSequences().size() < required)
1164     {
1165       JOptionPane.showMessageDialog(this,
1166               MessageManager.getString("warn.not_enough_sequences"));
1167       return false;
1168     }
1169     return true;
1170   }
1171
1172   @Override
1173   public void addDatabase_actionPerformed(ActionEvent e) throws IOException
1174   {
1175     if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
1176     {
1177       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1178       Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
1179     }
1180
1181     String path = openFileChooser(false);
1182     if (new File(path).exists())
1183     {
1184       IdentifyFile identifier = new IdentifyFile();
1185       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1186       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1187               || format == FileFormat.Pfam)
1188       {
1189         String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
1190         String currentDbPaths = Cache
1191                 .getProperty(Preferences.HMMSEARCH_DB_PATHS);
1192         currentDbPaths += " " + path;
1193
1194         String fileName = StringUtils.getLastToken(path, new String("/"));
1195         Scanner scanner = new Scanner(fileName).useDelimiter(".");
1196         String name = scanner.next();
1197         scanner.close();
1198         currentDbs += " " + path; // TODO remove path from file name
1199         scanner.close();
1200
1201         Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
1202         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1203       }
1204       else
1205       {
1206         JOptionPane.showMessageDialog(this,
1207                 MessageManager.getString("warn.invalid_format"));
1208       }
1209     }
1210     else
1211     {
1212       JOptionPane.showMessageDialog(this,
1213               MessageManager.getString("warn.not_enough_sequences"));
1214     }
1215   }
1216
1217   /**
1218    * Opens a file chooser
1219    *
1220    * @param forFolder
1221    * @return
1222    */
1223   protected String openFileChooser(boolean forFolder)
1224   {
1225     String choice = null;
1226     JFileChooser chooser = new JFileChooser();
1227     if (forFolder)
1228     {
1229       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1230     }
1231     chooser.setDialogTitle(
1232             MessageManager.getString("label.open_local_file"));
1233     chooser.setToolTipText(MessageManager.getString("action.open"));
1234
1235     int value = chooser.showOpenDialog(this);
1236
1237     if (value == JFileChooser.APPROVE_OPTION)
1238     {
1239       choice = chooser.getSelectedFile().getPath();
1240     }
1241     return choice;
1242   }
1243
1244   @Override
1245   public void reload_actionPerformed(ActionEvent e)
1246   {
1247     if (fileName != null)
1248     {
1249       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1250       // originating file's format
1251       // TODO: work out how to recover feature settings for correct view(s) when
1252       // file is reloaded.
1253       if (FileFormat.Jalview.equals(currentFileFormat))
1254       {
1255         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1256         for (int i = 0; i < frames.length; i++)
1257         {
1258           if (frames[i] instanceof AlignFrame && frames[i] != this
1259                   && ((AlignFrame) frames[i]).fileName != null
1260                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1261           {
1262             try
1263             {
1264               frames[i].setSelected(true);
1265               Desktop.instance.closeAssociatedWindows();
1266             } catch (java.beans.PropertyVetoException ex)
1267             {
1268             }
1269           }
1270
1271         }
1272         Desktop.instance.closeAssociatedWindows();
1273
1274         FileLoader loader = new FileLoader();
1275         DataSourceType protocol = fileName.startsWith("http:")
1276                 ? DataSourceType.URL
1277                 : DataSourceType.FILE;
1278         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1279       }
1280       else
1281       {
1282         Rectangle bounds = this.getBounds();
1283
1284         FileLoader loader = new FileLoader();
1285         DataSourceType protocol = fileName.startsWith("http:")
1286                 ? DataSourceType.URL
1287                 : DataSourceType.FILE;
1288         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1289                 protocol, currentFileFormat);
1290
1291         newframe.setBounds(bounds);
1292         if (featureSettings != null && featureSettings.isShowing())
1293         {
1294           final Rectangle fspos = featureSettings.frame.getBounds();
1295           // TODO: need a 'show feature settings' function that takes bounds -
1296           // need to refactor Desktop.addFrame
1297           newframe.featureSettings_actionPerformed(null);
1298           final FeatureSettings nfs = newframe.featureSettings;
1299           SwingUtilities.invokeLater(new Runnable()
1300           {
1301             @Override
1302             public void run()
1303             {
1304               nfs.frame.setBounds(fspos);
1305             }
1306           });
1307           this.featureSettings.close();
1308           this.featureSettings = null;
1309         }
1310         this.closeMenuItem_actionPerformed(true);
1311       }
1312     }
1313   }
1314
1315   @Override
1316   public void addFromText_actionPerformed(ActionEvent e)
1317   {
1318     Desktop.instance
1319             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1320   }
1321
1322   @Override
1323   public void addFromURL_actionPerformed(ActionEvent e)
1324   {
1325     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1326   }
1327
1328   @Override
1329   public void save_actionPerformed(ActionEvent e)
1330   {
1331     if (fileName == null || (currentFileFormat == null)
1332             || fileName.startsWith("http"))
1333     {
1334       saveAs_actionPerformed(null);
1335     }
1336     else
1337     {
1338       saveAlignment(fileName, currentFileFormat);
1339     }
1340   }
1341
1342   /**
1343    * DOCUMENT ME!
1344    *
1345    * @param e
1346    *          DOCUMENT ME!
1347    */
1348   @Override
1349   public void saveAs_actionPerformed(ActionEvent e)
1350   {
1351     String format = currentFileFormat == null ? null
1352             : currentFileFormat.getName();
1353     JalviewFileChooser chooser = JalviewFileChooser
1354             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1355
1356     chooser.setFileView(new JalviewFileView());
1357     chooser.setDialogTitle(
1358             MessageManager.getString("label.save_alignment_to_file"));
1359     chooser.setToolTipText(MessageManager.getString("action.save"));
1360
1361     int value = chooser.showSaveDialog(this);
1362
1363     if (value == JalviewFileChooser.APPROVE_OPTION)
1364     {
1365       currentFileFormat = chooser.getSelectedFormat();
1366       while (currentFileFormat == null)
1367       {
1368         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1369                 MessageManager.getString(
1370                         "label.select_file_format_before_saving"),
1371                 MessageManager.getString("label.file_format_not_specified"),
1372                 JvOptionPane.WARNING_MESSAGE);
1373         currentFileFormat = chooser.getSelectedFormat();
1374         value = chooser.showSaveDialog(this);
1375         if (value != JalviewFileChooser.APPROVE_OPTION)
1376         {
1377           return;
1378         }
1379       }
1380
1381       fileName = chooser.getSelectedFile().getPath();
1382
1383       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1384
1385       Cache.setProperty("LAST_DIRECTORY", fileName);
1386       saveAlignment(fileName, currentFileFormat);
1387     }
1388   }
1389
1390   public boolean saveAlignment(String file, FileFormatI format)
1391   {
1392     boolean success = true;
1393
1394     if (FileFormat.Jalview.equals(format))
1395     {
1396       String shortName = title;
1397
1398       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1399       {
1400         shortName = shortName.substring(
1401                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1402       }
1403
1404       success = new Jalview2XML().saveAlignment(this, file, shortName);
1405
1406       statusBar.setText(MessageManager.formatMessage(
1407               "label.successfully_saved_to_file_in_format", new Object[]
1408               { fileName, format }));
1409
1410     }
1411     else
1412     {
1413       AlignmentExportData exportData = getAlignmentForExport(format,
1414               viewport, null);
1415       if (exportData.getSettings().isCancelled())
1416       {
1417         return false;
1418       }
1419       FormatAdapter f = new FormatAdapter(alignPanel,
1420               exportData.getSettings());
1421       String output = f.formatSequences(format, exportData.getAlignment(), // class
1422                                                                            // cast
1423                                                                            // exceptions
1424                                                                            // will
1425               // occur in the distant future
1426               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1427               f.getCacheSuffixDefault(format),
1428               viewport.getAlignment().getHiddenColumns());
1429
1430       if (output == null)
1431       {
1432         success = false;
1433       }
1434       else
1435       {
1436         try
1437         {
1438           PrintWriter out = new PrintWriter(new FileWriter(file));
1439
1440           out.print(output);
1441           out.close();
1442           this.setTitle(file);
1443           statusBar.setText(MessageManager.formatMessage(
1444                   "label.successfully_saved_to_file_in_format", new Object[]
1445                   { fileName, format.getName() }));
1446         } catch (Exception ex)
1447         {
1448           success = false;
1449           ex.printStackTrace();
1450         }
1451       }
1452     }
1453
1454     if (!success)
1455     {
1456       JvOptionPane.showInternalMessageDialog(this, MessageManager
1457               .formatMessage("label.couldnt_save_file", new Object[]
1458               { fileName }),
1459               MessageManager.getString("label.error_saving_file"),
1460               JvOptionPane.WARNING_MESSAGE);
1461     }
1462
1463     return success;
1464   }
1465
1466   private void warningMessage(String warning, String title)
1467   {
1468     if (new jalview.util.Platform().isHeadless())
1469     {
1470       System.err.println("Warning: " + title + "\nWarning: " + warning);
1471
1472     }
1473     else
1474     {
1475       JvOptionPane.showInternalMessageDialog(this, warning, title,
1476               JvOptionPane.WARNING_MESSAGE);
1477     }
1478     return;
1479   }
1480
1481   /**
1482    * DOCUMENT ME!
1483    *
1484    * @param e
1485    *          DOCUMENT ME!
1486    */
1487   @Override
1488   protected void outputText_actionPerformed(ActionEvent e)
1489   {
1490     FileFormatI fileFormat = FileFormats.getInstance()
1491             .forName(e.getActionCommand());
1492     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1493             viewport, null);
1494     if (exportData.getSettings().isCancelled())
1495     {
1496       return;
1497     }
1498     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1499     cap.setForInput(null);
1500     try
1501     {
1502       FileFormatI format = fileFormat;
1503       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1504               .formatSequences(format, exportData.getAlignment(),
1505                       exportData.getOmitHidden(),
1506                       exportData.getStartEndPostions(),
1507                       viewport.getAlignment().getHiddenColumns()));
1508       Desktop.addInternalFrame(cap, MessageManager
1509               .formatMessage("label.alignment_output_command", new Object[]
1510               { e.getActionCommand() }), 600, 500);
1511     } catch (OutOfMemoryError oom)
1512     {
1513       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1514               oom);
1515       cap.dispose();
1516     }
1517
1518   }
1519
1520   public static AlignmentExportData getAlignmentForExport(
1521           FileFormatI format, AlignViewportI viewport,
1522           AlignExportSettingI exportSettings)
1523   {
1524     AlignmentI alignmentToExport = null;
1525     AlignExportSettingI settings = exportSettings;
1526     String[] omitHidden = null;
1527
1528     HiddenSequences hiddenSeqs = viewport.getAlignment()
1529             .getHiddenSequences();
1530
1531     alignmentToExport = viewport.getAlignment();
1532
1533     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1534     if (settings == null)
1535     {
1536       settings = new AlignExportSettings(hasHiddenSeqs,
1537               viewport.hasHiddenColumns(), format);
1538     }
1539     // settings.isExportAnnotations();
1540
1541     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1542     {
1543       omitHidden = viewport.getViewAsString(false,
1544               settings.isExportHiddenSequences());
1545     }
1546
1547     int[] alignmentStartEnd = new int[2];
1548     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1549     {
1550       alignmentToExport = hiddenSeqs.getFullAlignment();
1551     }
1552     else
1553     {
1554       alignmentToExport = viewport.getAlignment();
1555     }
1556     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1557             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1558     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1559             omitHidden, alignmentStartEnd, settings);
1560     return ed;
1561   }
1562
1563   /**
1564    * DOCUMENT ME!
1565    *
1566    * @param e
1567    *          DOCUMENT ME!
1568    */
1569   @Override
1570   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1571   {
1572     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1573     htmlSVG.exportHTML(null);
1574   }
1575
1576   @Override
1577   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1578   {
1579     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1580     bjs.exportHTML(null);
1581   }
1582
1583   public void createImageMap(File file, String image)
1584   {
1585     alignPanel.makePNGImageMap(file, image);
1586   }
1587
1588   /**
1589    * DOCUMENT ME!
1590    *
1591    * @param e
1592    *          DOCUMENT ME!
1593    */
1594   @Override
1595   public void createPNG(File f)
1596   {
1597     alignPanel.makePNG(f);
1598   }
1599
1600   /**
1601    * DOCUMENT ME!
1602    *
1603    * @param e
1604    *          DOCUMENT ME!
1605    */
1606   @Override
1607   public void createEPS(File f)
1608   {
1609     alignPanel.makeEPS(f);
1610   }
1611
1612   @Override
1613   public void createSVG(File f)
1614   {
1615     alignPanel.makeSVG(f);
1616   }
1617
1618   @Override
1619   public void pageSetup_actionPerformed(ActionEvent e)
1620   {
1621     PrinterJob printJob = PrinterJob.getPrinterJob();
1622     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1623   }
1624
1625   /**
1626    * DOCUMENT ME!
1627    *
1628    * @param e
1629    *          DOCUMENT ME!
1630    */
1631   @Override
1632   public void printMenuItem_actionPerformed(ActionEvent e)
1633   {
1634     // Putting in a thread avoids Swing painting problems
1635     PrintThread thread = new PrintThread(alignPanel);
1636     thread.start();
1637   }
1638
1639   @Override
1640   public void exportFeatures_actionPerformed(ActionEvent e)
1641   {
1642     new AnnotationExporter().exportFeatures(alignPanel);
1643   }
1644
1645   @Override
1646   public void exportAnnotations_actionPerformed(ActionEvent e)
1647   {
1648     new AnnotationExporter().exportAnnotations(alignPanel);
1649   }
1650
1651   @Override
1652   public void associatedData_actionPerformed(ActionEvent e)
1653           throws IOException, InterruptedException
1654   {
1655     // Pick the tree file
1656     JalviewFileChooser chooser = new JalviewFileChooser(
1657             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1658     chooser.setFileView(new JalviewFileView());
1659     chooser.setDialogTitle(
1660             MessageManager.getString("label.load_jalview_annotations"));
1661     chooser.setToolTipText(
1662             MessageManager.getString("label.load_jalview_annotations"));
1663
1664     int value = chooser.showOpenDialog(null);
1665
1666     if (value == JalviewFileChooser.APPROVE_OPTION)
1667     {
1668       String choice = chooser.getSelectedFile().getPath();
1669       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1670       loadJalviewDataFile(choice, null, null, null);
1671     }
1672
1673   }
1674
1675   /**
1676    * Close the current view or all views in the alignment frame. If the frame
1677    * only contains one view then the alignment will be removed from memory.
1678    *
1679    * @param closeAllTabs
1680    */
1681   @Override
1682   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1683   {
1684     if (alignPanels != null && alignPanels.size() < 2)
1685     {
1686       closeAllTabs = true;
1687     }
1688
1689     try
1690     {
1691       if (alignPanels != null)
1692       {
1693         if (closeAllTabs)
1694         {
1695           if (this.isClosed())
1696           {
1697             // really close all the windows - otherwise wait till
1698             // setClosed(true) is called
1699             for (int i = 0; i < alignPanels.size(); i++)
1700             {
1701               AlignmentPanel ap = alignPanels.get(i);
1702               ap.closePanel();
1703             }
1704           }
1705         }
1706         else
1707         {
1708           closeView(alignPanel);
1709         }
1710       }
1711
1712       if (closeAllTabs)
1713       {
1714         /*
1715          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1716          * be called recursively, with the frame now in 'closed' state
1717          */
1718         this.setClosed(true);
1719       }
1720     } catch (Exception ex)
1721     {
1722       ex.printStackTrace();
1723     }
1724   }
1725
1726   /**
1727    * Close the specified panel and close up tabs appropriately.
1728    *
1729    * @param panelToClose
1730    */
1731   public void closeView(AlignmentPanel panelToClose)
1732   {
1733     int index = tabbedPane.getSelectedIndex();
1734     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1735     alignPanels.remove(panelToClose);
1736     panelToClose.closePanel();
1737     panelToClose = null;
1738
1739     tabbedPane.removeTabAt(closedindex);
1740     tabbedPane.validate();
1741
1742     if (index > closedindex || index == tabbedPane.getTabCount())
1743     {
1744       // modify currently selected tab index if necessary.
1745       index--;
1746     }
1747
1748     this.tabSelectionChanged(index);
1749   }
1750
1751   /**
1752    * DOCUMENT ME!
1753    */
1754   void updateEditMenuBar()
1755   {
1756
1757     if (viewport.getHistoryList().size() > 0)
1758     {
1759       undoMenuItem.setEnabled(true);
1760       CommandI command = viewport.getHistoryList().peek();
1761       undoMenuItem.setText(MessageManager
1762               .formatMessage("label.undo_command", new Object[]
1763               { command.getDescription() }));
1764     }
1765     else
1766     {
1767       undoMenuItem.setEnabled(false);
1768       undoMenuItem.setText(MessageManager.getString("action.undo"));
1769     }
1770
1771     if (viewport.getRedoList().size() > 0)
1772     {
1773       redoMenuItem.setEnabled(true);
1774
1775       CommandI command = viewport.getRedoList().peek();
1776       redoMenuItem.setText(MessageManager
1777               .formatMessage("label.redo_command", new Object[]
1778               { command.getDescription() }));
1779     }
1780     else
1781     {
1782       redoMenuItem.setEnabled(false);
1783       redoMenuItem.setText(MessageManager.getString("action.redo"));
1784     }
1785   }
1786
1787   @Override
1788   public void addHistoryItem(CommandI command)
1789   {
1790     if (command.getSize() > 0)
1791     {
1792       viewport.addToHistoryList(command);
1793       viewport.clearRedoList();
1794       updateEditMenuBar();
1795       viewport.updateHiddenColumns();
1796       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1797       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1798       // viewport.getColumnSelection()
1799       // .getHiddenColumns().size() > 0);
1800     }
1801   }
1802
1803   /**
1804    *
1805    * @return alignment objects for all views
1806    */
1807   AlignmentI[] getViewAlignments()
1808   {
1809     if (alignPanels != null)
1810     {
1811       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1812       int i = 0;
1813       for (AlignmentPanel ap : alignPanels)
1814       {
1815         als[i++] = ap.av.getAlignment();
1816       }
1817       return als;
1818     }
1819     if (viewport != null)
1820     {
1821       return new AlignmentI[] { viewport.getAlignment() };
1822     }
1823     return null;
1824   }
1825
1826   /**
1827    * DOCUMENT ME!
1828    *
1829    * @param e
1830    *          DOCUMENT ME!
1831    */
1832   @Override
1833   protected void undoMenuItem_actionPerformed(ActionEvent e)
1834   {
1835     if (viewport.getHistoryList().isEmpty())
1836     {
1837       return;
1838     }
1839     CommandI command = viewport.getHistoryList().pop();
1840     viewport.addToRedoList(command);
1841     command.undoCommand(getViewAlignments());
1842
1843     AlignmentViewport originalSource = getOriginatingSource(command);
1844     updateEditMenuBar();
1845
1846     if (originalSource != null)
1847     {
1848       if (originalSource != viewport)
1849       {
1850         Cache.log.warn(
1851                 "Implementation worry: mismatch of viewport origin for undo");
1852       }
1853       originalSource.updateHiddenColumns();
1854       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1855       // null
1856       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1857       // viewport.getColumnSelection()
1858       // .getHiddenColumns().size() > 0);
1859       originalSource.firePropertyChange("alignment", null,
1860               originalSource.getAlignment().getSequences());
1861     }
1862   }
1863
1864   /**
1865    * DOCUMENT ME!
1866    *
1867    * @param e
1868    *          DOCUMENT ME!
1869    */
1870   @Override
1871   protected void redoMenuItem_actionPerformed(ActionEvent e)
1872   {
1873     if (viewport.getRedoList().size() < 1)
1874     {
1875       return;
1876     }
1877
1878     CommandI command = viewport.getRedoList().pop();
1879     viewport.addToHistoryList(command);
1880     command.doCommand(getViewAlignments());
1881
1882     AlignmentViewport originalSource = getOriginatingSource(command);
1883     updateEditMenuBar();
1884
1885     if (originalSource != null)
1886     {
1887
1888       if (originalSource != viewport)
1889       {
1890         Cache.log.warn(
1891                 "Implementation worry: mismatch of viewport origin for redo");
1892       }
1893       originalSource.updateHiddenColumns();
1894       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1895       // null
1896       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1897       // viewport.getColumnSelection()
1898       // .getHiddenColumns().size() > 0);
1899       originalSource.firePropertyChange("alignment", null,
1900               originalSource.getAlignment().getSequences());
1901     }
1902   }
1903
1904   AlignmentViewport getOriginatingSource(CommandI command)
1905   {
1906     AlignmentViewport originalSource = null;
1907     // For sequence removal and addition, we need to fire
1908     // the property change event FROM the viewport where the
1909     // original alignment was altered
1910     AlignmentI al = null;
1911     if (command instanceof EditCommand)
1912     {
1913       EditCommand editCommand = (EditCommand) command;
1914       al = editCommand.getAlignment();
1915       List<Component> comps = PaintRefresher.components
1916               .get(viewport.getSequenceSetId());
1917
1918       for (Component comp : comps)
1919       {
1920         if (comp instanceof AlignmentPanel)
1921         {
1922           if (al == ((AlignmentPanel) comp).av.getAlignment())
1923           {
1924             originalSource = ((AlignmentPanel) comp).av;
1925             break;
1926           }
1927         }
1928       }
1929     }
1930
1931     if (originalSource == null)
1932     {
1933       // The original view is closed, we must validate
1934       // the current view against the closed view first
1935       if (al != null)
1936       {
1937         PaintRefresher.validateSequences(al, viewport.getAlignment());
1938       }
1939
1940       originalSource = viewport;
1941     }
1942
1943     return originalSource;
1944   }
1945
1946   /**
1947    * DOCUMENT ME!
1948    *
1949    * @param up
1950    *          DOCUMENT ME!
1951    */
1952   public void moveSelectedSequences(boolean up)
1953   {
1954     SequenceGroup sg = viewport.getSelectionGroup();
1955
1956     if (sg == null)
1957     {
1958       return;
1959     }
1960     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1961             viewport.getHiddenRepSequences(), up);
1962     alignPanel.paintAlignment(true);
1963   }
1964
1965   synchronized void slideSequences(boolean right, int size)
1966   {
1967     List<SequenceI> sg = new ArrayList<>();
1968     if (viewport.cursorMode)
1969     {
1970       sg.add(viewport.getAlignment()
1971               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1972     }
1973     else if (viewport.getSelectionGroup() != null
1974             && viewport.getSelectionGroup().getSize() != viewport
1975                     .getAlignment().getHeight())
1976     {
1977       sg = viewport.getSelectionGroup()
1978               .getSequences(viewport.getHiddenRepSequences());
1979     }
1980
1981     if (sg.size() < 1)
1982     {
1983       return;
1984     }
1985
1986     List<SequenceI> invertGroup = new ArrayList<>();
1987
1988     for (SequenceI seq : viewport.getAlignment().getSequences())
1989     {
1990       if (!sg.contains(seq))
1991       {
1992         invertGroup.add(seq);
1993       }
1994     }
1995
1996     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1997
1998     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1999     for (int i = 0; i < invertGroup.size(); i++)
2000     {
2001       seqs2[i] = invertGroup.get(i);
2002     }
2003
2004     SlideSequencesCommand ssc;
2005     if (right)
2006     {
2007       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2008               viewport.getGapCharacter());
2009     }
2010     else
2011     {
2012       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2013               viewport.getGapCharacter());
2014     }
2015
2016     int groupAdjustment = 0;
2017     if (ssc.getGapsInsertedBegin() && right)
2018     {
2019       if (viewport.cursorMode)
2020       {
2021         alignPanel.getSeqPanel().moveCursor(size, 0);
2022       }
2023       else
2024       {
2025         groupAdjustment = size;
2026       }
2027     }
2028     else if (!ssc.getGapsInsertedBegin() && !right)
2029     {
2030       if (viewport.cursorMode)
2031       {
2032         alignPanel.getSeqPanel().moveCursor(-size, 0);
2033       }
2034       else
2035       {
2036         groupAdjustment = -size;
2037       }
2038     }
2039
2040     if (groupAdjustment != 0)
2041     {
2042       viewport.getSelectionGroup().setStartRes(
2043               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2044       viewport.getSelectionGroup().setEndRes(
2045               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2046     }
2047
2048     /*
2049      * just extend the last slide command if compatible; but not if in
2050      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2051      */
2052     boolean appendHistoryItem = false;
2053     Deque<CommandI> historyList = viewport.getHistoryList();
2054     boolean inSplitFrame = getSplitViewContainer() != null;
2055     if (!inSplitFrame && historyList != null && historyList.size() > 0
2056             && historyList.peek() instanceof SlideSequencesCommand)
2057     {
2058       appendHistoryItem = ssc.appendSlideCommand(
2059               (SlideSequencesCommand) historyList.peek());
2060     }
2061
2062     if (!appendHistoryItem)
2063     {
2064       addHistoryItem(ssc);
2065     }
2066
2067     repaint();
2068   }
2069
2070   /**
2071    * DOCUMENT ME!
2072    *
2073    * @param e
2074    *          DOCUMENT ME!
2075    */
2076   @Override
2077   protected void copy_actionPerformed(ActionEvent e)
2078   {
2079     System.gc();
2080     if (viewport.getSelectionGroup() == null)
2081     {
2082       return;
2083     }
2084     // TODO: preserve the ordering of displayed alignment annotation in any
2085     // internal paste (particularly sequence associated annotation)
2086     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2087     String[] omitHidden = null;
2088
2089     if (viewport.hasHiddenColumns())
2090     {
2091       omitHidden = viewport.getViewAsString(true);
2092     }
2093
2094     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2095             seqs, omitHidden, null);
2096
2097     StringSelection ss = new StringSelection(output);
2098
2099     try
2100     {
2101       jalview.gui.Desktop.internalCopy = true;
2102       // Its really worth setting the clipboard contents
2103       // to empty before setting the large StringSelection!!
2104       Toolkit.getDefaultToolkit().getSystemClipboard()
2105               .setContents(new StringSelection(""), null);
2106
2107       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2108               Desktop.instance);
2109     } catch (OutOfMemoryError er)
2110     {
2111       new OOMWarning("copying region", er);
2112       return;
2113     }
2114
2115     ArrayList<int[]> hiddenColumns = null;
2116     if (viewport.hasHiddenColumns())
2117     {
2118       hiddenColumns = new ArrayList<>();
2119
2120       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2121       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2122       ArrayList<int[]> hiddenRegions = viewport.getAlignment()
2123               .getHiddenColumns().getHiddenColumnsCopy();
2124       for (int[] region : hiddenRegions)
2125
2126       {
2127         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
2128         {
2129           hiddenColumns
2130                   .add(new int[]
2131                   { region[0] - hiddenOffset, region[1] - hiddenOffset });
2132         }
2133       }
2134     }
2135
2136     Desktop.jalviewClipboard = new Object[] { seqs,
2137         viewport.getAlignment().getDataset(), hiddenColumns };
2138     statusBar.setText(MessageManager.formatMessage(
2139             "label.copied_sequences_to_clipboard", new Object[]
2140             { Integer.valueOf(seqs.length).toString() }));
2141   }
2142
2143   /**
2144    * DOCUMENT ME!
2145    *
2146    * @param e
2147    *          DOCUMENT ME!
2148    * @throws InterruptedException
2149    * @throws IOException
2150    */
2151   @Override
2152   protected void pasteNew_actionPerformed(ActionEvent e)
2153           throws IOException, InterruptedException
2154   {
2155     paste(true);
2156   }
2157
2158   /**
2159    * DOCUMENT ME!
2160    *
2161    * @param e
2162    *          DOCUMENT ME!
2163    * @throws InterruptedException
2164    * @throws IOException
2165    */
2166   @Override
2167   protected void pasteThis_actionPerformed(ActionEvent e)
2168           throws IOException, InterruptedException
2169   {
2170     paste(false);
2171   }
2172
2173   /**
2174    * Paste contents of Jalview clipboard
2175    *
2176    * @param newAlignment
2177    *          true to paste to a new alignment, otherwise add to this.
2178    * @throws InterruptedException
2179    * @throws IOException
2180    */
2181   void paste(boolean newAlignment) throws IOException, InterruptedException
2182   {
2183     boolean externalPaste = true;
2184     try
2185     {
2186       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2187       Transferable contents = c.getContents(this);
2188
2189       if (contents == null)
2190       {
2191         return;
2192       }
2193
2194       String str;
2195       FileFormatI format;
2196       try
2197       {
2198         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2199         if (str.length() < 1)
2200         {
2201           return;
2202         }
2203
2204         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2205
2206       } catch (OutOfMemoryError er)
2207       {
2208         new OOMWarning("Out of memory pasting sequences!!", er);
2209         return;
2210       }
2211
2212       SequenceI[] sequences;
2213       boolean annotationAdded = false;
2214       AlignmentI alignment = null;
2215
2216       if (Desktop.jalviewClipboard != null)
2217       {
2218         // The clipboard was filled from within Jalview, we must use the
2219         // sequences
2220         // And dataset from the copied alignment
2221         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2222         // be doubly sure that we create *new* sequence objects.
2223         sequences = new SequenceI[newseq.length];
2224         for (int i = 0; i < newseq.length; i++)
2225         {
2226           sequences[i] = new Sequence(newseq[i]);
2227         }
2228         alignment = new Alignment(sequences);
2229         externalPaste = false;
2230       }
2231       else
2232       {
2233         // parse the clipboard as an alignment.
2234         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2235                 format);
2236         sequences = alignment.getSequencesArray();
2237       }
2238
2239       int alwidth = 0;
2240       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2241       int fgroup = -1;
2242
2243       if (newAlignment)
2244       {
2245
2246         if (Desktop.jalviewClipboard != null)
2247         {
2248           // dataset is inherited
2249           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2250         }
2251         else
2252         {
2253           // new dataset is constructed
2254           alignment.setDataset(null);
2255         }
2256         alwidth = alignment.getWidth() + 1;
2257       }
2258       else
2259       {
2260         AlignmentI pastedal = alignment; // preserve pasted alignment object
2261         // Add pasted sequences and dataset into existing alignment.
2262         alignment = viewport.getAlignment();
2263         alwidth = alignment.getWidth() + 1;
2264         // decide if we need to import sequences from an existing dataset
2265         boolean importDs = Desktop.jalviewClipboard != null
2266                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2267         // importDs==true instructs us to copy over new dataset sequences from
2268         // an existing alignment
2269         Vector newDs = (importDs) ? new Vector() : null; // used to create
2270         // minimum dataset set
2271
2272         for (int i = 0; i < sequences.length; i++)
2273         {
2274           if (importDs)
2275           {
2276             newDs.addElement(null);
2277           }
2278           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2279           // paste
2280           if (importDs && ds != null)
2281           {
2282             if (!newDs.contains(ds))
2283             {
2284               newDs.setElementAt(ds, i);
2285               ds = new Sequence(ds);
2286               // update with new dataset sequence
2287               sequences[i].setDatasetSequence(ds);
2288             }
2289             else
2290             {
2291               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2292             }
2293           }
2294           else
2295           {
2296             // copy and derive new dataset sequence
2297             sequences[i] = sequences[i].deriveSequence();
2298             alignment.getDataset()
2299                     .addSequence(sequences[i].getDatasetSequence());
2300             // TODO: avoid creation of duplicate dataset sequences with a
2301             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2302           }
2303           alignment.addSequence(sequences[i]); // merges dataset
2304         }
2305         if (newDs != null)
2306         {
2307           newDs.clear(); // tidy up
2308         }
2309         if (alignment.getAlignmentAnnotation() != null)
2310         {
2311           for (AlignmentAnnotation alan : alignment
2312                   .getAlignmentAnnotation())
2313           {
2314             if (alan.graphGroup > fgroup)
2315             {
2316               fgroup = alan.graphGroup;
2317             }
2318           }
2319         }
2320         if (pastedal.getAlignmentAnnotation() != null)
2321         {
2322           // Add any annotation attached to alignment.
2323           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2324           for (int i = 0; i < alann.length; i++)
2325           {
2326             annotationAdded = true;
2327             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2328             {
2329               AlignmentAnnotation newann = new AlignmentAnnotation(
2330                       alann[i]);
2331               if (newann.graphGroup > -1)
2332               {
2333                 if (newGraphGroups.size() <= newann.graphGroup
2334                         || newGraphGroups.get(newann.graphGroup) == null)
2335                 {
2336                   for (int q = newGraphGroups
2337                           .size(); q <= newann.graphGroup; q++)
2338                   {
2339                     newGraphGroups.add(q, null);
2340                   }
2341                   newGraphGroups.set(newann.graphGroup,
2342                           new Integer(++fgroup));
2343                 }
2344                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2345                         .intValue();
2346               }
2347
2348               newann.padAnnotation(alwidth);
2349               alignment.addAnnotation(newann);
2350             }
2351           }
2352         }
2353       }
2354       if (!newAlignment)
2355       {
2356         // /////
2357         // ADD HISTORY ITEM
2358         //
2359         addHistoryItem(new EditCommand(
2360                 MessageManager.getString("label.add_sequences"),
2361                 Action.PASTE, sequences, 0, alignment.getWidth(),
2362                 alignment));
2363       }
2364       // Add any annotations attached to sequences
2365       for (int i = 0; i < sequences.length; i++)
2366       {
2367         if (sequences[i].getAnnotation() != null)
2368         {
2369           AlignmentAnnotation newann;
2370           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2371           {
2372             annotationAdded = true;
2373             newann = sequences[i].getAnnotation()[a];
2374             newann.adjustForAlignment();
2375             newann.padAnnotation(alwidth);
2376             if (newann.graphGroup > -1)
2377             {
2378               if (newann.graphGroup > -1)
2379               {
2380                 if (newGraphGroups.size() <= newann.graphGroup
2381                         || newGraphGroups.get(newann.graphGroup) == null)
2382                 {
2383                   for (int q = newGraphGroups
2384                           .size(); q <= newann.graphGroup; q++)
2385                   {
2386                     newGraphGroups.add(q, null);
2387                   }
2388                   newGraphGroups.set(newann.graphGroup,
2389                           new Integer(++fgroup));
2390                 }
2391                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2392                         .intValue();
2393               }
2394             }
2395             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2396             // was
2397             // duplicated
2398             // earlier
2399             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2400                     a);
2401           }
2402         }
2403       }
2404       if (!newAlignment)
2405       {
2406
2407         // propagate alignment changed.
2408         vpRanges.setEndSeq(alignment.getHeight());
2409         if (annotationAdded)
2410         {
2411           // Duplicate sequence annotation in all views.
2412           AlignmentI[] alview = this.getViewAlignments();
2413           for (int i = 0; i < sequences.length; i++)
2414           {
2415             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2416             if (sann == null)
2417             {
2418               continue;
2419             }
2420             for (int avnum = 0; avnum < alview.length; avnum++)
2421             {
2422               if (alview[avnum] != alignment)
2423               {
2424                 // duplicate in a view other than the one with input focus
2425                 int avwidth = alview[avnum].getWidth() + 1;
2426                 // this relies on sann being preserved after we
2427                 // modify the sequence's annotation array for each duplication
2428                 for (int a = 0; a < sann.length; a++)
2429                 {
2430                   AlignmentAnnotation newann = new AlignmentAnnotation(
2431                           sann[a]);
2432                   sequences[i].addAlignmentAnnotation(newann);
2433                   newann.padAnnotation(avwidth);
2434                   alview[avnum].addAnnotation(newann); // annotation was
2435                   // duplicated earlier
2436                   // TODO JAL-1145 graphGroups are not updated for sequence
2437                   // annotation added to several views. This may cause
2438                   // strangeness
2439                   alview[avnum].setAnnotationIndex(newann, a);
2440                 }
2441               }
2442             }
2443           }
2444           buildSortByAnnotationScoresMenu();
2445         }
2446         viewport.firePropertyChange("alignment", null,
2447                 alignment.getSequences());
2448         if (alignPanels != null)
2449         {
2450           for (AlignmentPanel ap : alignPanels)
2451           {
2452             ap.validateAnnotationDimensions(false);
2453           }
2454         }
2455         else
2456         {
2457           alignPanel.validateAnnotationDimensions(false);
2458         }
2459
2460       }
2461       else
2462       {
2463         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2464                 DEFAULT_HEIGHT);
2465         String newtitle = new String("Copied sequences");
2466
2467         if (Desktop.jalviewClipboard != null
2468                 && Desktop.jalviewClipboard[2] != null)
2469         {
2470           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2471           for (int[] region : hc)
2472           {
2473             af.viewport.hideColumns(region[0], region[1]);
2474           }
2475         }
2476
2477         // >>>This is a fix for the moment, until a better solution is
2478         // found!!<<<
2479         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2480                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2481                         .getFeatureRenderer());
2482
2483         // TODO: maintain provenance of an alignment, rather than just make the
2484         // title a concatenation of operations.
2485         if (!externalPaste)
2486         {
2487           if (title.startsWith("Copied sequences"))
2488           {
2489             newtitle = title;
2490           }
2491           else
2492           {
2493             newtitle = newtitle.concat("- from " + title);
2494           }
2495         }
2496         else
2497         {
2498           newtitle = new String("Pasted sequences");
2499         }
2500
2501         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2502                 DEFAULT_HEIGHT);
2503
2504       }
2505
2506     } catch (Exception ex)
2507     {
2508       ex.printStackTrace();
2509       System.out.println("Exception whilst pasting: " + ex);
2510       // could be anything being pasted in here
2511     }
2512   }
2513
2514   @Override
2515   protected void expand_newalign(ActionEvent e)
2516   {
2517     try
2518     {
2519       AlignmentI alignment = AlignmentUtils
2520               .expandContext(getViewport().getAlignment(), -1);
2521       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2522               DEFAULT_HEIGHT);
2523       String newtitle = new String("Flanking alignment");
2524
2525       if (Desktop.jalviewClipboard != null
2526               && Desktop.jalviewClipboard[2] != null)
2527       {
2528         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2529         for (int region[] : hc)
2530         {
2531           af.viewport.hideColumns(region[0], region[1]);
2532         }
2533       }
2534
2535       // >>>This is a fix for the moment, until a better solution is
2536       // found!!<<<
2537       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2538               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2539                       .getFeatureRenderer());
2540
2541       // TODO: maintain provenance of an alignment, rather than just make the
2542       // title a concatenation of operations.
2543       {
2544         if (title.startsWith("Copied sequences"))
2545         {
2546           newtitle = title;
2547         }
2548         else
2549         {
2550           newtitle = newtitle.concat("- from " + title);
2551         }
2552       }
2553
2554       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2555
2556     } catch (Exception ex)
2557     {
2558       ex.printStackTrace();
2559       System.out.println("Exception whilst pasting: " + ex);
2560       // could be anything being pasted in here
2561     } catch (OutOfMemoryError oom)
2562     {
2563       new OOMWarning("Viewing flanking region of alignment", oom);
2564     }
2565   }
2566
2567   /**
2568    * DOCUMENT ME!
2569    *
2570    * @param e
2571    *          DOCUMENT ME!
2572    */
2573   @Override
2574   protected void cut_actionPerformed(ActionEvent e)
2575   {
2576     copy_actionPerformed(null);
2577     delete_actionPerformed(null);
2578   }
2579
2580   /**
2581    * DOCUMENT ME!
2582    *
2583    * @param e
2584    *          DOCUMENT ME!
2585    */
2586   @Override
2587   protected void delete_actionPerformed(ActionEvent evt)
2588   {
2589
2590     SequenceGroup sg = viewport.getSelectionGroup();
2591     if (sg == null)
2592     {
2593       return;
2594     }
2595
2596     /*
2597      * If the cut affects all sequences, warn, remove highlighted columns
2598      */
2599     if (sg.getSize() == viewport.getAlignment().getHeight())
2600     {
2601       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2602               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2603       if (isEntireAlignWidth)
2604       {
2605         int confirm = JvOptionPane.showConfirmDialog(this,
2606                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2607                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2608                 JvOptionPane.OK_CANCEL_OPTION);
2609
2610         if (confirm == JvOptionPane.CANCEL_OPTION
2611                 || confirm == JvOptionPane.CLOSED_OPTION)
2612         {
2613           return;
2614         }
2615       }
2616       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2617               sg.getEndRes() + 1);
2618     }
2619     SequenceI[] cut = sg.getSequences()
2620             .toArray(new SequenceI[sg.getSize()]);
2621
2622     addHistoryItem(new EditCommand(
2623             MessageManager.getString("label.cut_sequences"), Action.CUT,
2624             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2625             viewport.getAlignment()));
2626
2627     viewport.setSelectionGroup(null);
2628     viewport.sendSelection();
2629     viewport.getAlignment().deleteGroup(sg);
2630
2631     viewport.firePropertyChange("alignment", null,
2632             viewport.getAlignment().getSequences());
2633     if (viewport.getAlignment().getHeight() < 1)
2634     {
2635       try
2636       {
2637         this.setClosed(true);
2638       } catch (Exception ex)
2639       {
2640       }
2641     }
2642   }
2643
2644   /**
2645    * DOCUMENT ME!
2646    *
2647    * @param e
2648    *          DOCUMENT ME!
2649    */
2650   @Override
2651   protected void deleteGroups_actionPerformed(ActionEvent e)
2652   {
2653     if (avc.deleteGroups())
2654     {
2655       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2656       alignPanel.updateAnnotation();
2657       alignPanel.paintAlignment(true);
2658     }
2659   }
2660
2661   /**
2662    * DOCUMENT ME!
2663    *
2664    * @param e
2665    *          DOCUMENT ME!
2666    */
2667   @Override
2668   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2669   {
2670     SequenceGroup sg = new SequenceGroup();
2671
2672     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2673     {
2674       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2675     }
2676
2677     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2678     viewport.setSelectionGroup(sg);
2679     viewport.sendSelection();
2680     // JAL-2034 - should delegate to
2681     // alignPanel to decide if overview needs
2682     // updating.
2683     alignPanel.paintAlignment(false);
2684     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2685   }
2686
2687   /**
2688    * DOCUMENT ME!
2689    *
2690    * @param e
2691    *          DOCUMENT ME!
2692    */
2693   @Override
2694   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2695   {
2696     if (viewport.cursorMode)
2697     {
2698       alignPanel.getSeqPanel().keyboardNo1 = null;
2699       alignPanel.getSeqPanel().keyboardNo2 = null;
2700     }
2701     viewport.setSelectionGroup(null);
2702     viewport.getColumnSelection().clear();
2703     viewport.setSelectionGroup(null);
2704     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2705     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2706     // JAL-2034 - should delegate to
2707     // alignPanel to decide if overview needs
2708     // updating.
2709     alignPanel.paintAlignment(false);
2710     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2711     viewport.sendSelection();
2712   }
2713
2714   /**
2715    * DOCUMENT ME!
2716    *
2717    * @param e
2718    *          DOCUMENT ME!
2719    */
2720   @Override
2721   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2722   {
2723     SequenceGroup sg = viewport.getSelectionGroup();
2724
2725     if (sg == null)
2726     {
2727       selectAllSequenceMenuItem_actionPerformed(null);
2728
2729       return;
2730     }
2731
2732     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2733     {
2734       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2735     }
2736     // JAL-2034 - should delegate to
2737     // alignPanel to decide if overview needs
2738     // updating.
2739
2740     alignPanel.paintAlignment(true);
2741     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2742     viewport.sendSelection();
2743   }
2744
2745   @Override
2746   public void invertColSel_actionPerformed(ActionEvent e)
2747   {
2748     viewport.invertColumnSelection();
2749     alignPanel.paintAlignment(true);
2750     viewport.sendSelection();
2751   }
2752
2753   /**
2754    * DOCUMENT ME!
2755    *
2756    * @param e
2757    *          DOCUMENT ME!
2758    */
2759   @Override
2760   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2761   {
2762     trimAlignment(true);
2763   }
2764
2765   /**
2766    * DOCUMENT ME!
2767    *
2768    * @param e
2769    *          DOCUMENT ME!
2770    */
2771   @Override
2772   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2773   {
2774     trimAlignment(false);
2775   }
2776
2777   void trimAlignment(boolean trimLeft)
2778   {
2779     ColumnSelection colSel = viewport.getColumnSelection();
2780     int column;
2781
2782     if (!colSel.isEmpty())
2783     {
2784       if (trimLeft)
2785       {
2786         column = colSel.getMin();
2787       }
2788       else
2789       {
2790         column = colSel.getMax();
2791       }
2792
2793       SequenceI[] seqs;
2794       if (viewport.getSelectionGroup() != null)
2795       {
2796         seqs = viewport.getSelectionGroup()
2797                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2798       }
2799       else
2800       {
2801         seqs = viewport.getAlignment().getSequencesArray();
2802       }
2803
2804       TrimRegionCommand trimRegion;
2805       if (trimLeft)
2806       {
2807         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2808                 column, viewport.getAlignment());
2809         vpRanges.setStartRes(0);
2810       }
2811       else
2812       {
2813         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2814                 column, viewport.getAlignment());
2815       }
2816
2817       statusBar.setText(MessageManager
2818               .formatMessage("label.removed_columns", new String[]
2819               { Integer.valueOf(trimRegion.getSize()).toString() }));
2820
2821       addHistoryItem(trimRegion);
2822
2823       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2824       {
2825         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2826                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2827         {
2828           viewport.getAlignment().deleteGroup(sg);
2829         }
2830       }
2831
2832       viewport.firePropertyChange("alignment", null,
2833               viewport.getAlignment().getSequences());
2834     }
2835   }
2836
2837   /**
2838    * DOCUMENT ME!
2839    *
2840    * @param e
2841    *          DOCUMENT ME!
2842    */
2843   @Override
2844   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2845   {
2846     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2847
2848     SequenceI[] seqs;
2849     if (viewport.getSelectionGroup() != null)
2850     {
2851       seqs = viewport.getSelectionGroup()
2852               .getSequencesAsArray(viewport.getHiddenRepSequences());
2853       start = viewport.getSelectionGroup().getStartRes();
2854       end = viewport.getSelectionGroup().getEndRes();
2855     }
2856     else
2857     {
2858       seqs = viewport.getAlignment().getSequencesArray();
2859     }
2860
2861     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2862             "Remove Gapped Columns", seqs, start, end,
2863             viewport.getAlignment());
2864
2865     addHistoryItem(removeGapCols);
2866
2867     statusBar.setText(MessageManager
2868             .formatMessage("label.removed_empty_columns", new Object[]
2869             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2870
2871     // This is to maintain viewport position on first residue
2872     // of first sequence
2873     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2874     int startRes = seq.findPosition(vpRanges.getStartRes());
2875     // ShiftList shifts;
2876     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2877     // edit.alColumnChanges=shifts.getInverse();
2878     // if (viewport.hasHiddenColumns)
2879     // viewport.getColumnSelection().compensateForEdits(shifts);
2880     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2881     viewport.firePropertyChange("alignment", null,
2882             viewport.getAlignment().getSequences());
2883
2884   }
2885
2886   /**
2887    * DOCUMENT ME!
2888    *
2889    * @param e
2890    *          DOCUMENT ME!
2891    */
2892   @Override
2893   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2894   {
2895     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2896
2897     SequenceI[] seqs;
2898     if (viewport.getSelectionGroup() != null)
2899     {
2900       seqs = viewport.getSelectionGroup()
2901               .getSequencesAsArray(viewport.getHiddenRepSequences());
2902       start = viewport.getSelectionGroup().getStartRes();
2903       end = viewport.getSelectionGroup().getEndRes();
2904     }
2905     else
2906     {
2907       seqs = viewport.getAlignment().getSequencesArray();
2908     }
2909
2910     // This is to maintain viewport position on first residue
2911     // of first sequence
2912     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2913     int startRes = seq.findPosition(vpRanges.getStartRes());
2914
2915     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2916             viewport.getAlignment()));
2917
2918     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2919
2920     viewport.firePropertyChange("alignment", null,
2921             viewport.getAlignment().getSequences());
2922
2923   }
2924
2925   /**
2926    * DOCUMENT ME!
2927    *
2928    * @param e
2929    *          DOCUMENT ME!
2930    */
2931   @Override
2932   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2933   {
2934     viewport.setPadGaps(padGapsMenuitem.isSelected());
2935     viewport.firePropertyChange("alignment", null,
2936             viewport.getAlignment().getSequences());
2937   }
2938
2939   /**
2940    * DOCUMENT ME!
2941    *
2942    * @param e
2943    *          DOCUMENT ME!
2944    */
2945   @Override
2946   public void findMenuItem_actionPerformed(ActionEvent e)
2947   {
2948     new Finder();
2949   }
2950
2951   /**
2952    * Create a new view of the current alignment.
2953    */
2954   @Override
2955   public void newView_actionPerformed(ActionEvent e)
2956   {
2957     newView(null, true);
2958   }
2959
2960   /**
2961    * Creates and shows a new view of the current alignment.
2962    *
2963    * @param viewTitle
2964    *          title of newly created view; if null, one will be generated
2965    * @param copyAnnotation
2966    *          if true then duplicate all annnotation, groups and settings
2967    * @return new alignment panel, already displayed.
2968    */
2969   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2970   {
2971     /*
2972      * Create a new AlignmentPanel (with its own, new Viewport)
2973      */
2974     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2975             true);
2976     if (!copyAnnotation)
2977     {
2978       /*
2979        * remove all groups and annotation except for the automatic stuff
2980        */
2981       newap.av.getAlignment().deleteAllGroups();
2982       newap.av.getAlignment().deleteAllAnnotations(false);
2983     }
2984
2985     newap.av.setGatherViewsHere(false);
2986
2987     if (viewport.viewName == null)
2988     {
2989       viewport.viewName = MessageManager
2990               .getString("label.view_name_original");
2991     }
2992
2993     /*
2994      * Views share the same edits undo and redo stacks
2995      */
2996     newap.av.setHistoryList(viewport.getHistoryList());
2997     newap.av.setRedoList(viewport.getRedoList());
2998
2999     /*
3000      * Views share the same mappings; need to deregister any new mappings
3001      * created by copyAlignPanel, and register the new reference to the shared
3002      * mappings
3003      */
3004     newap.av.replaceMappings(viewport.getAlignment());
3005
3006     /*
3007      * start up cDNA consensus (if applicable) now mappings are in place
3008      */
3009     if (newap.av.initComplementConsensus())
3010     {
3011       newap.refresh(true); // adjust layout of annotations
3012     }
3013
3014     newap.av.viewName = getNewViewName(viewTitle);
3015
3016     addAlignmentPanel(newap, true);
3017     newap.alignmentChanged();
3018
3019     if (alignPanels.size() == 2)
3020     {
3021       viewport.setGatherViewsHere(true);
3022     }
3023     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3024     return newap;
3025   }
3026
3027   /**
3028    * Make a new name for the view, ensuring it is unique within the current
3029    * sequenceSetId. (This used to be essential for Jalview Project archives, but
3030    * these now use viewId. Unique view names are still desirable for usability.)
3031    *
3032    * @param viewTitle
3033    * @return
3034    */
3035   protected String getNewViewName(String viewTitle)
3036   {
3037     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3038     boolean addFirstIndex = false;
3039     if (viewTitle == null || viewTitle.trim().length() == 0)
3040     {
3041       viewTitle = MessageManager.getString("action.view");
3042       addFirstIndex = true;
3043     }
3044     else
3045     {
3046       index = 1;// we count from 1 if given a specific name
3047     }
3048     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3049
3050     List<Component> comps = PaintRefresher.components
3051             .get(viewport.getSequenceSetId());
3052
3053     List<String> existingNames = getExistingViewNames(comps);
3054
3055     while (existingNames.contains(newViewName))
3056     {
3057       newViewName = viewTitle + " " + (++index);
3058     }
3059     return newViewName;
3060   }
3061
3062   /**
3063    * Returns a list of distinct view names found in the given list of
3064    * components. View names are held on the viewport of an AlignmentPanel.
3065    *
3066    * @param comps
3067    * @return
3068    */
3069   protected List<String> getExistingViewNames(List<Component> comps)
3070   {
3071     List<String> existingNames = new ArrayList<>();
3072     for (Component comp : comps)
3073     {
3074       if (comp instanceof AlignmentPanel)
3075       {
3076         AlignmentPanel ap = (AlignmentPanel) comp;
3077         if (!existingNames.contains(ap.av.viewName))
3078         {
3079           existingNames.add(ap.av.viewName);
3080         }
3081       }
3082     }
3083     return existingNames;
3084   }
3085
3086   /**
3087    * Explode tabbed views into separate windows.
3088    */
3089   @Override
3090   public void expandViews_actionPerformed(ActionEvent e)
3091   {
3092     Desktop.explodeViews(this);
3093   }
3094
3095   /**
3096    * Gather views in separate windows back into a tabbed presentation.
3097    */
3098   @Override
3099   public void gatherViews_actionPerformed(ActionEvent e)
3100   {
3101     Desktop.instance.gatherViews(this);
3102   }
3103
3104   /**
3105    * DOCUMENT ME!
3106    *
3107    * @param e
3108    *          DOCUMENT ME!
3109    */
3110   @Override
3111   public void font_actionPerformed(ActionEvent e)
3112   {
3113     new FontChooser(alignPanel);
3114   }
3115
3116   /**
3117    * DOCUMENT ME!
3118    *
3119    * @param e
3120    *          DOCUMENT ME!
3121    */
3122   @Override
3123   protected void seqLimit_actionPerformed(ActionEvent e)
3124   {
3125     viewport.setShowJVSuffix(seqLimits.isSelected());
3126
3127     alignPanel.getIdPanel().getIdCanvas()
3128             .setPreferredSize(alignPanel.calculateIdWidth());
3129     alignPanel.paintAlignment(true);
3130   }
3131
3132   @Override
3133   public void idRightAlign_actionPerformed(ActionEvent e)
3134   {
3135     viewport.setRightAlignIds(idRightAlign.isSelected());
3136     alignPanel.paintAlignment(true);
3137   }
3138
3139   @Override
3140   public void centreColumnLabels_actionPerformed(ActionEvent e)
3141   {
3142     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3143     alignPanel.paintAlignment(true);
3144   }
3145
3146   /*
3147    * (non-Javadoc)
3148    *
3149    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3150    */
3151   @Override
3152   protected void followHighlight_actionPerformed()
3153   {
3154     /*
3155      * Set the 'follow' flag on the Viewport (and scroll to position if now
3156      * true).
3157      */
3158     final boolean state = this.followHighlightMenuItem.getState();
3159     viewport.setFollowHighlight(state);
3160     if (state)
3161     {
3162       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3163     }
3164   }
3165
3166   /**
3167    * DOCUMENT ME!
3168    *
3169    * @param e
3170    *          DOCUMENT ME!
3171    */
3172   @Override
3173   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3174   {
3175     viewport.setColourText(colourTextMenuItem.isSelected());
3176     alignPanel.paintAlignment(true);
3177   }
3178
3179   /**
3180    * DOCUMENT ME!
3181    *
3182    * @param e
3183    *          DOCUMENT ME!
3184    */
3185   @Override
3186   public void wrapMenuItem_actionPerformed(ActionEvent e)
3187   {
3188     scaleAbove.setVisible(wrapMenuItem.isSelected());
3189     scaleLeft.setVisible(wrapMenuItem.isSelected());
3190     scaleRight.setVisible(wrapMenuItem.isSelected());
3191     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3192     alignPanel.updateLayout();
3193   }
3194
3195   @Override
3196   public void showAllSeqs_actionPerformed(ActionEvent e)
3197   {
3198     viewport.showAllHiddenSeqs();
3199   }
3200
3201   @Override
3202   public void showAllColumns_actionPerformed(ActionEvent e)
3203   {
3204     viewport.showAllHiddenColumns();
3205     alignPanel.paintAlignment(true);
3206     viewport.sendSelection();
3207   }
3208
3209   @Override
3210   public void hideSelSequences_actionPerformed(ActionEvent e)
3211   {
3212     viewport.hideAllSelectedSeqs();
3213   }
3214
3215   /**
3216    * called by key handler and the hide all/show all menu items
3217    *
3218    * @param toggleSeqs
3219    * @param toggleCols
3220    */
3221   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3222   {
3223
3224     boolean hide = false;
3225     SequenceGroup sg = viewport.getSelectionGroup();
3226     if (!toggleSeqs && !toggleCols)
3227     {
3228       // Hide everything by the current selection - this is a hack - we do the
3229       // invert and then hide
3230       // first check that there will be visible columns after the invert.
3231       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3232               && sg.getStartRes() <= sg.getEndRes()))
3233       {
3234         // now invert the sequence set, if required - empty selection implies
3235         // that no hiding is required.
3236         if (sg != null)
3237         {
3238           invertSequenceMenuItem_actionPerformed(null);
3239           sg = viewport.getSelectionGroup();
3240           toggleSeqs = true;
3241
3242         }
3243         viewport.expandColSelection(sg, true);
3244         // finally invert the column selection and get the new sequence
3245         // selection.
3246         invertColSel_actionPerformed(null);
3247         toggleCols = true;
3248       }
3249     }
3250
3251     if (toggleSeqs)
3252     {
3253       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3254       {
3255         hideSelSequences_actionPerformed(null);
3256         hide = true;
3257       }
3258       else if (!(toggleCols && viewport.hasSelectedColumns()))
3259       {
3260         showAllSeqs_actionPerformed(null);
3261       }
3262     }
3263
3264     if (toggleCols)
3265     {
3266       if (viewport.hasSelectedColumns())
3267       {
3268         hideSelColumns_actionPerformed(null);
3269         if (!toggleSeqs)
3270         {
3271           viewport.setSelectionGroup(sg);
3272         }
3273       }
3274       else if (!hide)
3275       {
3276         showAllColumns_actionPerformed(null);
3277       }
3278     }
3279   }
3280
3281   /*
3282    * (non-Javadoc)
3283    *
3284    * @see
3285    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3286    * event.ActionEvent)
3287    */
3288   @Override
3289   public void hideAllButSelection_actionPerformed(ActionEvent e)
3290   {
3291     toggleHiddenRegions(false, false);
3292     viewport.sendSelection();
3293   }
3294
3295   /*
3296    * (non-Javadoc)
3297    *
3298    * @see
3299    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3300    * .ActionEvent)
3301    */
3302   @Override
3303   public void hideAllSelection_actionPerformed(ActionEvent e)
3304   {
3305     SequenceGroup sg = viewport.getSelectionGroup();
3306     viewport.expandColSelection(sg, false);
3307     viewport.hideAllSelectedSeqs();
3308     viewport.hideSelectedColumns();
3309     alignPanel.paintAlignment(true);
3310     viewport.sendSelection();
3311   }
3312
3313   /*
3314    * (non-Javadoc)
3315    *
3316    * @see
3317    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3318    * ActionEvent)
3319    */
3320   @Override
3321   public void showAllhidden_actionPerformed(ActionEvent e)
3322   {
3323     viewport.showAllHiddenColumns();
3324     viewport.showAllHiddenSeqs();
3325     alignPanel.paintAlignment(true);
3326     viewport.sendSelection();
3327   }
3328
3329   @Override
3330   public void hideSelColumns_actionPerformed(ActionEvent e)
3331   {
3332     viewport.hideSelectedColumns();
3333     alignPanel.paintAlignment(true);
3334     viewport.sendSelection();
3335   }
3336
3337   @Override
3338   public void hiddenMarkers_actionPerformed(ActionEvent e)
3339   {
3340     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3341     repaint();
3342   }
3343
3344   /**
3345    * DOCUMENT ME!
3346    *
3347    * @param e
3348    *          DOCUMENT ME!
3349    */
3350   @Override
3351   protected void scaleAbove_actionPerformed(ActionEvent e)
3352   {
3353     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3354     alignPanel.paintAlignment(true);
3355   }
3356
3357   /**
3358    * DOCUMENT ME!
3359    *
3360    * @param e
3361    *          DOCUMENT ME!
3362    */
3363   @Override
3364   protected void scaleLeft_actionPerformed(ActionEvent e)
3365   {
3366     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3367     alignPanel.paintAlignment(true);
3368   }
3369
3370   /**
3371    * DOCUMENT ME!
3372    *
3373    * @param e
3374    *          DOCUMENT ME!
3375    */
3376   @Override
3377   protected void scaleRight_actionPerformed(ActionEvent e)
3378   {
3379     viewport.setScaleRightWrapped(scaleRight.isSelected());
3380     alignPanel.paintAlignment(true);
3381   }
3382
3383   /**
3384    * DOCUMENT ME!
3385    *
3386    * @param e
3387    *          DOCUMENT ME!
3388    */
3389   @Override
3390   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3391   {
3392     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3393     alignPanel.paintAlignment(true);
3394   }
3395
3396   /**
3397    * DOCUMENT ME!
3398    *
3399    * @param e
3400    *          DOCUMENT ME!
3401    */
3402   @Override
3403   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3404   {
3405     viewport.setShowText(viewTextMenuItem.isSelected());
3406     alignPanel.paintAlignment(true);
3407   }
3408
3409   /**
3410    * DOCUMENT ME!
3411    *
3412    * @param e
3413    *          DOCUMENT ME!
3414    */
3415   @Override
3416   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3417   {
3418     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3419     alignPanel.paintAlignment(true);
3420   }
3421
3422   public FeatureSettings featureSettings;
3423
3424   @Override
3425   public FeatureSettingsControllerI getFeatureSettingsUI()
3426   {
3427     return featureSettings;
3428   }
3429
3430   @Override
3431   public void featureSettings_actionPerformed(ActionEvent e)
3432   {
3433     if (featureSettings != null)
3434     {
3435       featureSettings.close();
3436       featureSettings = null;
3437     }
3438     if (!showSeqFeatures.isSelected())
3439     {
3440       // make sure features are actually displayed
3441       showSeqFeatures.setSelected(true);
3442       showSeqFeatures_actionPerformed(null);
3443     }
3444     featureSettings = new FeatureSettings(this);
3445   }
3446
3447   /**
3448    * Set or clear 'Show Sequence Features'
3449    *
3450    * @param evt
3451    *          DOCUMENT ME!
3452    */
3453   @Override
3454   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3455   {
3456     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3457     alignPanel.paintAlignment(true);
3458   }
3459
3460   /**
3461    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3462    * the annotations panel as a whole.
3463    *
3464    * The options to show/hide all annotations should be enabled when the panel
3465    * is shown, and disabled when the panel is hidden.
3466    *
3467    * @param e
3468    */
3469   @Override
3470   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3471   {
3472     final boolean setVisible = annotationPanelMenuItem.isSelected();
3473     viewport.setShowAnnotation(setVisible);
3474     this.showAllSeqAnnotations.setEnabled(setVisible);
3475     this.hideAllSeqAnnotations.setEnabled(setVisible);
3476     this.showAllAlAnnotations.setEnabled(setVisible);
3477     this.hideAllAlAnnotations.setEnabled(setVisible);
3478     alignPanel.updateLayout();
3479   }
3480
3481   @Override
3482   public void alignmentProperties()
3483   {
3484     JEditorPane editPane = new JEditorPane("text/html", "");
3485     editPane.setEditable(false);
3486     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3487             .formatAsHtml();
3488     editPane.setText(
3489             MessageManager.formatMessage("label.html_content", new Object[]
3490             { contents.toString() }));
3491     JInternalFrame frame = new JInternalFrame();
3492     frame.getContentPane().add(new JScrollPane(editPane));
3493
3494     Desktop.addInternalFrame(frame, MessageManager
3495             .formatMessage("label.alignment_properties", new Object[]
3496             { getTitle() }), 500, 400);
3497   }
3498
3499   /**
3500    * DOCUMENT ME!
3501    *
3502    * @param e
3503    *          DOCUMENT ME!
3504    */
3505   @Override
3506   public void overviewMenuItem_actionPerformed(ActionEvent e)
3507   {
3508     if (alignPanel.overviewPanel != null)
3509     {
3510       return;
3511     }
3512
3513     JInternalFrame frame = new JInternalFrame();
3514     final OverviewPanel overview = new OverviewPanel(alignPanel);
3515     frame.setContentPane(overview);
3516     Desktop.addInternalFrame(frame, MessageManager
3517             .formatMessage("label.overview_params", new Object[]
3518             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3519             true, true);
3520     frame.pack();
3521     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3522     frame.addInternalFrameListener(
3523             new javax.swing.event.InternalFrameAdapter()
3524             {
3525               @Override
3526               public void internalFrameClosed(
3527                       javax.swing.event.InternalFrameEvent evt)
3528               {
3529                 overview.dispose();
3530                 alignPanel.setOverviewPanel(null);
3531               };
3532             });
3533
3534     alignPanel.setOverviewPanel(overview);
3535   }
3536
3537   @Override
3538   public void textColour_actionPerformed()
3539   {
3540     new TextColourChooser().chooseColour(alignPanel, null);
3541   }
3542
3543   /*
3544    * public void covariationColour_actionPerformed() {
3545    * changeColour(new
3546    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3547    * ()[0])); }
3548    */
3549   @Override
3550   public void annotationColour_actionPerformed()
3551   {
3552     new AnnotationColourChooser(viewport, alignPanel);
3553   }
3554
3555   @Override
3556   public void annotationColumn_actionPerformed(ActionEvent e)
3557   {
3558     new AnnotationColumnChooser(viewport, alignPanel);
3559   }
3560
3561   /**
3562    * Action on the user checking or unchecking the option to apply the selected
3563    * colour scheme to all groups. If unchecked, groups may have their own
3564    * independent colour schemes.
3565    *
3566    * @param selected
3567    */
3568   @Override
3569   public void applyToAllGroups_actionPerformed(boolean selected)
3570   {
3571     viewport.setColourAppliesToAllGroups(selected);
3572   }
3573
3574   /**
3575    * Action on user selecting a colour from the colour menu
3576    *
3577    * @param name
3578    *          the name (not the menu item label!) of the colour scheme
3579    */
3580   @Override
3581   public void changeColour_actionPerformed(String name)
3582   {
3583     /*
3584      * 'User Defined' opens a panel to configure or load a
3585      * user-defined colour scheme
3586      */
3587     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3588     {
3589       new UserDefinedColours(alignPanel);
3590       return;
3591     }
3592
3593     /*
3594      * otherwise set the chosen colour scheme (or null for 'None')
3595      */
3596     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3597             viewport.getAlignment(), viewport.getHiddenRepSequences());
3598     changeColour(cs);
3599   }
3600
3601   /**
3602    * Actions on setting or changing the alignment colour scheme
3603    *
3604    * @param cs
3605    */
3606   @Override
3607   public void changeColour(ColourSchemeI cs)
3608   {
3609     // TODO: pull up to controller method
3610     ColourMenuHelper.setColourSelected(colourMenu, cs);
3611
3612     viewport.setGlobalColourScheme(cs);
3613
3614     alignPanel.paintAlignment(true);
3615   }
3616
3617   /**
3618    * Show the PID threshold slider panel
3619    */
3620   @Override
3621   protected void modifyPID_actionPerformed()
3622   {
3623     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3624             alignPanel.getViewName());
3625     SliderPanel.showPIDSlider();
3626   }
3627
3628   /**
3629    * Show the Conservation slider panel
3630    */
3631   @Override
3632   protected void modifyConservation_actionPerformed()
3633   {
3634     SliderPanel.setConservationSlider(alignPanel,
3635             viewport.getResidueShading(), alignPanel.getViewName());
3636     SliderPanel.showConservationSlider();
3637   }
3638
3639   /**
3640    * Action on selecting or deselecting (Colour) By Conservation
3641    */
3642   @Override
3643   public void conservationMenuItem_actionPerformed(boolean selected)
3644   {
3645     modifyConservation.setEnabled(selected);
3646     viewport.setConservationSelected(selected);
3647     viewport.getResidueShading().setConservationApplied(selected);
3648
3649     changeColour(viewport.getGlobalColourScheme());
3650     if (selected)
3651     {
3652       modifyConservation_actionPerformed();
3653     }
3654     else
3655     {
3656       SliderPanel.hideConservationSlider();
3657     }
3658   }
3659
3660   /**
3661    * Action on selecting or deselecting (Colour) Above PID Threshold
3662    */
3663   @Override
3664   public void abovePIDThreshold_actionPerformed(boolean selected)
3665   {
3666     modifyPID.setEnabled(selected);
3667     viewport.setAbovePIDThreshold(selected);
3668     if (!selected)
3669     {
3670       viewport.getResidueShading().setThreshold(0,
3671               viewport.isIgnoreGapsConsensus());
3672     }
3673
3674     changeColour(viewport.getGlobalColourScheme());
3675     if (selected)
3676     {
3677       modifyPID_actionPerformed();
3678     }
3679     else
3680     {
3681       SliderPanel.hidePIDSlider();
3682     }
3683   }
3684
3685   /**
3686    * DOCUMENT ME!
3687    *
3688    * @param e
3689    *          DOCUMENT ME!
3690    */
3691   @Override
3692   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3693   {
3694     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3695     AlignmentSorter.sortByPID(viewport.getAlignment(),
3696             viewport.getAlignment().getSequenceAt(0));
3697     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3698             viewport.getAlignment()));
3699     alignPanel.paintAlignment(true);
3700   }
3701
3702   /**
3703    * DOCUMENT ME!
3704    *
3705    * @param e
3706    *          DOCUMENT ME!
3707    */
3708   @Override
3709   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3710   {
3711     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3712     AlignmentSorter.sortByID(viewport.getAlignment());
3713     addHistoryItem(
3714             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3715     alignPanel.paintAlignment(true);
3716   }
3717
3718   /**
3719    * DOCUMENT ME!
3720    *
3721    * @param e
3722    *          DOCUMENT ME!
3723    */
3724   @Override
3725   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3726   {
3727     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3728     AlignmentSorter.sortByLength(viewport.getAlignment());
3729     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3730             viewport.getAlignment()));
3731     alignPanel.paintAlignment(true);
3732   }
3733
3734   /**
3735    * DOCUMENT ME!
3736    *
3737    * @param e
3738    *          DOCUMENT ME!
3739    */
3740   @Override
3741   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3742   {
3743     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3744     AlignmentSorter.sortByGroup(viewport.getAlignment());
3745     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3746             viewport.getAlignment()));
3747
3748     alignPanel.paintAlignment(true);
3749   }
3750
3751   /**
3752    * DOCUMENT ME!
3753    *
3754    * @param e
3755    *          DOCUMENT ME!
3756    */
3757   @Override
3758   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3759   {
3760     new RedundancyPanel(alignPanel, this);
3761   }
3762
3763   /**
3764    * DOCUMENT ME!
3765    *
3766    * @param e
3767    *          DOCUMENT ME!
3768    */
3769   @Override
3770   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3771   {
3772     if ((viewport.getSelectionGroup() == null)
3773             || (viewport.getSelectionGroup().getSize() < 2))
3774     {
3775       JvOptionPane.showInternalMessageDialog(this,
3776               MessageManager.getString(
3777                       "label.you_must_select_least_two_sequences"),
3778               MessageManager.getString("label.invalid_selection"),
3779               JvOptionPane.WARNING_MESSAGE);
3780     }
3781     else
3782     {
3783       JInternalFrame frame = new JInternalFrame();
3784       frame.setContentPane(new PairwiseAlignPanel(viewport));
3785       Desktop.addInternalFrame(frame,
3786               MessageManager.getString("action.pairwise_alignment"), 600,
3787               500);
3788     }
3789   }
3790
3791   @Override
3792   public void autoCalculate_actionPerformed(ActionEvent e)
3793   {
3794     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3795     if (viewport.autoCalculateConsensus)
3796     {
3797       viewport.firePropertyChange("alignment", null,
3798               viewport.getAlignment().getSequences());
3799     }
3800   }
3801
3802   @Override
3803   public void sortByTreeOption_actionPerformed(ActionEvent e)
3804   {
3805     viewport.sortByTree = sortByTree.isSelected();
3806   }
3807
3808   @Override
3809   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3810   {
3811     viewport.followSelection = listenToViewSelections.isSelected();
3812   }
3813
3814   /**
3815    * Constructs a tree panel and adds it to the desktop
3816    *
3817    * @param type
3818    *          tree type (NJ or AV)
3819    * @param modelName
3820    *          name of score model used to compute the tree
3821    * @param options
3822    *          parameters for the distance or similarity calculation
3823    */
3824   void newTreePanel(String type, String modelName,
3825           SimilarityParamsI options)
3826   {
3827     String frameTitle = "";
3828     TreePanel tp;
3829
3830     boolean onSelection = false;
3831     if (viewport.getSelectionGroup() != null
3832             && viewport.getSelectionGroup().getSize() > 0)
3833     {
3834       SequenceGroup sg = viewport.getSelectionGroup();
3835
3836       /* Decide if the selection is a column region */
3837       for (SequenceI _s : sg.getSequences())
3838       {
3839         if (_s.getLength() < sg.getEndRes())
3840         {
3841           JvOptionPane.showMessageDialog(Desktop.desktop,
3842                   MessageManager.getString(
3843                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3844                   MessageManager.getString(
3845                           "label.sequences_selection_not_aligned"),
3846                   JvOptionPane.WARNING_MESSAGE);
3847
3848           return;
3849         }
3850       }
3851       onSelection = true;
3852     }
3853     else
3854     {
3855       if (viewport.getAlignment().getHeight() < 2)
3856       {
3857         return;
3858       }
3859     }
3860
3861     tp = new TreePanel(alignPanel, type, modelName, options);
3862     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3863
3864     frameTitle += " from ";
3865
3866     if (viewport.viewName != null)
3867     {
3868       frameTitle += viewport.viewName + " of ";
3869     }
3870
3871     frameTitle += this.title;
3872
3873     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3874   }
3875
3876   /**
3877    * DOCUMENT ME!
3878    *
3879    * @param title
3880    *          DOCUMENT ME!
3881    * @param order
3882    *          DOCUMENT ME!
3883    */
3884   public void addSortByOrderMenuItem(String title,
3885           final AlignmentOrder order)
3886   {
3887     final JMenuItem item = new JMenuItem(MessageManager
3888             .formatMessage("action.by_title_param", new Object[]
3889             { title }));
3890     sort.add(item);
3891     item.addActionListener(new java.awt.event.ActionListener()
3892     {
3893       @Override
3894       public void actionPerformed(ActionEvent e)
3895       {
3896         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3897
3898         // TODO: JBPNote - have to map order entries to curent SequenceI
3899         // pointers
3900         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3901
3902         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3903                 viewport.getAlignment()));
3904
3905         alignPanel.paintAlignment(true);
3906       }
3907     });
3908   }
3909
3910   /**
3911    * Add a new sort by annotation score menu item
3912    *
3913    * @param sort
3914    *          the menu to add the option to
3915    * @param scoreLabel
3916    *          the label used to retrieve scores for each sequence on the
3917    *          alignment
3918    */
3919   public void addSortByAnnotScoreMenuItem(JMenu sort,
3920           final String scoreLabel)
3921   {
3922     final JMenuItem item = new JMenuItem(scoreLabel);
3923     sort.add(item);
3924     item.addActionListener(new java.awt.event.ActionListener()
3925     {
3926       @Override
3927       public void actionPerformed(ActionEvent e)
3928       {
3929         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3930         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3931                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3932         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3933                 viewport.getAlignment()));
3934         alignPanel.paintAlignment(true);
3935       }
3936     });
3937   }
3938
3939   /**
3940    * last hash for alignment's annotation array - used to minimise cost of
3941    * rebuild.
3942    */
3943   protected int _annotationScoreVectorHash;
3944
3945   /**
3946    * search the alignment and rebuild the sort by annotation score submenu the
3947    * last alignment annotation vector hash is stored to minimize cost of
3948    * rebuilding in subsequence calls.
3949    *
3950    */
3951   @Override
3952   public void buildSortByAnnotationScoresMenu()
3953   {
3954     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3955     {
3956       return;
3957     }
3958
3959     if (viewport.getAlignment().getAlignmentAnnotation()
3960             .hashCode() != _annotationScoreVectorHash)
3961     {
3962       sortByAnnotScore.removeAll();
3963       // almost certainly a quicker way to do this - but we keep it simple
3964       Hashtable scoreSorts = new Hashtable();
3965       AlignmentAnnotation aann[];
3966       for (SequenceI sqa : viewport.getAlignment().getSequences())
3967       {
3968         aann = sqa.getAnnotation();
3969         for (int i = 0; aann != null && i < aann.length; i++)
3970         {
3971           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3972           {
3973             scoreSorts.put(aann[i].label, aann[i].label);
3974           }
3975         }
3976       }
3977       Enumeration labels = scoreSorts.keys();
3978       while (labels.hasMoreElements())
3979       {
3980         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3981                 (String) labels.nextElement());
3982       }
3983       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3984       scoreSorts.clear();
3985
3986       _annotationScoreVectorHash = viewport.getAlignment()
3987               .getAlignmentAnnotation().hashCode();
3988     }
3989   }
3990
3991   /**
3992    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3993    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3994    * call. Listeners are added to remove the menu item when the treePanel is
3995    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3996    * modified.
3997    */
3998   @Override
3999   public void buildTreeSortMenu()
4000   {
4001     sortByTreeMenu.removeAll();
4002
4003     List<Component> comps = PaintRefresher.components
4004             .get(viewport.getSequenceSetId());
4005     List<TreePanel> treePanels = new ArrayList<>();
4006     for (Component comp : comps)
4007     {
4008       if (comp instanceof TreePanel)
4009       {
4010         treePanels.add((TreePanel) comp);
4011       }
4012     }
4013
4014     if (treePanels.size() < 1)
4015     {
4016       sortByTreeMenu.setVisible(false);
4017       return;
4018     }
4019
4020     sortByTreeMenu.setVisible(true);
4021
4022     for (final TreePanel tp : treePanels)
4023     {
4024       final JMenuItem item = new JMenuItem(tp.getTitle());
4025       item.addActionListener(new java.awt.event.ActionListener()
4026       {
4027         @Override
4028         public void actionPerformed(ActionEvent e)
4029         {
4030           tp.sortByTree_actionPerformed();
4031           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4032
4033         }
4034       });
4035
4036       sortByTreeMenu.add(item);
4037     }
4038   }
4039
4040   public boolean sortBy(AlignmentOrder alorder, String undoname)
4041   {
4042     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4043     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4044     if (undoname != null)
4045     {
4046       addHistoryItem(new OrderCommand(undoname, oldOrder,
4047               viewport.getAlignment()));
4048     }
4049     alignPanel.paintAlignment(true);
4050     return true;
4051   }
4052
4053   /**
4054    * Work out whether the whole set of sequences or just the selected set will
4055    * be submitted for multiple alignment.
4056    *
4057    */
4058   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4059   {
4060     // Now, check we have enough sequences
4061     AlignmentView msa = null;
4062
4063     if ((viewport.getSelectionGroup() != null)
4064             && (viewport.getSelectionGroup().getSize() > 1))
4065     {
4066       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4067       // some common interface!
4068       /*
4069        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4070        * SequenceI[sz = seqs.getSize(false)];
4071        *
4072        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4073        * seqs.getSequenceAt(i); }
4074        */
4075       msa = viewport.getAlignmentView(true);
4076     }
4077     else if (viewport.getSelectionGroup() != null
4078             && viewport.getSelectionGroup().getSize() == 1)
4079     {
4080       int option = JvOptionPane.showConfirmDialog(this,
4081               MessageManager.getString("warn.oneseq_msainput_selection"),
4082               MessageManager.getString("label.invalid_selection"),
4083               JvOptionPane.OK_CANCEL_OPTION);
4084       if (option == JvOptionPane.OK_OPTION)
4085       {
4086         msa = viewport.getAlignmentView(false);
4087       }
4088     }
4089     else
4090     {
4091       msa = viewport.getAlignmentView(false);
4092     }
4093     return msa;
4094   }
4095
4096   /**
4097    * Decides what is submitted to a secondary structure prediction service: the
4098    * first sequence in the alignment, or in the current selection, or, if the
4099    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4100    * region or the whole alignment. (where the first sequence in the set is the
4101    * one that the prediction will be for).
4102    */
4103   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4104   {
4105     AlignmentView seqs = null;
4106
4107     if ((viewport.getSelectionGroup() != null)
4108             && (viewport.getSelectionGroup().getSize() > 0))
4109     {
4110       seqs = viewport.getAlignmentView(true);
4111     }
4112     else
4113     {
4114       seqs = viewport.getAlignmentView(false);
4115     }
4116     // limit sequences - JBPNote in future - could spawn multiple prediction
4117     // jobs
4118     // TODO: viewport.getAlignment().isAligned is a global state - the local
4119     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4120     if (!viewport.getAlignment().isAligned(false))
4121     {
4122       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4123       // TODO: if seqs.getSequences().length>1 then should really have warned
4124       // user!
4125
4126     }
4127     return seqs;
4128   }
4129
4130   /**
4131    * DOCUMENT ME!
4132    *
4133    * @param e
4134    *          DOCUMENT ME!
4135    */
4136   @Override
4137   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4138   {
4139     // Pick the tree file
4140     JalviewFileChooser chooser = new JalviewFileChooser(
4141             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4142     chooser.setFileView(new JalviewFileView());
4143     chooser.setDialogTitle(
4144             MessageManager.getString("label.select_newick_like_tree_file"));
4145     chooser.setToolTipText(
4146             MessageManager.getString("label.load_tree_file"));
4147
4148     int value = chooser.showOpenDialog(null);
4149
4150     if (value == JalviewFileChooser.APPROVE_OPTION)
4151     {
4152       String filePath = chooser.getSelectedFile().getPath();
4153       Cache.setProperty("LAST_DIRECTORY", filePath);
4154       NewickFile fin = null;
4155       try
4156       {
4157         fin = new NewickFile(filePath, DataSourceType.FILE);
4158         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4159       } catch (Exception ex)
4160       {
4161         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4162                 MessageManager.getString("label.problem_reading_tree_file"),
4163                 JvOptionPane.WARNING_MESSAGE);
4164         ex.printStackTrace();
4165       }
4166       if (fin != null && fin.hasWarningMessage())
4167       {
4168         JvOptionPane.showMessageDialog(Desktop.desktop,
4169                 fin.getWarningMessage(),
4170                 MessageManager
4171                         .getString("label.possible_problem_with_tree_file"),
4172                 JvOptionPane.WARNING_MESSAGE);
4173       }
4174     }
4175   }
4176
4177   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4178   {
4179     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4180   }
4181
4182   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4183           int h, int x, int y)
4184   {
4185     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4186   }
4187
4188   /**
4189    * Add a treeviewer for the tree extracted from a Newick file object to the
4190    * current alignment view
4191    *
4192    * @param nf
4193    *          the tree
4194    * @param title
4195    *          tree viewer title
4196    * @param input
4197    *          Associated alignment input data (or null)
4198    * @param w
4199    *          width
4200    * @param h
4201    *          height
4202    * @param x
4203    *          position
4204    * @param y
4205    *          position
4206    * @return TreePanel handle
4207    */
4208   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4209           AlignmentView input, int w, int h, int x, int y)
4210   {
4211     TreePanel tp = null;
4212
4213     try
4214     {
4215       nf.parse();
4216
4217       if (nf.getTree() != null)
4218       {
4219         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4220
4221         tp.setSize(w, h);
4222
4223         if (x > 0 && y > 0)
4224         {
4225           tp.setLocation(x, y);
4226         }
4227
4228         Desktop.addInternalFrame(tp, treeTitle, w, h);
4229       }
4230     } catch (Exception ex)
4231     {
4232       ex.printStackTrace();
4233     }
4234
4235     return tp;
4236   }
4237
4238   private boolean buildingMenu = false;
4239
4240   /**
4241    * Generates menu items and listener event actions for web service clients
4242    *
4243    */
4244   public void BuildWebServiceMenu()
4245   {
4246     while (buildingMenu)
4247     {
4248       try
4249       {
4250         System.err.println("Waiting for building menu to finish.");
4251         Thread.sleep(10);
4252       } catch (Exception e)
4253       {
4254       }
4255     }
4256     final AlignFrame me = this;
4257     buildingMenu = true;
4258     new Thread(new Runnable()
4259     {
4260       @Override
4261       public void run()
4262       {
4263         final List<JMenuItem> legacyItems = new ArrayList<>();
4264         try
4265         {
4266           // System.err.println("Building ws menu again "
4267           // + Thread.currentThread());
4268           // TODO: add support for context dependent disabling of services based
4269           // on
4270           // alignment and current selection
4271           // TODO: add additional serviceHandle parameter to specify abstract
4272           // handler
4273           // class independently of AbstractName
4274           // TODO: add in rediscovery GUI function to restart discoverer
4275           // TODO: group services by location as well as function and/or
4276           // introduce
4277           // object broker mechanism.
4278           final Vector<JMenu> wsmenu = new Vector<>();
4279           final IProgressIndicator af = me;
4280
4281           /*
4282            * do not i18n these strings - they are hard-coded in class
4283            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4284            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4285            */
4286           final JMenu msawsmenu = new JMenu("Alignment");
4287           final JMenu secstrmenu = new JMenu(
4288                   "Secondary Structure Prediction");
4289           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4290           final JMenu analymenu = new JMenu("Analysis");
4291           final JMenu dismenu = new JMenu("Protein Disorder");
4292           // JAL-940 - only show secondary structure prediction services from
4293           // the legacy server
4294           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4295               // &&
4296           Discoverer.services != null && (Discoverer.services.size() > 0))
4297           {
4298             // TODO: refactor to allow list of AbstractName/Handler bindings to
4299             // be
4300             // stored or retrieved from elsewhere
4301             // No MSAWS used any more:
4302             // Vector msaws = null; // (Vector)
4303             // Discoverer.services.get("MsaWS");
4304             Vector secstrpr = (Vector) Discoverer.services
4305                     .get("SecStrPred");
4306             if (secstrpr != null)
4307             {
4308               // Add any secondary structure prediction services
4309               for (int i = 0, j = secstrpr.size(); i < j; i++)
4310               {
4311                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4312                         .get(i);
4313                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4314                         .getServiceClient(sh);
4315                 int p = secstrmenu.getItemCount();
4316                 impl.attachWSMenuEntry(secstrmenu, me);
4317                 int q = secstrmenu.getItemCount();
4318                 for (int litm = p; litm < q; litm++)
4319                 {
4320                   legacyItems.add(secstrmenu.getItem(litm));
4321                 }
4322               }
4323             }
4324           }
4325
4326           // Add all submenus in the order they should appear on the web
4327           // services menu
4328           wsmenu.add(msawsmenu);
4329           wsmenu.add(secstrmenu);
4330           wsmenu.add(dismenu);
4331           wsmenu.add(analymenu);
4332           // No search services yet
4333           // wsmenu.add(seqsrchmenu);
4334
4335           javax.swing.SwingUtilities.invokeLater(new Runnable()
4336           {
4337             @Override
4338             public void run()
4339             {
4340               try
4341               {
4342                 webService.removeAll();
4343                 // first, add discovered services onto the webservices menu
4344                 if (wsmenu.size() > 0)
4345                 {
4346                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4347                   {
4348                     webService.add(wsmenu.get(i));
4349                   }
4350                 }
4351                 else
4352                 {
4353                   webService.add(me.webServiceNoServices);
4354                 }
4355                 // TODO: move into separate menu builder class.
4356                 boolean new_sspred = false;
4357                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4358                 {
4359                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4360                   if (jws2servs != null)
4361                   {
4362                     if (jws2servs.hasServices())
4363                     {
4364                       jws2servs.attachWSMenuEntry(webService, me);
4365                       for (Jws2Instance sv : jws2servs.getServices())
4366                       {
4367                         if (sv.description.toLowerCase().contains("jpred"))
4368                         {
4369                           for (JMenuItem jmi : legacyItems)
4370                           {
4371                             jmi.setVisible(false);
4372                           }
4373                         }
4374                       }
4375
4376                     }
4377                     if (jws2servs.isRunning())
4378                     {
4379                       JMenuItem tm = new JMenuItem(
4380                               "Still discovering JABA Services");
4381                       tm.setEnabled(false);
4382                       webService.add(tm);
4383                     }
4384                   }
4385                 }
4386                 build_urlServiceMenu(me.webService);
4387                 build_fetchdbmenu(webService);
4388                 for (JMenu item : wsmenu)
4389                 {
4390                   if (item.getItemCount() == 0)
4391                   {
4392                     item.setEnabled(false);
4393                   }
4394                   else
4395                   {
4396                     item.setEnabled(true);
4397                   }
4398                 }
4399               } catch (Exception e)
4400               {
4401                 Cache.log.debug(
4402                         "Exception during web service menu building process.",
4403                         e);
4404               }
4405             }
4406           });
4407         } catch (Exception e)
4408         {
4409         }
4410         buildingMenu = false;
4411       }
4412     }).start();
4413
4414   }
4415
4416   /**
4417    * construct any groupURL type service menu entries.
4418    *
4419    * @param webService
4420    */
4421   private void build_urlServiceMenu(JMenu webService)
4422   {
4423     // TODO: remove this code when 2.7 is released
4424     // DEBUG - alignmentView
4425     /*
4426      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4427      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4428      *
4429      * @Override public void actionPerformed(ActionEvent e) {
4430      * jalview.datamodel.AlignmentView
4431      * .testSelectionViews(af.viewport.getAlignment(),
4432      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4433      *
4434      * }); webService.add(testAlView);
4435      */
4436     // TODO: refactor to RestClient discoverer and merge menu entries for
4437     // rest-style services with other types of analysis/calculation service
4438     // SHmmr test client - still being implemented.
4439     // DEBUG - alignmentView
4440
4441     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4442             .getRestClients())
4443     {
4444       client.attachWSMenuEntry(
4445               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4446               this);
4447     }
4448   }
4449
4450   /**
4451    * Searches the alignment sequences for xRefs and builds the Show
4452    * Cross-References menu (formerly called Show Products), with database
4453    * sources for which cross-references are found (protein sources for a
4454    * nucleotide alignment and vice versa)
4455    *
4456    * @return true if Show Cross-references menu should be enabled
4457    */
4458   public boolean canShowProducts()
4459   {
4460     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4461     AlignmentI dataset = viewport.getAlignment().getDataset();
4462
4463     showProducts.removeAll();
4464     final boolean dna = viewport.getAlignment().isNucleotide();
4465
4466     if (seqs == null || seqs.length == 0)
4467     {
4468       // nothing to see here.
4469       return false;
4470     }
4471
4472     boolean showp = false;
4473     try
4474     {
4475       List<String> ptypes = new CrossRef(seqs, dataset)
4476               .findXrefSourcesForSequences(dna);
4477
4478       for (final String source : ptypes)
4479       {
4480         showp = true;
4481         final AlignFrame af = this;
4482         JMenuItem xtype = new JMenuItem(source);
4483         xtype.addActionListener(new ActionListener()
4484         {
4485           @Override
4486           public void actionPerformed(ActionEvent e)
4487           {
4488             showProductsFor(af.viewport.getSequenceSelection(), dna,
4489                     source);
4490           }
4491         });
4492         showProducts.add(xtype);
4493       }
4494       showProducts.setVisible(showp);
4495       showProducts.setEnabled(showp);
4496     } catch (Exception e)
4497     {
4498       Cache.log.warn(
4499               "canShowProducts threw an exception - please report to help@jalview.org",
4500               e);
4501       return false;
4502     }
4503     return showp;
4504   }
4505
4506   /**
4507    * Finds and displays cross-references for the selected sequences (protein
4508    * products for nucleotide sequences, dna coding sequences for peptides).
4509    *
4510    * @param sel
4511    *          the sequences to show cross-references for
4512    * @param dna
4513    *          true if from a nucleotide alignment (so showing proteins)
4514    * @param source
4515    *          the database to show cross-references for
4516    */
4517   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4518           final String source)
4519   {
4520     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4521             .start();
4522   }
4523
4524   /**
4525    * Construct and display a new frame containing the translation of this
4526    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4527    */
4528   @Override
4529   public void showTranslation_actionPerformed(ActionEvent e)
4530   {
4531     AlignmentI al = null;
4532     try
4533     {
4534       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4535
4536       al = dna.translateCdna();
4537     } catch (Exception ex)
4538     {
4539       jalview.bin.Cache.log.error(
4540               "Exception during translation. Please report this !", ex);
4541       final String msg = MessageManager.getString(
4542               "label.error_when_translating_sequences_submit_bug_report");
4543       final String errorTitle = MessageManager
4544               .getString("label.implementation_error")
4545               + MessageManager.getString("label.translation_failed");
4546       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4547               JvOptionPane.ERROR_MESSAGE);
4548       return;
4549     }
4550     if (al == null || al.getHeight() == 0)
4551     {
4552       final String msg = MessageManager.getString(
4553               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4554       final String errorTitle = MessageManager
4555               .getString("label.translation_failed");
4556       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4557               JvOptionPane.WARNING_MESSAGE);
4558     }
4559     else
4560     {
4561       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4562       af.setFileFormat(this.currentFileFormat);
4563       final String newTitle = MessageManager
4564               .formatMessage("label.translation_of_params", new Object[]
4565               { this.getTitle() });
4566       af.setTitle(newTitle);
4567       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4568       {
4569         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4570         viewport.openSplitFrame(af, new Alignment(seqs));
4571       }
4572       else
4573       {
4574         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4575                 DEFAULT_HEIGHT);
4576       }
4577     }
4578   }
4579
4580   /**
4581    * Set the file format
4582    *
4583    * @param format
4584    */
4585   public void setFileFormat(FileFormatI format)
4586   {
4587     this.currentFileFormat = format;
4588   }
4589
4590   /**
4591    * Try to load a features file onto the alignment.
4592    *
4593    * @param file
4594    *          contents or path to retrieve file
4595    * @param sourceType
4596    *          access mode of file (see jalview.io.AlignFile)
4597    * @return true if features file was parsed correctly.
4598    */
4599   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4600   {
4601     return avc.parseFeaturesFile(file, sourceType,
4602             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4603
4604   }
4605
4606   @Override
4607   public void refreshFeatureUI(boolean enableIfNecessary)
4608   {
4609     // note - currently this is only still here rather than in the controller
4610     // because of the featureSettings hard reference that is yet to be
4611     // abstracted
4612     if (enableIfNecessary)
4613     {
4614       viewport.setShowSequenceFeatures(true);
4615       showSeqFeatures.setSelected(true);
4616     }
4617
4618   }
4619
4620   @Override
4621   public void dragEnter(DropTargetDragEvent evt)
4622   {
4623   }
4624
4625   @Override
4626   public void dragExit(DropTargetEvent evt)
4627   {
4628   }
4629
4630   @Override
4631   public void dragOver(DropTargetDragEvent evt)
4632   {
4633   }
4634
4635   @Override
4636   public void dropActionChanged(DropTargetDragEvent evt)
4637   {
4638   }
4639
4640   @Override
4641   public void drop(DropTargetDropEvent evt)
4642   {
4643     // JAL-1552 - acceptDrop required before getTransferable call for
4644     // Java's Transferable for native dnd
4645     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4646     Transferable t = evt.getTransferable();
4647     List<String> files = new ArrayList<>();
4648     List<DataSourceType> protocols = new ArrayList<>();
4649
4650     try
4651     {
4652       Desktop.transferFromDropTarget(files, protocols, evt, t);
4653     } catch (Exception e)
4654     {
4655       e.printStackTrace();
4656     }
4657     if (files != null)
4658     {
4659       try
4660       {
4661         // check to see if any of these files have names matching sequences in
4662         // the alignment
4663         SequenceIdMatcher idm = new SequenceIdMatcher(
4664                 viewport.getAlignment().getSequencesArray());
4665         /**
4666          * Object[] { String,SequenceI}
4667          */
4668         ArrayList<Object[]> filesmatched = new ArrayList<>();
4669         ArrayList<String> filesnotmatched = new ArrayList<>();
4670         for (int i = 0; i < files.size(); i++)
4671         {
4672           String file = files.get(i).toString();
4673           String pdbfn = "";
4674           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4675           if (protocol == DataSourceType.FILE)
4676           {
4677             File fl = new File(file);
4678             pdbfn = fl.getName();
4679           }
4680           else if (protocol == DataSourceType.URL)
4681           {
4682             URL url = new URL(file);
4683             pdbfn = url.getFile();
4684           }
4685           if (pdbfn.length() > 0)
4686           {
4687             // attempt to find a match in the alignment
4688             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4689             int l = 0, c = pdbfn.indexOf(".");
4690             while (mtch == null && c != -1)
4691             {
4692               do
4693               {
4694                 l = c;
4695               } while ((c = pdbfn.indexOf(".", l)) > l);
4696               if (l > -1)
4697               {
4698                 pdbfn = pdbfn.substring(0, l);
4699               }
4700               mtch = idm.findAllIdMatches(pdbfn);
4701             }
4702             if (mtch != null)
4703             {
4704               FileFormatI type = null;
4705               try
4706               {
4707                 type = new IdentifyFile().identify(file, protocol);
4708               } catch (Exception ex)
4709               {
4710                 type = null;
4711               }
4712               if (type != null && type.isStructureFile())
4713               {
4714                 filesmatched.add(new Object[] { file, protocol, mtch });
4715                 continue;
4716               }
4717             }
4718             // File wasn't named like one of the sequences or wasn't a PDB file.
4719             filesnotmatched.add(file);
4720           }
4721         }
4722         int assocfiles = 0;
4723         if (filesmatched.size() > 0)
4724         {
4725           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4726                   || JvOptionPane.showConfirmDialog(this,
4727                           MessageManager.formatMessage(
4728                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4729                                   new Object[]
4730                                   { Integer.valueOf(filesmatched.size())
4731                                           .toString() }),
4732                           MessageManager.getString(
4733                                   "label.automatically_associate_structure_files_by_name"),
4734                           JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4735
4736           {
4737             for (Object[] fm : filesmatched)
4738             {
4739               // try and associate
4740               // TODO: may want to set a standard ID naming formalism for
4741               // associating PDB files which have no IDs.
4742               for (SequenceI toassoc : (SequenceI[]) fm[2])
4743               {
4744                 PDBEntry pe = new AssociatePdbFileWithSeq()
4745                         .associatePdbWithSeq((String) fm[0],
4746                                 (DataSourceType) fm[1], toassoc, false,
4747                                 Desktop.instance);
4748                 if (pe != null)
4749                 {
4750                   System.err.println("Associated file : " + ((String) fm[0])
4751                           + " with " + toassoc.getDisplayId(true));
4752                   assocfiles++;
4753                 }
4754               }
4755               alignPanel.paintAlignment(true);
4756             }
4757           }
4758         }
4759         if (filesnotmatched.size() > 0)
4760         {
4761           if (assocfiles > 0 && (Cache.getDefault(
4762                   "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4763                   || JvOptionPane.showConfirmDialog(this,
4764                           "<html>" + MessageManager.formatMessage(
4765                                   "label.ignore_unmatched_dropped_files_info",
4766                                   new Object[]
4767                                   { Integer.valueOf(filesnotmatched.size())
4768                                           .toString() })
4769                                   + "</html>",
4770                           MessageManager.getString(
4771                                   "label.ignore_unmatched_dropped_files"),
4772                           JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4773           {
4774             return;
4775           }
4776           for (String fn : filesnotmatched)
4777           {
4778             loadJalviewDataFile(fn, null, null, null);
4779           }
4780
4781         }
4782       } catch (Exception ex)
4783       {
4784         ex.printStackTrace();
4785       }
4786     }
4787   }
4788
4789   /**
4790    * Attempt to load a "dropped" file or URL string, by testing in turn for
4791    * <ul>
4792    * <li>an Annotation file</li>
4793    * <li>a JNet file</li>
4794    * <li>a features file</li>
4795    * <li>else try to interpret as an alignment file</li>
4796    * </ul>
4797    *
4798    * @param file
4799    *          either a filename or a URL string.
4800    * @throws InterruptedException
4801    * @throws IOException
4802    */
4803   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4804           FileFormatI format, SequenceI assocSeq)
4805   {
4806     try
4807     {
4808       if (sourceType == null)
4809       {
4810         sourceType = FormatAdapter.checkProtocol(file);
4811       }
4812       // if the file isn't identified, or not positively identified as some
4813       // other filetype (PFAM is default unidentified alignment file type) then
4814       // try to parse as annotation.
4815       boolean isAnnotation = (format == null
4816               || FileFormat.Pfam.equals(format))
4817                       ? new AnnotationFile().annotateAlignmentView(viewport,
4818                               file, sourceType)
4819                       : false;
4820
4821       if (!isAnnotation)
4822       {
4823         // first see if its a T-COFFEE score file
4824         TCoffeeScoreFile tcf = null;
4825         try
4826         {
4827           tcf = new TCoffeeScoreFile(file, sourceType);
4828           if (tcf.isValid())
4829           {
4830             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4831             {
4832               buildColourMenu();
4833               changeColour(
4834                       new TCoffeeColourScheme(viewport.getAlignment()));
4835               isAnnotation = true;
4836               statusBar.setText(MessageManager.getString(
4837                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4838             }
4839             else
4840             {
4841               // some problem - if no warning its probable that the ID matching
4842               // process didn't work
4843               JvOptionPane.showMessageDialog(Desktop.desktop,
4844                       tcf.getWarningMessage() == null
4845                               ? MessageManager.getString(
4846                                       "label.check_file_matches_sequence_ids_alignment")
4847                               : tcf.getWarningMessage(),
4848                       MessageManager.getString(
4849                               "label.problem_reading_tcoffee_score_file"),
4850                       JvOptionPane.WARNING_MESSAGE);
4851             }
4852           }
4853           else
4854           {
4855             tcf = null;
4856           }
4857         } catch (Exception x)
4858         {
4859           Cache.log.debug(
4860                   "Exception when processing data source as T-COFFEE score file",
4861                   x);
4862           tcf = null;
4863         }
4864         if (tcf == null)
4865         {
4866           // try to see if its a JNet 'concise' style annotation file *before*
4867           // we
4868           // try to parse it as a features file
4869           if (format == null)
4870           {
4871             format = new IdentifyFile().identify(file, sourceType);
4872           }
4873           if (FileFormat.ScoreMatrix == format)
4874           {
4875             ScoreMatrixFile sm = new ScoreMatrixFile(
4876                     new FileParse(file, sourceType));
4877             sm.parse();
4878             // todo: i18n this message
4879             statusBar.setText(MessageManager.formatMessage(
4880                     "label.successfully_loaded_matrix",
4881                     sm.getMatrixName()));
4882           }
4883           else if (FileFormat.Jnet.equals(format))
4884           {
4885             JPredFile predictions = new JPredFile(file, sourceType);
4886             new JnetAnnotationMaker();
4887             JnetAnnotationMaker.add_annotation(predictions,
4888                     viewport.getAlignment(), 0, false);
4889             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4890             viewport.getAlignment().setSeqrep(repseq);
4891             HiddenColumns cs = new HiddenColumns();
4892             cs.hideInsertionsFor(repseq);
4893             viewport.getAlignment().setHiddenColumns(cs);
4894             isAnnotation = true;
4895           }
4896           // else if (IdentifyFile.FeaturesFile.equals(format))
4897           else if (FileFormat.Features.equals(format))
4898           {
4899             if (parseFeaturesFile(file, sourceType))
4900             {
4901               alignPanel.paintAlignment(true);
4902             }
4903           }
4904           else
4905           {
4906             new FileLoader().LoadFile(viewport, file, sourceType, format);
4907           }
4908         }
4909       }
4910       if (isAnnotation)
4911       {
4912         alignPanel.adjustAnnotationHeight();
4913         viewport.updateSequenceIdColours();
4914         buildSortByAnnotationScoresMenu();
4915         alignPanel.paintAlignment(true);
4916       }
4917     } catch (Exception ex)
4918     {
4919       ex.printStackTrace();
4920     } catch (OutOfMemoryError oom)
4921     {
4922       try
4923       {
4924         System.gc();
4925       } catch (Exception x)
4926       {
4927       }
4928       new OOMWarning(
4929               "loading data "
4930                       + (sourceType != null
4931                               ? (sourceType == DataSourceType.PASTE
4932                                       ? "from clipboard."
4933                                       : "using " + sourceType + " from "
4934                                               + file)
4935                               : ".")
4936                       + (format != null
4937                               ? "(parsing as '" + format + "' file)"
4938                               : ""),
4939               oom, Desktop.desktop);
4940     }
4941   }
4942
4943   /**
4944    * Method invoked by the ChangeListener on the tabbed pane, in other words
4945    * when a different tabbed pane is selected by the user or programmatically.
4946    */
4947   @Override
4948   public void tabSelectionChanged(int index)
4949   {
4950     if (index > -1)
4951     {
4952       alignPanel = alignPanels.get(index);
4953       viewport = alignPanel.av;
4954       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4955       setMenusFromViewport(viewport);
4956     }
4957
4958     /*
4959      * 'focus' any colour slider that is open to the selected viewport
4960      */
4961     if (viewport.getConservationSelected())
4962     {
4963       SliderPanel.setConservationSlider(alignPanel,
4964               viewport.getResidueShading(), alignPanel.getViewName());
4965     }
4966     else
4967     {
4968       SliderPanel.hideConservationSlider();
4969     }
4970     if (viewport.getAbovePIDThreshold())
4971     {
4972       SliderPanel.setPIDSliderSource(alignPanel,
4973               viewport.getResidueShading(), alignPanel.getViewName());
4974     }
4975     else
4976     {
4977       SliderPanel.hidePIDSlider();
4978     }
4979
4980     /*
4981      * If there is a frame linked to this one in a SplitPane, switch it to the
4982      * same view tab index. No infinite recursion of calls should happen, since
4983      * tabSelectionChanged() should not get invoked on setting the selected
4984      * index to an unchanged value. Guard against setting an invalid index
4985      * before the new view peer tab has been created.
4986      */
4987     final AlignViewportI peer = viewport.getCodingComplement();
4988     if (peer != null)
4989     {
4990       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4991               .getAlignPanel().alignFrame;
4992       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4993       {
4994         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4995       }
4996     }
4997   }
4998
4999   /**
5000    * On right mouse click on view tab, prompt for and set new view name.
5001    */
5002   @Override
5003   public void tabbedPane_mousePressed(MouseEvent e)
5004   {
5005     if (e.isPopupTrigger())
5006     {
5007       String msg = MessageManager.getString("label.enter_view_name");
5008       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5009               JvOptionPane.QUESTION_MESSAGE);
5010
5011       if (reply != null)
5012       {
5013         viewport.viewName = reply;
5014         // TODO warn if reply is in getExistingViewNames()?
5015         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5016       }
5017     }
5018   }
5019
5020   public AlignViewport getCurrentView()
5021   {
5022     return viewport;
5023   }
5024
5025   /**
5026    * Open the dialog for regex description parsing.
5027    */
5028   @Override
5029   protected void extractScores_actionPerformed(ActionEvent e)
5030   {
5031     ParseProperties pp = new jalview.analysis.ParseProperties(
5032             viewport.getAlignment());
5033     // TODO: verify regex and introduce GUI dialog for version 2.5
5034     // if (pp.getScoresFromDescription("col", "score column ",
5035     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5036     // true)>0)
5037     if (pp.getScoresFromDescription("description column",
5038             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5039     {
5040       buildSortByAnnotationScoresMenu();
5041     }
5042   }
5043
5044   /*
5045    * (non-Javadoc)
5046    *
5047    * @see
5048    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5049    * )
5050    */
5051   @Override
5052   protected void showDbRefs_actionPerformed(ActionEvent e)
5053   {
5054     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5055   }
5056
5057   /*
5058    * (non-Javadoc)
5059    *
5060    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5061    * ActionEvent)
5062    */
5063   @Override
5064   protected void showNpFeats_actionPerformed(ActionEvent e)
5065   {
5066     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5067   }
5068
5069   /**
5070    * find the viewport amongst the tabs in this alignment frame and close that
5071    * tab
5072    *
5073    * @param av
5074    */
5075   public boolean closeView(AlignViewportI av)
5076   {
5077     if (viewport == av)
5078     {
5079       this.closeMenuItem_actionPerformed(false);
5080       return true;
5081     }
5082     Component[] comp = tabbedPane.getComponents();
5083     for (int i = 0; comp != null && i < comp.length; i++)
5084     {
5085       if (comp[i] instanceof AlignmentPanel)
5086       {
5087         if (((AlignmentPanel) comp[i]).av == av)
5088         {
5089           // close the view.
5090           closeView((AlignmentPanel) comp[i]);
5091           return true;
5092         }
5093       }
5094     }
5095     return false;
5096   }
5097
5098   protected void build_fetchdbmenu(JMenu webService)
5099   {
5100     // Temporary hack - DBRef Fetcher always top level ws entry.
5101     // TODO We probably want to store a sequence database checklist in
5102     // preferences and have checkboxes.. rather than individual sources selected
5103     // here
5104     final JMenu rfetch = new JMenu(
5105             MessageManager.getString("action.fetch_db_references"));
5106     rfetch.setToolTipText(MessageManager.getString(
5107             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5108     webService.add(rfetch);
5109
5110     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5111             MessageManager.getString("option.trim_retrieved_seqs"));
5112     trimrs.setToolTipText(
5113             MessageManager.getString("label.trim_retrieved_sequences"));
5114     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5115     trimrs.addActionListener(new ActionListener()
5116     {
5117       @Override
5118       public void actionPerformed(ActionEvent e)
5119       {
5120         trimrs.setSelected(trimrs.isSelected());
5121         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5122                 Boolean.valueOf(trimrs.isSelected()).toString());
5123       };
5124     });
5125     rfetch.add(trimrs);
5126     JMenuItem fetchr = new JMenuItem(
5127             MessageManager.getString("label.standard_databases"));
5128     fetchr.setToolTipText(
5129             MessageManager.getString("label.fetch_embl_uniprot"));
5130     fetchr.addActionListener(new ActionListener()
5131     {
5132
5133       @Override
5134       public void actionPerformed(ActionEvent e)
5135       {
5136         new Thread(new Runnable()
5137         {
5138           @Override
5139           public void run()
5140           {
5141             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5142                     .getAlignment().isNucleotide();
5143             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5144                     alignPanel.av.getSequenceSelection(),
5145                     alignPanel.alignFrame, null,
5146                     alignPanel.alignFrame.featureSettings, isNucleotide);
5147             dbRefFetcher.addListener(new FetchFinishedListenerI()
5148             {
5149               @Override
5150               public void finished()
5151               {
5152                 AlignFrame.this.setMenusForViewport();
5153               }
5154             });
5155             dbRefFetcher.fetchDBRefs(false);
5156           }
5157         }).start();
5158
5159       }
5160
5161     });
5162     rfetch.add(fetchr);
5163     final AlignFrame me = this;
5164     new Thread(new Runnable()
5165     {
5166       @Override
5167       public void run()
5168       {
5169         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5170                 .getSequenceFetcherSingleton(me);
5171         javax.swing.SwingUtilities.invokeLater(new Runnable()
5172         {
5173           @Override
5174           public void run()
5175           {
5176             String[] dbclasses = sf.getOrderedSupportedSources();
5177             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5178             // jalview.util.QuickSort.sort(otherdb, otherdb);
5179             List<DbSourceProxy> otherdb;
5180             JMenu dfetch = new JMenu();
5181             JMenu ifetch = new JMenu();
5182             JMenuItem fetchr = null;
5183             int comp = 0, icomp = 0, mcomp = 15;
5184             String mname = null;
5185             int dbi = 0;
5186             for (String dbclass : dbclasses)
5187             {
5188               otherdb = sf.getSourceProxy(dbclass);
5189               // add a single entry for this class, or submenu allowing 'fetch
5190               // all' or pick one
5191               if (otherdb == null || otherdb.size() < 1)
5192               {
5193                 continue;
5194               }
5195               // List<DbSourceProxy> dbs=otherdb;
5196               // otherdb=new ArrayList<DbSourceProxy>();
5197               // for (DbSourceProxy db:dbs)
5198               // {
5199               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5200               // }
5201               if (mname == null)
5202               {
5203                 mname = "From " + dbclass;
5204               }
5205               if (otherdb.size() == 1)
5206               {
5207                 final DbSourceProxy[] dassource = otherdb
5208                         .toArray(new DbSourceProxy[0]);
5209                 DbSourceProxy src = otherdb.get(0);
5210                 fetchr = new JMenuItem(src.getDbSource());
5211                 fetchr.addActionListener(new ActionListener()
5212                 {
5213
5214                   @Override
5215                   public void actionPerformed(ActionEvent e)
5216                   {
5217                     new Thread(new Runnable()
5218                     {
5219
5220                       @Override
5221                       public void run()
5222                       {
5223                         boolean isNucleotide = alignPanel.alignFrame
5224                                 .getViewport().getAlignment()
5225                                 .isNucleotide();
5226                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5227                                 alignPanel.av.getSequenceSelection(),
5228                                 alignPanel.alignFrame, dassource,
5229                                 alignPanel.alignFrame.featureSettings,
5230                                 isNucleotide);
5231                         dbRefFetcher
5232                                 .addListener(new FetchFinishedListenerI()
5233                                 {
5234                                   @Override
5235                                   public void finished()
5236                                   {
5237                                     AlignFrame.this.setMenusForViewport();
5238                                   }
5239                                 });
5240                         dbRefFetcher.fetchDBRefs(false);
5241                       }
5242                     }).start();
5243                   }
5244
5245                 });
5246                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5247                         MessageManager.formatMessage(
5248                                 "label.fetch_retrieve_from", new Object[]
5249                                 { src.getDbName() })));
5250                 dfetch.add(fetchr);
5251                 comp++;
5252               }
5253               else
5254               {
5255                 final DbSourceProxy[] dassource = otherdb
5256                         .toArray(new DbSourceProxy[0]);
5257                 // fetch all entry
5258                 DbSourceProxy src = otherdb.get(0);
5259                 fetchr = new JMenuItem(MessageManager
5260                         .formatMessage("label.fetch_all_param", new Object[]
5261                         { src.getDbSource() }));
5262                 fetchr.addActionListener(new ActionListener()
5263                 {
5264                   @Override
5265                   public void actionPerformed(ActionEvent e)
5266                   {
5267                     new Thread(new Runnable()
5268                     {
5269
5270                       @Override
5271                       public void run()
5272                       {
5273                         boolean isNucleotide = alignPanel.alignFrame
5274                                 .getViewport().getAlignment()
5275                                 .isNucleotide();
5276                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5277                                 alignPanel.av.getSequenceSelection(),
5278                                 alignPanel.alignFrame, dassource,
5279                                 alignPanel.alignFrame.featureSettings,
5280                                 isNucleotide);
5281                         dbRefFetcher
5282                                 .addListener(new FetchFinishedListenerI()
5283                                 {
5284                                   @Override
5285                                   public void finished()
5286                                   {
5287                                     AlignFrame.this.setMenusForViewport();
5288                                   }
5289                                 });
5290                         dbRefFetcher.fetchDBRefs(false);
5291                       }
5292                     }).start();
5293                   }
5294                 });
5295
5296                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5297                         MessageManager.formatMessage(
5298                                 "label.fetch_retrieve_from_all_sources",
5299                                 new Object[]
5300                                 { Integer.valueOf(otherdb.size())
5301                                         .toString(),
5302                                     src.getDbSource(), src.getDbName() })));
5303                 dfetch.add(fetchr);
5304                 comp++;
5305                 // and then build the rest of the individual menus
5306                 ifetch = new JMenu(MessageManager.formatMessage(
5307                         "label.source_from_db_source", new Object[]
5308                         { src.getDbSource() }));
5309                 icomp = 0;
5310                 String imname = null;
5311                 int i = 0;
5312                 for (DbSourceProxy sproxy : otherdb)
5313                 {
5314                   String dbname = sproxy.getDbName();
5315                   String sname = dbname.length() > 5
5316                           ? dbname.substring(0, 5) + "..."
5317                           : dbname;
5318                   String msname = dbname.length() > 10
5319                           ? dbname.substring(0, 10) + "..."
5320                           : dbname;
5321                   if (imname == null)
5322                   {
5323                     imname = MessageManager
5324                             .formatMessage("label.from_msname", new Object[]
5325                             { sname });
5326                   }
5327                   fetchr = new JMenuItem(msname);
5328                   final DbSourceProxy[] dassrc = { sproxy };
5329                   fetchr.addActionListener(new ActionListener()
5330                   {
5331
5332                     @Override
5333                     public void actionPerformed(ActionEvent e)
5334                     {
5335                       new Thread(new Runnable()
5336                       {
5337
5338                         @Override
5339                         public void run()
5340                         {
5341                           boolean isNucleotide = alignPanel.alignFrame
5342                                   .getViewport().getAlignment()
5343                                   .isNucleotide();
5344                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5345                                   alignPanel.av.getSequenceSelection(),
5346                                   alignPanel.alignFrame, dassrc,
5347                                   alignPanel.alignFrame.featureSettings,
5348                                   isNucleotide);
5349                           dbRefFetcher
5350                                   .addListener(new FetchFinishedListenerI()
5351                                   {
5352                                     @Override
5353                                     public void finished()
5354                                     {
5355                                       AlignFrame.this.setMenusForViewport();
5356                                     }
5357                                   });
5358                           dbRefFetcher.fetchDBRefs(false);
5359                         }
5360                       }).start();
5361                     }
5362
5363                   });
5364                   fetchr.setToolTipText(
5365                           "<html>" + MessageManager.formatMessage(
5366                                   "label.fetch_retrieve_from", new Object[]
5367                                   { dbname }));
5368                   ifetch.add(fetchr);
5369                   ++i;
5370                   if (++icomp >= mcomp || i == (otherdb.size()))
5371                   {
5372                     ifetch.setText(MessageManager.formatMessage(
5373                             "label.source_to_target", imname, sname));
5374                     dfetch.add(ifetch);
5375                     ifetch = new JMenu();
5376                     imname = null;
5377                     icomp = 0;
5378                     comp++;
5379                   }
5380                 }
5381               }
5382               ++dbi;
5383               if (comp >= mcomp || dbi >= (dbclasses.length))
5384               {
5385                 dfetch.setText(MessageManager.formatMessage(
5386                         "label.source_to_target", mname, dbclass));
5387                 rfetch.add(dfetch);
5388                 dfetch = new JMenu();
5389                 mname = null;
5390                 comp = 0;
5391               }
5392             }
5393           }
5394         });
5395       }
5396     }).start();
5397
5398   }
5399
5400   /**
5401    * Left justify the whole alignment.
5402    */
5403   @Override
5404   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5405   {
5406     AlignmentI al = viewport.getAlignment();
5407     al.justify(false);
5408     viewport.firePropertyChange("alignment", null, al);
5409   }
5410
5411   /**
5412    * Right justify the whole alignment.
5413    */
5414   @Override
5415   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5416   {
5417     AlignmentI al = viewport.getAlignment();
5418     al.justify(true);
5419     viewport.firePropertyChange("alignment", null, al);
5420   }
5421
5422   @Override
5423   public void setShowSeqFeatures(boolean b)
5424   {
5425     showSeqFeatures.setSelected(b);
5426     viewport.setShowSequenceFeatures(b);
5427   }
5428
5429   /*
5430    * (non-Javadoc)
5431    *
5432    * @see
5433    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5434    * awt.event.ActionEvent)
5435    */
5436   @Override
5437   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5438   {
5439     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5440     alignPanel.paintAlignment(true);
5441   }
5442
5443   /*
5444    * (non-Javadoc)
5445    *
5446    * @see
5447    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5448    * .ActionEvent)
5449    */
5450   @Override
5451   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5452   {
5453     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5454     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5455
5456   }
5457
5458   /*
5459    * (non-Javadoc)
5460    *
5461    * @see
5462    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5463    * .event.ActionEvent)
5464    */
5465   @Override
5466   protected void showGroupConservation_actionPerformed(ActionEvent e)
5467   {
5468     viewport.setShowGroupConservation(showGroupConservation.getState());
5469     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5470   }
5471
5472   /*
5473    * (non-Javadoc)
5474    *
5475    * @see
5476    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5477    * .event.ActionEvent)
5478    */
5479   @Override
5480   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5481   {
5482     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5483     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5484   }
5485
5486   /*
5487    * (non-Javadoc)
5488    *
5489    * @see
5490    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5491    * .event.ActionEvent)
5492    */
5493   @Override
5494   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5495   {
5496     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5497     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5498   }
5499
5500   @Override
5501   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5502   {
5503     showSequenceLogo.setState(true);
5504     viewport.setShowSequenceLogo(true);
5505     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5506     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5507   }
5508
5509   @Override
5510   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5511   {
5512     viewport.setShowInformationHistogram(
5513             showInformationHistogram.getState());
5514     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5515   }
5516
5517   @Override
5518   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5519   {
5520     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5521     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5522   }
5523
5524   @Override
5525   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5526   {
5527     showHMMSequenceLogo.setState(true);
5528     viewport.setShowHMMSequenceLogo(true);
5529     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5530     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5531   }
5532
5533   @Override
5534   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5535   {
5536     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5537   }
5538
5539   /*
5540    * (non-Javadoc)
5541    *
5542    * @see
5543    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5544    * .event.ActionEvent)
5545    */
5546   @Override
5547   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5548   {
5549     if (avc.makeGroupsFromSelection())
5550     {
5551       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5552       alignPanel.updateAnnotation();
5553       alignPanel.paintAlignment(true);
5554     }
5555   }
5556
5557   public void clearAlignmentSeqRep()
5558   {
5559     // TODO refactor alignmentseqrep to controller
5560     if (viewport.getAlignment().hasSeqrep())
5561     {
5562       viewport.getAlignment().setSeqrep(null);
5563       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5564       alignPanel.updateAnnotation();
5565       alignPanel.paintAlignment(true);
5566     }
5567   }
5568
5569   @Override
5570   protected void createGroup_actionPerformed(ActionEvent e)
5571   {
5572     if (avc.createGroup())
5573     {
5574       alignPanel.alignmentChanged();
5575     }
5576   }
5577
5578   @Override
5579   protected void unGroup_actionPerformed(ActionEvent e)
5580   {
5581     if (avc.unGroup())
5582     {
5583       alignPanel.alignmentChanged();
5584     }
5585   }
5586
5587   /**
5588    * make the given alignmentPanel the currently selected tab
5589    *
5590    * @param alignmentPanel
5591    */
5592   public void setDisplayedView(AlignmentPanel alignmentPanel)
5593   {
5594     if (!viewport.getSequenceSetId()
5595             .equals(alignmentPanel.av.getSequenceSetId()))
5596     {
5597       throw new Error(MessageManager.getString(
5598               "error.implementation_error_cannot_show_view_alignment_frame"));
5599     }
5600     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5601             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5602     {
5603       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5604     }
5605   }
5606
5607   /**
5608    * Action on selection of menu options to Show or Hide annotations.
5609    *
5610    * @param visible
5611    * @param forSequences
5612    *          update sequence-related annotations
5613    * @param forAlignment
5614    *          update non-sequence-related annotations
5615    */
5616   @Override
5617   protected void setAnnotationsVisibility(boolean visible,
5618           boolean forSequences, boolean forAlignment)
5619   {
5620     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5621             .getAlignmentAnnotation();
5622     if (anns == null)
5623     {
5624       return;
5625     }
5626     for (AlignmentAnnotation aa : anns)
5627     {
5628       /*
5629        * don't display non-positional annotations on an alignment
5630        */
5631       if (aa.annotations == null)
5632       {
5633         continue;
5634       }
5635       boolean apply = (aa.sequenceRef == null && forAlignment)
5636               || (aa.sequenceRef != null && forSequences);
5637       if (apply)
5638       {
5639         aa.visible = visible;
5640       }
5641     }
5642     alignPanel.validateAnnotationDimensions(true);
5643     alignPanel.alignmentChanged();
5644   }
5645
5646   /**
5647    * Store selected annotation sort order for the view and repaint.
5648    */
5649   @Override
5650   protected void sortAnnotations_actionPerformed()
5651   {
5652     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5653     this.alignPanel.av
5654             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5655     alignPanel.paintAlignment(true);
5656   }
5657
5658   /**
5659    *
5660    * @return alignment panels in this alignment frame
5661    */
5662   public List<? extends AlignmentViewPanel> getAlignPanels()
5663   {
5664     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5665   }
5666
5667   /**
5668    * Open a new alignment window, with the cDNA associated with this (protein)
5669    * alignment, aligned as is the protein.
5670    */
5671   protected void viewAsCdna_actionPerformed()
5672   {
5673     // TODO no longer a menu action - refactor as required
5674     final AlignmentI alignment = getViewport().getAlignment();
5675     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5676     if (mappings == null)
5677     {
5678       return;
5679     }
5680     List<SequenceI> cdnaSeqs = new ArrayList<>();
5681     for (SequenceI aaSeq : alignment.getSequences())
5682     {
5683       for (AlignedCodonFrame acf : mappings)
5684       {
5685         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5686         if (dnaSeq != null)
5687         {
5688           /*
5689            * There is a cDNA mapping for this protein sequence - add to new
5690            * alignment. It will share the same dataset sequence as other mapped
5691            * cDNA (no new mappings need to be created).
5692            */
5693           final Sequence newSeq = new Sequence(dnaSeq);
5694           newSeq.setDatasetSequence(dnaSeq);
5695           cdnaSeqs.add(newSeq);
5696         }
5697       }
5698     }
5699     if (cdnaSeqs.size() == 0)
5700     {
5701       // show a warning dialog no mapped cDNA
5702       return;
5703     }
5704     AlignmentI cdna = new Alignment(
5705             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5706     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5707             AlignFrame.DEFAULT_HEIGHT);
5708     cdna.alignAs(alignment);
5709     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5710             + this.title;
5711     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5712             AlignFrame.DEFAULT_HEIGHT);
5713   }
5714
5715   /**
5716    * Set visibility of dna/protein complement view (available when shown in a
5717    * split frame).
5718    *
5719    * @param show
5720    */
5721   @Override
5722   protected void showComplement_actionPerformed(boolean show)
5723   {
5724     SplitContainerI sf = getSplitViewContainer();
5725     if (sf != null)
5726     {
5727       sf.setComplementVisible(this, show);
5728     }
5729   }
5730
5731   /**
5732    * Generate the reverse (optionally complemented) of the selected sequences,
5733    * and add them to the alignment
5734    */
5735   @Override
5736   protected void showReverse_actionPerformed(boolean complement)
5737   {
5738     AlignmentI al = null;
5739     try
5740     {
5741       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5742       al = dna.reverseCdna(complement);
5743       viewport.addAlignment(al, "");
5744       addHistoryItem(new EditCommand(
5745               MessageManager.getString("label.add_sequences"), Action.PASTE,
5746               al.getSequencesArray(), 0, al.getWidth(),
5747               viewport.getAlignment()));
5748     } catch (Exception ex)
5749     {
5750       System.err.println(ex.getMessage());
5751       return;
5752     }
5753   }
5754
5755   /**
5756    * Try to run a script in the Groovy console, having first ensured that this
5757    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5758    * be targeted at this alignment.
5759    */
5760   @Override
5761   protected void runGroovy_actionPerformed()
5762   {
5763     Jalview.setCurrentAlignFrame(this);
5764     groovy.ui.Console console = Desktop.getGroovyConsole();
5765     if (console != null)
5766     {
5767       try
5768       {
5769         console.runScript();
5770       } catch (Exception ex)
5771       {
5772         System.err.println((ex.toString()));
5773         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5774                 MessageManager.getString("label.couldnt_run_groovy_script"),
5775                 MessageManager.getString("label.groovy_support_failed"),
5776                 JvOptionPane.ERROR_MESSAGE);
5777       }
5778     }
5779     else
5780     {
5781       System.err.println("Can't run Groovy script as console not found");
5782     }
5783   }
5784
5785   /**
5786    * Hides columns containing (or not containing) a specified feature, provided
5787    * that would not leave all columns hidden
5788    *
5789    * @param featureType
5790    * @param columnsContaining
5791    * @return
5792    */
5793   public boolean hideFeatureColumns(String featureType,
5794           boolean columnsContaining)
5795   {
5796     boolean notForHiding = avc.markColumnsContainingFeatures(
5797             columnsContaining, false, false, featureType);
5798     if (notForHiding)
5799     {
5800       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5801               false, featureType))
5802       {
5803         getViewport().hideSelectedColumns();
5804         return true;
5805       }
5806     }
5807     return false;
5808   }
5809
5810   @Override
5811   protected void selectHighlightedColumns_actionPerformed(
5812           ActionEvent actionEvent)
5813   {
5814     // include key modifier check in case user selects from menu
5815     avc.markHighlightedColumns(
5816             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5817             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5818                     | ActionEvent.CTRL_MASK)) != 0);
5819   }
5820
5821   /**
5822    * Rebuilds the Colour menu, including any user-defined colours which have
5823    * been loaded either on startup or during the session
5824    */
5825   public void buildColourMenu()
5826   {
5827     colourMenu.removeAll();
5828
5829     colourMenu.add(applyToAllGroups);
5830     colourMenu.add(textColour);
5831     colourMenu.addSeparator();
5832
5833     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5834             false);
5835
5836     colourMenu.addSeparator();
5837     colourMenu.add(conservationMenuItem);
5838     colourMenu.add(modifyConservation);
5839     colourMenu.add(abovePIDThreshold);
5840     colourMenu.add(modifyPID);
5841     colourMenu.add(annotationColour);
5842
5843     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5844     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5845   }
5846
5847   /**
5848    * Open a dialog (if not already open) that allows the user to select and
5849    * calculate PCA or Tree analysis
5850    */
5851   protected void openTreePcaDialog()
5852   {
5853     if (alignPanel.getCalculationDialog() == null)
5854     {
5855       new CalculationChooser(AlignFrame.this);
5856     }
5857   }
5858
5859   /**
5860    * Sets the status of the HMMER menu
5861    *
5862    * @param status
5863    */
5864   public void updateHMMERStatus(boolean status)
5865   {
5866     hmmerMenu.setEnabled(status);
5867   }
5868
5869   /**
5870    * Returns the selected hidden Markov model.
5871    *
5872    * @return
5873    */
5874   public HiddenMarkovModel getSelectedHMM()
5875   {
5876     if (selectedHMMSequence == null)
5877     {
5878       return null;
5879     }
5880     return selectedHMMSequence.getHMM();
5881   }
5882
5883   /**
5884    * Returns the selected hidden Markov model.
5885    *
5886    * @return
5887    */
5888   public SequenceI getSelectedHMMSequence()
5889   {
5890     return selectedHMMSequence;
5891   }
5892
5893   /**
5894    * Sets the selected hidden Markov model
5895    *
5896    * @param selectedHMM
5897    */
5898   public void setSelectedHMMSequence(SequenceI selectedHMM)
5899   {
5900     this.selectedHMMSequence = selectedHMM;
5901     hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5902             + selectedHMM.getHMM().getName());
5903     hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5904             + selectedHMM.getHMM().getName());
5905   }
5906
5907   @Override
5908   public void hmmerMenu_actionPerformed(ActionEvent e)
5909   {
5910     SequenceGroup grp = getViewport().getSelectionGroup();
5911     if (grp != null)
5912     {
5913       hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5914               + grp.getName());
5915     }
5916     else
5917     {
5918       hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5919               + " from Alignment");
5920     }
5921   }
5922
5923 }
5924
5925 class PrintThread extends Thread
5926 {
5927   AlignmentPanel ap;
5928
5929   public PrintThread(AlignmentPanel ap)
5930   {
5931     this.ap = ap;
5932   }
5933
5934   static PageFormat pf;
5935
5936   @Override
5937   public void run()
5938   {
5939     PrinterJob printJob = PrinterJob.getPrinterJob();
5940
5941     if (pf != null)
5942     {
5943       printJob.setPrintable(ap, pf);
5944     }
5945     else
5946     {
5947       printJob.setPrintable(ap);
5948     }
5949
5950     if (printJob.printDialog())
5951     {
5952       try
5953       {
5954         printJob.print();
5955       } catch (Exception PrintException)
5956       {
5957         PrintException.printStackTrace();
5958       }
5959     }
5960   }
5961 }