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.GeneticCodeI;
  28 import jalview.analysis.ParseProperties;
  29 import jalview.analysis.SequenceIdMatcher;
  30 import jalview.api.AlignExportSettingI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.FeatureSettingsModelI;
  37 import jalview.api.SplitContainerI;
  38 import jalview.api.ViewStyleI;
  39 import jalview.api.analysis.SimilarityParamsI;
  40 import jalview.bin.Cache;
  41 import jalview.bin.Jalview;
  42 import jalview.commands.CommandI;
  43 import jalview.commands.EditCommand;
  44 import jalview.commands.EditCommand.Action;
  45 import jalview.commands.OrderCommand;
  46 import jalview.commands.RemoveGapColCommand;
  47 import jalview.commands.RemoveGapsCommand;
  48 import jalview.commands.SlideSequencesCommand;
  49 import jalview.commands.TrimRegionCommand;
  50 import jalview.datamodel.AlignedCodonFrame;
  51 import jalview.datamodel.Alignment;
  52 import jalview.datamodel.AlignmentAnnotation;
  53 import jalview.datamodel.AlignmentExportData;
  54 import jalview.datamodel.AlignmentI;
  55 import jalview.datamodel.AlignmentOrder;
  56 import jalview.datamodel.AlignmentView;
  57 import jalview.datamodel.ColumnSelection;
  58 import jalview.datamodel.HiddenColumns;
  59 import jalview.datamodel.HiddenSequences;
  60 import jalview.datamodel.PDBEntry;
  61 import jalview.datamodel.SeqCigar;
  62 import jalview.datamodel.Sequence;
  63 import jalview.datamodel.SequenceGroup;
  64 import jalview.datamodel.SequenceI;
  65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  67 import jalview.hmmer.HMMAlign;
  68 import jalview.hmmer.HMMBuild;
  69 import jalview.hmmer.HMMERParamStore;
  70 import jalview.hmmer.HMMERPreset;
  71 import jalview.hmmer.HMMSearch;
  72 import jalview.hmmer.HmmerCommand;
  73 import jalview.hmmer.JackHMMER;
  74 import jalview.io.AlignmentProperties;
  75 import jalview.io.AnnotationFile;
  76 import jalview.io.BackupFiles;
  77 import jalview.io.BioJsHTMLOutput;
  78 import jalview.io.DataSourceType;
  79 import jalview.io.FileFormat;
  80 import jalview.io.FileFormatI;
  81 import jalview.io.FileFormats;
  82 import jalview.io.FileLoader;
  83 import jalview.io.FileParse;
  84 import jalview.io.FormatAdapter;
  85 import jalview.io.HtmlSvgOutput;
  86 import jalview.io.IdentifyFile;
  87 import jalview.io.JPredFile;
  88 import jalview.io.JalviewFileChooser;
  89 import jalview.io.JalviewFileView;
  90 import jalview.io.JnetAnnotationMaker;
  91 import jalview.io.NewickFile;
  92 import jalview.io.ScoreMatrixFile;
  93 import jalview.io.TCoffeeScoreFile;
  94 import jalview.io.vcf.VCFLoader;
  95 import jalview.jbgui.GAlignFrame;
  96 import jalview.schemes.ColourSchemeI;
  97 import jalview.schemes.ColourSchemes;
  98 import jalview.schemes.ResidueColourScheme;
  99 import jalview.schemes.TCoffeeColourScheme;
 100 import jalview.util.MessageManager;
 101 import jalview.viewmodel.AlignmentViewport;
 102 import jalview.viewmodel.ViewportRanges;
 103 import jalview.ws.DBRefFetcher;
 104 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 105 import jalview.ws.jws1.Discoverer;
 106 import jalview.ws.jws2.Jws2Discoverer;
 107 import jalview.ws.jws2.jabaws2.Jws2Instance;
 108 import jalview.ws.params.ArgumentI;
 109 import jalview.ws.params.ParamDatastoreI;
 110 import jalview.ws.params.WsParamSetI;
 111 import jalview.ws.seqfetcher.DbSourceProxy;
 112
 113 import java.awt.BorderLayout;
 114 import java.awt.Component;
 115 import java.awt.Rectangle;
 116 import java.awt.Toolkit;
 117 import java.awt.datatransfer.Clipboard;
 118 import java.awt.datatransfer.DataFlavor;
 119 import java.awt.datatransfer.StringSelection;
 120 import java.awt.datatransfer.Transferable;
 121 import java.awt.dnd.DnDConstants;
 122 import java.awt.dnd.DropTargetDragEvent;
 123 import java.awt.dnd.DropTargetDropEvent;
 124 import java.awt.dnd.DropTargetEvent;
 125 import java.awt.dnd.DropTargetListener;
 126 import java.awt.event.ActionEvent;
 127 import java.awt.event.ActionListener;
 128 import java.awt.event.FocusAdapter;
 129 import java.awt.event.FocusEvent;
 130 import java.awt.event.ItemEvent;
 131 import java.awt.event.ItemListener;
 132 import java.awt.event.KeyAdapter;
 133 import java.awt.event.KeyEvent;
 134 import java.awt.event.MouseEvent;
 135 import java.awt.print.PageFormat;
 136 import java.awt.print.PrinterJob;
 137 import java.beans.PropertyChangeEvent;
 138 import java.io.File;
 139 import java.io.FileWriter;
 140 import java.io.IOException;
 141 import java.io.PrintWriter;
 142 import java.net.URL;
 143 import java.util.ArrayList;
 144 import java.util.Arrays;
 145 import java.util.Deque;
 146 import java.util.HashSet;
 147 import java.util.List;
 148 import java.util.Set;
 149 import java.util.Vector;
 150
 151 import javax.swing.ButtonGroup;
 152 import javax.swing.JCheckBoxMenuItem;
 153 import javax.swing.JEditorPane;
 154 import javax.swing.JFileChooser;
 155 import javax.swing.JInternalFrame;
 156 import javax.swing.JLayeredPane;
 157 import javax.swing.JMenu;
 158 import javax.swing.JMenuItem;
 159 import javax.swing.JOptionPane;
 160 import javax.swing.JScrollPane;
 161 import javax.swing.SwingUtilities;
 162
 163 /**
 164  * DOCUMENT ME!
 165  *
 166  * @author $author$
 167  * @version $Revision$
 168  */
 169 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 170         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 171 {
 172   public static final int DEFAULT_WIDTH = 700;
 173
 174   public static final int DEFAULT_HEIGHT = 500;
 175
 176   /*
 177    * The currently displayed panel (selected tabbed view if more than one)
 178    */
 179   public AlignmentPanel alignPanel;
 180
 181   AlignViewport viewport;
 182
 183   public AlignViewControllerI avc;
 184
 185   List<AlignmentPanel> alignPanels = new ArrayList<>();
 186
 187   /**
 188    * Last format used to load or save alignments in this window
 189    */
 190   FileFormatI currentFileFormat = null;
 191
 192   /**
 193    * Current filename for this alignment
 194    */
 195   String fileName = null;
 196
 197
 198   /**
 199    * Creates a new AlignFrame object with specific width and height.
 200    *
 201    * @param al
 202    * @param width
 203    * @param height
 204    */
 205   public AlignFrame(AlignmentI al, int width, int height)
 206   {
 207     this(al, null, width, height);
 208   }
 209
 210   /**
 211    * Creates a new AlignFrame object with specific width, height and
 212    * sequenceSetId
 213    *
 214    * @param al
 215    * @param width
 216    * @param height
 217    * @param sequenceSetId
 218    */
 219   public AlignFrame(AlignmentI al, int width, int height,
 220           String sequenceSetId)
 221   {
 222     this(al, null, width, height, sequenceSetId);
 223   }
 224
 225   /**
 226    * Creates a new AlignFrame object with specific width, height and
 227    * sequenceSetId
 228    *
 229    * @param al
 230    * @param width
 231    * @param height
 232    * @param sequenceSetId
 233    * @param viewId
 234    */
 235   public AlignFrame(AlignmentI al, int width, int height,
 236           String sequenceSetId, String viewId)
 237   {
 238     this(al, null, width, height, sequenceSetId, viewId);
 239   }
 240
 241   /**
 242    * new alignment window with hidden columns
 243    *
 244    * @param al
 245    *          AlignmentI
 246    * @param hiddenColumns
 247    *          ColumnSelection or null
 248    * @param width
 249    *          Width of alignment frame
 250    * @param height
 251    *          height of frame.
 252    */
 253   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 254           int height)
 255   {
 256     this(al, hiddenColumns, width, height, null);
 257   }
 258
 259   /**
 260    * Create alignment frame for al with hiddenColumns, a specific width and
 261    * height, and specific sequenceId
 262    *
 263    * @param al
 264    * @param hiddenColumns
 265    * @param width
 266    * @param height
 267    * @param sequenceSetId
 268    *          (may be null)
 269    */
 270   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 271           int height, String sequenceSetId)
 272   {
 273     this(al, hiddenColumns, width, height, sequenceSetId, null);
 274   }
 275
 276   /**
 277    * Create alignment frame for al with hiddenColumns, a specific width and
 278    * height, and specific sequenceId
 279    *
 280    * @param al
 281    * @param hiddenColumns
 282    * @param width
 283    * @param height
 284    * @param sequenceSetId
 285    *          (may be null)
 286    * @param viewId
 287    *          (may be null)
 288    */
 289   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 290           int height, String sequenceSetId, String viewId)
 291   {
 292     setSize(width, height);
 293
 294     if (al.getDataset() == null)
 295     {
 296       al.setDataset(null);
 297     }
 298
 299     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 300
 301     alignPanel = new AlignmentPanel(this, viewport);
 302
 303     addAlignmentPanel(alignPanel, true);
 304     init();
 305   }
 306
 307   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 308           HiddenColumns hiddenColumns, int width, int height)
 309   {
 310     setSize(width, height);
 311
 312     if (al.getDataset() == null)
 313     {
 314       al.setDataset(null);
 315     }
 316
 317     viewport = new AlignViewport(al, hiddenColumns);
 318
 319     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 320     {
 321       viewport.hideSequence(hiddenSeqs);
 322     }
 323     alignPanel = new AlignmentPanel(this, viewport);
 324     addAlignmentPanel(alignPanel, true);
 325     init();
 326   }
 327
 328   /**
 329    * Make a new AlignFrame from existing alignmentPanels
 330    *
 331    * @param ap
 332    *          AlignmentPanel
 333    * @param av
 334    *          AlignViewport
 335    */
 336   public AlignFrame(AlignmentPanel ap)
 337   {
 338     viewport = ap.av;
 339     alignPanel = ap;
 340     addAlignmentPanel(ap, false);
 341     init();
 342   }
 343
 344   /**
 345    * initalise the alignframe from the underlying viewport data and the
 346    * configurations
 347    */
 348   void init()
 349   {
 350     if (!Jalview.isHeadlessMode())
 351     {
 352       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 353     }
 354
 355     avc = new jalview.controller.AlignViewController(this, viewport,
 356             alignPanel);
 357     if (viewport.getAlignmentConservationAnnotation() == null)
 358     {
 359       // BLOSUM62Colour.setEnabled(false);
 360       conservationMenuItem.setEnabled(false);
 361       modifyConservation.setEnabled(false);
 362       // PIDColour.setEnabled(false);
 363       // abovePIDThreshold.setEnabled(false);
 364       // modifyPID.setEnabled(false);
 365     }
 366
 367     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 368             "No sort");
 369
 370     if (sortby.equals("Id"))
 371     {
 372       sortIDMenuItem_actionPerformed(null);
 373     }
 374     else if (sortby.equals("Pairwise Identity"))
 375     {
 376       sortPairwiseMenuItem_actionPerformed(null);
 377     }
 378
 379     this.alignPanel.av
 380             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 381
 382     setMenusFromViewport(viewport);
 383     buildSortByAnnotationScoresMenu();
 384     calculateTree.addActionListener(new ActionListener()
 385     {
 386
 387       @Override
 388       public void actionPerformed(ActionEvent e)
 389       {
 390         openTreePcaDialog();
 391       }
 392     });
 393     buildColourMenu();
 394
 395     if (Desktop.desktop != null)
 396     {
 397       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 398       addServiceListeners();
 399       setGUINucleotide();
 400     }
 401
 402     if (viewport.getWrapAlignment())
 403     {
 404       wrapMenuItem_actionPerformed(null);
 405     }
 406
 407     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 408     {
 409       this.overviewMenuItem_actionPerformed(null);
 410     }
 411
 412     addKeyListener();
 413
 414     final List<AlignmentPanel> selviews = new ArrayList<>();
 415     final List<AlignmentPanel> origview = new ArrayList<>();
 416     final String menuLabel = MessageManager
 417             .getString("label.copy_format_from");
 418     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 419             new ViewSetProvider()
 420             {
 421
 422               @Override
 423               public AlignmentPanel[] getAllAlignmentPanels()
 424               {
 425                 origview.clear();
 426                 origview.add(alignPanel);
 427                 // make an array of all alignment panels except for this one
 428                 List<AlignmentPanel> aps = new ArrayList<>(
 429                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 430                 aps.remove(AlignFrame.this.alignPanel);
 431                 return aps.toArray(new AlignmentPanel[aps.size()]);
 432               }
 433             }, selviews, new ItemListener()
 434             {
 435
 436               @Override
 437               public void itemStateChanged(ItemEvent e)
 438               {
 439                 if (origview.size() > 0)
 440                 {
 441                   final AlignmentPanel ap = origview.get(0);
 442
 443                   /*
 444                    * Copy the ViewStyle of the selected panel to 'this one'.
 445                    * Don't change value of 'scaleProteinAsCdna' unless copying
 446                    * from a SplitFrame.
 447                    */
 448                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 449                           .getViewStyle();
 450                   boolean fromSplitFrame = selviews.get(0)
 451                           .getAlignViewport().getCodingComplement() != null;
 452                   if (!fromSplitFrame)
 453                   {
 454                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 455                             .getViewStyle().isScaleProteinAsCdna());
 456                   }
 457                   ap.getAlignViewport().setViewStyle(vs);
 458
 459                   /*
 460                    * Also rescale ViewStyle of SplitFrame complement if there is
 461                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 462                    * the whole ViewStyle (allow cDNA protein to have different
 463                    * fonts)
 464                    */
 465                   AlignViewportI complement = ap.getAlignViewport()
 466                           .getCodingComplement();
 467                   if (complement != null && vs.isScaleProteinAsCdna())
 468                   {
 469                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 470                     ((SplitFrame) af.getSplitViewContainer())
 471                             .adjustLayout();
 472                     af.setMenusForViewport();
 473                   }
 474
 475                   ap.updateLayout();
 476                   ap.setSelected(true);
 477                   ap.alignFrame.setMenusForViewport();
 478
 479                 }
 480               }
 481             });
 482     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 483             .indexOf("devel") > -1
 484             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 485                     .indexOf("test") > -1)
 486     {
 487       formatMenu.add(vsel);
 488     }
 489     addFocusListener(new FocusAdapter()
 490     {
 491       @Override
 492       public void focusGained(FocusEvent e)
 493       {
 494         Jalview.setCurrentAlignFrame(AlignFrame.this);
 495       }
 496     });
 497
 498   }
 499
 500   /**
 501    * Change the filename and format for the alignment, and enable the 'reload'
 502    * button functionality.
 503    *
 504    * @param file
 505    *          valid filename
 506    * @param format
 507    *          format of file
 508    */
 509   public void setFileName(String file, FileFormatI format)
 510   {
 511     fileName = file;
 512     setFileFormat(format);
 513     reload.setEnabled(true);
 514   }
 515
 516   /**
 517    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 518    * events
 519    */
 520   void addKeyListener()
 521   {
 522     addKeyListener(new KeyAdapter()
 523     {
 524       @Override
 525       public void keyPressed(KeyEvent evt)
 526       {
 527         if (viewport.cursorMode
 528                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 529                         && evt.getKeyCode() <= KeyEvent.VK_9)
 530                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 531                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 532                 && Character.isDigit(evt.getKeyChar()))
 533         {
 534           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 535         }
 536
 537         switch (evt.getKeyCode())
 538         {
 539
 540         case 27: // escape key
 541           deselectAllSequenceMenuItem_actionPerformed(null);
 542
 543           break;
 544
 545         case KeyEvent.VK_DOWN:
 546           if (evt.isAltDown() || !viewport.cursorMode)
 547           {
 548             moveSelectedSequences(false);
 549           }
 550           if (viewport.cursorMode)
 551           {
 552             alignPanel.getSeqPanel().moveCursor(0, 1);
 553           }
 554           break;
 555
 556         case KeyEvent.VK_UP:
 557           if (evt.isAltDown() || !viewport.cursorMode)
 558           {
 559             moveSelectedSequences(true);
 560           }
 561           if (viewport.cursorMode)
 562           {
 563             alignPanel.getSeqPanel().moveCursor(0, -1);
 564           }
 565
 566           break;
 567
 568         case KeyEvent.VK_LEFT:
 569           if (evt.isAltDown() || !viewport.cursorMode)
 570           {
 571             slideSequences(false,
 572                     alignPanel.getSeqPanel().getKeyboardNo1());
 573           }
 574           else
 575           {
 576             alignPanel.getSeqPanel().moveCursor(-1, 0);
 577           }
 578
 579           break;
 580
 581         case KeyEvent.VK_RIGHT:
 582           if (evt.isAltDown() || !viewport.cursorMode)
 583           {
 584             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 585           }
 586           else
 587           {
 588             alignPanel.getSeqPanel().moveCursor(1, 0);
 589           }
 590           break;
 591
 592         case KeyEvent.VK_SPACE:
 593           if (viewport.cursorMode)
 594           {
 595             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 596                     || evt.isShiftDown() || evt.isAltDown());
 597           }
 598           break;
 599
 600         // case KeyEvent.VK_A:
 601         // if (viewport.cursorMode)
 602         // {
 603         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 604         // //System.out.println("A");
 605         // }
 606         // break;
 607         /*
 608          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 609          * System.out.println("closing bracket"); } break;
 610          */
 611         case KeyEvent.VK_DELETE:
 612         case KeyEvent.VK_BACK_SPACE:
 613           if (!viewport.cursorMode)
 614           {
 615             cut_actionPerformed(null);
 616           }
 617           else
 618           {
 619             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 620                     || evt.isShiftDown() || evt.isAltDown());
 621           }
 622
 623           break;
 624
 625         case KeyEvent.VK_S:
 626           if (viewport.cursorMode)
 627           {
 628             alignPanel.getSeqPanel().setCursorRow();
 629           }
 630           break;
 631         case KeyEvent.VK_C:
 632           if (viewport.cursorMode && !evt.isControlDown())
 633           {
 634             alignPanel.getSeqPanel().setCursorColumn();
 635           }
 636           break;
 637         case KeyEvent.VK_P:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setCursorPosition();
 641           }
 642           break;
 643
 644         case KeyEvent.VK_ENTER:
 645         case KeyEvent.VK_COMMA:
 646           if (viewport.cursorMode)
 647           {
 648             alignPanel.getSeqPanel().setCursorRowAndColumn();
 649           }
 650           break;
 651
 652         case KeyEvent.VK_Q:
 653           if (viewport.cursorMode)
 654           {
 655             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 656           }
 657           break;
 658         case KeyEvent.VK_M:
 659           if (viewport.cursorMode)
 660           {
 661             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 662           }
 663           break;
 664
 665         case KeyEvent.VK_F2:
 666           viewport.cursorMode = !viewport.cursorMode;
 667           statusBar.setText(MessageManager
 668                   .formatMessage("label.keyboard_editing_mode", new String[]
 669                   { (viewport.cursorMode ? "on" : "off") }));
 670           if (viewport.cursorMode)
 671           {
 672             ViewportRanges ranges = viewport.getRanges();
 673             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 674                     .getStartRes();
 675             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 676                     .getStartSeq();
 677           }
 678           alignPanel.getSeqPanel().seqCanvas.repaint();
 679           break;
 680
 681         case KeyEvent.VK_F1:
 682           try
 683           {
 684             Help.showHelpWindow();
 685           } catch (Exception ex)
 686           {
 687             ex.printStackTrace();
 688           }
 689           break;
 690         case KeyEvent.VK_H:
 691         {
 692           boolean toggleSeqs = !evt.isControlDown();
 693           boolean toggleCols = !evt.isShiftDown();
 694           toggleHiddenRegions(toggleSeqs, toggleCols);
 695           break;
 696         }
 697         case KeyEvent.VK_B:
 698         {
 699           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 700           boolean modifyExisting = true; // always modify, don't clear
 701                                          // evt.isShiftDown();
 702           boolean invertHighlighted = evt.isAltDown();
 703           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 704                   toggleSel);
 705           break;
 706         }
 707         case KeyEvent.VK_PAGE_UP:
 708           viewport.getRanges().pageUp();
 709           break;
 710         case KeyEvent.VK_PAGE_DOWN:
 711           viewport.getRanges().pageDown();
 712           break;
 713         }
 714       }
 715
 716       @Override
 717       public void keyReleased(KeyEvent evt)
 718       {
 719         switch (evt.getKeyCode())
 720         {
 721         case KeyEvent.VK_LEFT:
 722           if (evt.isAltDown() || !viewport.cursorMode)
 723           {
 724             viewport.firePropertyChange("alignment", null,
 725                     viewport.getAlignment().getSequences());
 726           }
 727           break;
 728
 729         case KeyEvent.VK_RIGHT:
 730           if (evt.isAltDown() || !viewport.cursorMode)
 731           {
 732             viewport.firePropertyChange("alignment", null,
 733                     viewport.getAlignment().getSequences());
 734           }
 735           break;
 736         }
 737       }
 738     });
 739   }
 740
 741   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 742   {
 743     ap.alignFrame = this;
 744     avc = new jalview.controller.AlignViewController(this, viewport,
 745             alignPanel);
 746
 747     alignPanels.add(ap);
 748
 749     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 750
 751     int aSize = alignPanels.size();
 752
 753     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 754
 755     if (aSize == 1 && ap.av.getViewName() == null)
 756     {
 757       this.getContentPane().add(ap, BorderLayout.CENTER);
 758     }
 759     else
 760     {
 761       if (aSize == 2)
 762       {
 763         setInitialTabVisible();
 764       }
 765
 766       expandViews.setEnabled(true);
 767       gatherViews.setEnabled(true);
 768       tabbedPane.addTab(ap.av.getViewName(), ap);
 769
 770       ap.setVisible(false);
 771     }
 772
 773     if (newPanel)
 774     {
 775       if (ap.av.isPadGaps())
 776       {
 777         ap.av.getAlignment().padGaps();
 778       }
 779       ap.av.updateConservation(ap);
 780       ap.av.updateConsensus(ap);
 781       ap.av.updateStrucConsensus(ap);
 782       ap.av.initInformationWorker(ap);
 783     }
 784   }
 785
 786   public void setInitialTabVisible()
 787   {
 788     expandViews.setEnabled(true);
 789     gatherViews.setEnabled(true);
 790     tabbedPane.setVisible(true);
 791     AlignmentPanel first = alignPanels.get(0);
 792     tabbedPane.addTab(first.av.getViewName(), first);
 793     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 794   }
 795
 796   public AlignViewport getViewport()
 797   {
 798     return viewport;
 799   }
 800
 801   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 802   private void addServiceListeners()
 803   {
 804     final java.beans.PropertyChangeListener thisListener;
 805     Desktop.instance.addJalviewPropertyChangeListener("services",
 806             thisListener = new java.beans.PropertyChangeListener()
 807             {
 808               @Override
 809               public void propertyChange(PropertyChangeEvent evt)
 810               {
 811                 // // System.out.println("Discoverer property change.");
 812                 // if (evt.getPropertyName().equals("services"))
 813                 {
 814                   SwingUtilities.invokeLater(new Runnable()
 815                   {
 816
 817                     @Override
 818                     public void run()
 819                     {
 820                       System.err.println(
 821                               "Rebuild WS Menu for service change");
 822                       BuildWebServiceMenu();
 823                     }
 824
 825                   });
 826                 }
 827               }
 828             });
 829     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 830     {
 831       @Override
 832       public void internalFrameClosed(
 833               javax.swing.event.InternalFrameEvent evt)
 834       {
 835         // System.out.println("deregistering discoverer listener");
 836         Desktop.instance.removeJalviewPropertyChangeListener("services",
 837                 thisListener);
 838         closeMenuItem_actionPerformed(true);
 839       };
 840     });
 841     // Finally, build the menu once to get current service state
 842     new Thread(new Runnable()
 843     {
 844       @Override
 845       public void run()
 846       {
 847         BuildWebServiceMenu();
 848       }
 849     }).start();
 850   }
 851
 852   /**
 853    * Configure menu items that vary according to whether the alignment is
 854    * nucleotide or protein
 855    */
 856   public void setGUINucleotide()
 857   {
 858     AlignmentI al = getViewport().getAlignment();
 859     boolean nucleotide = al.isNucleotide();
 860
 861     loadVcf.setVisible(nucleotide);
 862     showTranslation.setVisible(nucleotide);
 863     showReverse.setVisible(nucleotide);
 864     showReverseComplement.setVisible(nucleotide);
 865     conservationMenuItem.setEnabled(!nucleotide);
 866     modifyConservation
 867             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 868     showGroupConservation.setEnabled(!nucleotide);
 869
 870     showComplementMenuItem
 871             .setText(nucleotide ? MessageManager.getString("label.protein")
 872                     : MessageManager.getString("label.nucleotide"));
 873   }
 874
 875   /**
 876    * set up menus for the current viewport. This may be called after any
 877    * operation that affects the data in the current view (selection changed,
 878    * etc) to update the menus to reflect the new state.
 879    */
 880   @Override
 881   public void setMenusForViewport()
 882   {
 883     setMenusFromViewport(viewport);
 884   }
 885
 886   /**
 887    * Need to call this method when tabs are selected for multiple views, or when
 888    * loading from Jalview2XML.java
 889    *
 890    * @param av
 891    *          AlignViewport
 892    */
 893   public void setMenusFromViewport(AlignViewport av)
 894   {
 895     padGapsMenuitem.setSelected(av.isPadGaps());
 896     colourTextMenuItem.setSelected(av.isShowColourText());
 897     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 898     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 899     conservationMenuItem.setSelected(av.getConservationSelected());
 900     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 901     seqLimits.setSelected(av.getShowJVSuffix());
 902     idRightAlign.setSelected(av.isRightAlignIds());
 903     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 904     renderGapsMenuItem.setSelected(av.isRenderGaps());
 905     wrapMenuItem.setSelected(av.getWrapAlignment());
 906     scaleAbove.setVisible(av.getWrapAlignment());
 907     scaleLeft.setVisible(av.getWrapAlignment());
 908     scaleRight.setVisible(av.getWrapAlignment());
 909     annotationPanelMenuItem.setState(av.isShowAnnotation());
 910     /*
 911      * Show/hide annotations only enabled if annotation panel is shown
 912      */
 913     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 914     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 915     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 916     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 917     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 918     viewTextMenuItem.setSelected(av.getShowText());
 919     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 920     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 921     showGroupConservation.setSelected(av.isShowGroupConservation());
 922     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 923     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 924     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 925     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 926     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 927     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 928
 929     ColourMenuHelper.setColourSelected(colourMenu,
 930             av.getGlobalColourScheme());
 931
 932     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 933     hiddenMarkers.setState(av.getShowHiddenMarkers());
 934     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 935     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 936     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 937     autoCalculate.setSelected(av.autoCalculateConsensus);
 938     sortByTree.setSelected(av.sortByTree);
 939     listenToViewSelections.setSelected(av.followSelection);
 940
 941     showProducts.setEnabled(canShowProducts());
 942     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 943
 944     updateEditMenuBar();
 945   }
 946
 947   /**
 948    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 949    *
 950    * @param b
 951    */
 952   public void setGroovyEnabled(boolean b)
 953   {
 954     runGroovy.setEnabled(b);
 955   }
 956
 957   private IProgressIndicator progressBar;
 958
 959   /*
 960    * (non-Javadoc)
 961    *
 962    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 963    */
 964   @Override
 965   public void setProgressBar(String message, long id)
 966   {
 967     progressBar.setProgressBar(message, id);
 968   }
 969
 970   @Override
 971   public void registerHandler(final long id,
 972           final IProgressIndicatorHandler handler)
 973   {
 974     progressBar.registerHandler(id, handler);
 975   }
 976
 977   /**
 978    *
 979    * @return true if any progress bars are still active
 980    */
 981   @Override
 982   public boolean operationInProgress()
 983   {
 984     return progressBar.operationInProgress();
 985   }
 986
 987   /**
 988    * Sets the text of the status bar. Note that setting a null or empty value
 989    * will cause the status bar to be hidden, with possibly undesirable flicker
 990    * of the screen layout.
 991    */
 992   @Override
 993   public void setStatus(String text)
 994   {
 995     statusBar.setText(text == null || text.isEmpty() ? " " : text);
 996   }
 997
 998   /*
 999    * Added so Castor Mapping file can obtain Jalview Version
1000    */
1001   public String getVersion()
1002   {
1003     return jalview.bin.Cache.getProperty("VERSION");
1004   }
1005
1006   public FeatureRenderer getFeatureRenderer()
1007   {
1008     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1009   }
1010
1011   @Override
1012   public void fetchSequence_actionPerformed(ActionEvent e)
1013   {
1014     new jalview.gui.SequenceFetcher(this);
1015   }
1016
1017   @Override
1018   public void addFromFile_actionPerformed(ActionEvent e)
1019   {
1020     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1021   }
1022
1023   @Override
1024   public void hmmBuild_actionPerformed(boolean withDefaults)
1025   {
1026     if (!alignmentIsSufficient(1))
1027     {
1028       return;
1029     }
1030
1031     /*
1032      * get default parameters, and optionally show a dialog
1033      * to allow them to be modified
1034      */
1035     ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
1036     List<ArgumentI> args = store.getServiceParameters();
1037
1038     if (!withDefaults)
1039     {
1040       WsParamSetI set = new HMMERPreset();
1041       WsJobParameters params = new WsJobParameters(store, set, args);
1042       if (params.showRunDialog())
1043       {
1044         args = params.getJobParams();
1045       }
1046       else
1047       {
1048         return; // user cancelled
1049       }
1050     }
1051     new Thread(new HMMBuild(this, args)).start();
1052   }
1053
1054   @Override
1055   public void hmmAlign_actionPerformed(boolean withDefaults)
1056   {
1057     if (!(checkForHMM() && alignmentIsSufficient(2)))
1058     {
1059       return;
1060     }
1061
1062     /*
1063      * get default parameters, and optionally show a dialog
1064      * to allow them to be modified
1065      */
1066     ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
1067     List<ArgumentI> args = store.getServiceParameters();
1068
1069     if (!withDefaults)
1070     {
1071       WsParamSetI set = new HMMERPreset();
1072       WsJobParameters params = new WsJobParameters(store, set, args);
1073       if (params.showRunDialog())
1074       {
1075         args = params.getJobParams();
1076       }
1077       else
1078       {
1079         return; // user cancelled
1080       }
1081     }
1082     new Thread(new HMMAlign(this, args)).start();
1083   }
1084
1085   @Override
1086   public void hmmSearch_actionPerformed(boolean withDefaults)
1087   {
1088     if (!checkForHMM())
1089     {
1090       return;
1091     }
1092
1093     /*
1094      * get default parameters, and (if requested) show
1095      * dialog to allow modification
1096      */
1097     ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
1098     List<ArgumentI> args = store.getServiceParameters();
1099
1100     if (!withDefaults)
1101     {
1102       WsParamSetI set = new HMMERPreset();
1103       WsJobParameters params = new WsJobParameters(store, set, args);
1104       if (params.showRunDialog())
1105       {
1106         args = params.getJobParams();
1107       }
1108       else
1109       {
1110         return; // user cancelled
1111       }
1112     }
1113     new Thread(new HMMSearch(this, args)).start();
1114     alignPanel.repaint();
1115   }
1116
1117   @Override
1118   public void jackhmmer_actionPerformed(boolean withDefaults)
1119   {
1120
1121     /*
1122      * get default parameters, and (if requested) show
1123      * dialog to allow modification
1124      */
1125
1126     ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
1127     List<ArgumentI> args = store.getServiceParameters();
1128
1129     if (!withDefaults)
1130     {
1131       WsParamSetI set = new HMMERPreset();
1132       WsJobParameters params = new WsJobParameters(store, set, args);
1133       if (params.showRunDialog())
1134       {
1135         args = params.getJobParams();
1136       }
1137       else
1138       {
1139         return; // user cancelled
1140       }
1141     }
1142     new Thread(new JackHMMER(this, args)).start();
1143     alignPanel.repaint();
1144
1145   }
1146
1147   /**
1148    * Checks if the alignment has at least one hidden Markov model, if not shows
1149    * a dialog advising to run hmmbuild or load an HMM profile
1150    *
1151    * @return
1152    */
1153   private boolean checkForHMM()
1154   {
1155     if (viewport.getAlignment().getHmmSequences().isEmpty())
1156     {
1157       JOptionPane.showMessageDialog(this,
1158               MessageManager.getString("warn.no_hmm"));
1159       return false;
1160     }
1161     return true;
1162   }
1163
1164   @Override
1165   protected void filterByEValue_actionPerformed()
1166   {
1167     viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
1168   }
1169
1170   @Override
1171   protected void filterByScore_actionPerformed()
1172   {
1173     viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
1174   }
1175
1176   private double inputDouble(String message)
1177   {
1178     String str = null;
1179     Double d = null;
1180     while(d == null || d <= 0)
1181     {
1182       str = JOptionPane.showInputDialog(this.alignPanel, message);
1183       try
1184       {
1185         d = Double.valueOf(str);
1186       }
1187       catch (NumberFormatException e)
1188       {
1189       }
1190     }
1191     return d;
1192   }
1193
1194   /**
1195    * Checks if the alignment contains the required number of sequences.
1196    *
1197    * @param required
1198    * @return
1199    */
1200   public boolean alignmentIsSufficient(int required)
1201   {
1202     if (getViewport().getAlignment().getSequences().size() < required)
1203     {
1204       JOptionPane.showMessageDialog(this,
1205               MessageManager.getString("label.not_enough_sequences"));
1206       return false;
1207     }
1208     return true;
1209   }
1210
1211   /**
1212    * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
1213    * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
1214    * comma-separated list)
1215    */
1216   @Override
1217   public void addDatabase_actionPerformed() throws IOException
1218   {
1219     if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
1220     {
1221       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1222     }
1223
1224     String path = openFileChooser(false);
1225     if (path != null && new File(path).exists())
1226     {
1227       IdentifyFile identifier = new IdentifyFile();
1228       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1229       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1230               || format == FileFormat.Pfam)
1231       {
1232         String currentDbPaths = Cache
1233                 .getProperty(Preferences.HMMSEARCH_DBS);
1234         currentDbPaths += Preferences.COMMA + path;
1235         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1236       }
1237       else
1238       {
1239         JOptionPane.showMessageDialog(this,
1240                 MessageManager.getString("warn.invalid_format"));
1241       }
1242     }
1243   }
1244
1245   /**
1246    * Opens a file chooser, optionally restricted to selecting folders
1247    * (directories) only. Answers the path to the selected file or folder, or
1248    * null if none is chosen.
1249    *
1250    * @param
1251    * @return
1252    */
1253   protected String openFileChooser(boolean forFolder)
1254   {
1255     // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
1256     String choice = null;
1257     JFileChooser chooser = new JFileChooser();
1258     if (forFolder)
1259     {
1260       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1261     }
1262     chooser.setDialogTitle(
1263             MessageManager.getString("label.open_local_file"));
1264     chooser.setToolTipText(MessageManager.getString("action.open"));
1265
1266     int value = chooser.showOpenDialog(this);
1267
1268     if (value == JFileChooser.APPROVE_OPTION)
1269     {
1270       choice = chooser.getSelectedFile().getPath();
1271     }
1272     return choice;
1273   }
1274
1275   @Override
1276   public void reload_actionPerformed(ActionEvent e)
1277   {
1278     if (fileName != null)
1279     {
1280       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1281       // originating file's format
1282       // TODO: work out how to recover feature settings for correct view(s) when
1283       // file is reloaded.
1284       if (FileFormat.Jalview.equals(currentFileFormat))
1285       {
1286         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1287         for (int i = 0; i < frames.length; i++)
1288         {
1289           if (frames[i] instanceof AlignFrame && frames[i] != this
1290                   && ((AlignFrame) frames[i]).fileName != null
1291                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1292           {
1293             try
1294             {
1295               frames[i].setSelected(true);
1296               Desktop.instance.closeAssociatedWindows();
1297             } catch (java.beans.PropertyVetoException ex)
1298             {
1299             }
1300           }
1301
1302         }
1303         Desktop.instance.closeAssociatedWindows();
1304
1305         FileLoader loader = new FileLoader();
1306         DataSourceType protocol = fileName.startsWith("http:")
1307                 ? DataSourceType.URL
1308                 : DataSourceType.FILE;
1309         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1310       }
1311       else
1312       {
1313         Rectangle bounds = this.getBounds();
1314
1315         FileLoader loader = new FileLoader();
1316         DataSourceType protocol = fileName.startsWith("http:")
1317                 ? DataSourceType.URL
1318                 : DataSourceType.FILE;
1319         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1320                 protocol, currentFileFormat);
1321
1322         newframe.setBounds(bounds);
1323         if (featureSettings != null && featureSettings.isShowing())
1324         {
1325           final Rectangle fspos = featureSettings.frame.getBounds();
1326           // TODO: need a 'show feature settings' function that takes bounds -
1327           // need to refactor Desktop.addFrame
1328           newframe.featureSettings_actionPerformed(null);
1329           final FeatureSettings nfs = newframe.featureSettings;
1330           SwingUtilities.invokeLater(new Runnable()
1331           {
1332             @Override
1333             public void run()
1334             {
1335               nfs.frame.setBounds(fspos);
1336             }
1337           });
1338           this.featureSettings.close();
1339           this.featureSettings = null;
1340         }
1341         this.closeMenuItem_actionPerformed(true);
1342       }
1343     }
1344   }
1345
1346   @Override
1347   public void addFromText_actionPerformed(ActionEvent e)
1348   {
1349     Desktop.instance
1350             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1351   }
1352
1353   @Override
1354   public void addFromURL_actionPerformed(ActionEvent e)
1355   {
1356     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1357   }
1358
1359   @Override
1360   public void save_actionPerformed(ActionEvent e)
1361   {
1362     if (fileName == null || (currentFileFormat == null)
1363             || fileName.startsWith("http"))
1364     {
1365       saveAs_actionPerformed(null);
1366     }
1367     else
1368     {
1369       saveAlignment(fileName, currentFileFormat);
1370     }
1371   }
1372
1373   /**
1374    * DOCUMENT ME!
1375    *
1376    * @param e
1377    *          DOCUMENT ME!
1378    */
1379   @Override
1380   public void saveAs_actionPerformed(ActionEvent e)
1381   {
1382     String format = currentFileFormat == null ? null
1383             : currentFileFormat.getName();
1384     JalviewFileChooser chooser = JalviewFileChooser
1385             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1386
1387     chooser.setFileView(new JalviewFileView());
1388     chooser.setDialogTitle(
1389             MessageManager.getString("label.save_alignment_to_file"));
1390     chooser.setToolTipText(MessageManager.getString("action.save"));
1391
1392     int value = chooser.showSaveDialog(this);
1393
1394     if (value == JalviewFileChooser.APPROVE_OPTION)
1395     {
1396       currentFileFormat = chooser.getSelectedFormat();
1397       while (currentFileFormat == null)
1398       {
1399         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1400                 MessageManager.getString(
1401                         "label.select_file_format_before_saving"),
1402                 MessageManager.getString("label.file_format_not_specified"),
1403                 JvOptionPane.WARNING_MESSAGE);
1404         currentFileFormat = chooser.getSelectedFormat();
1405         value = chooser.showSaveDialog(this);
1406         if (value != JalviewFileChooser.APPROVE_OPTION)
1407         {
1408           return;
1409         }
1410       }
1411
1412       fileName = chooser.getSelectedFile().getPath();
1413
1414       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1415
1416       Cache.setProperty("LAST_DIRECTORY", fileName);
1417       saveAlignment(fileName, currentFileFormat);
1418     }
1419   }
1420
1421   public boolean saveAlignment(String file, FileFormatI format)
1422   {
1423     boolean success = true;
1424
1425     if (FileFormat.Jalview.equals(format))
1426     {
1427       String shortName = title;
1428
1429       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1430       {
1431         shortName = shortName.substring(
1432                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1433       }
1434
1435       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1436               shortName);
1437
1438       statusBar.setText(MessageManager.formatMessage(
1439               "label.successfully_saved_to_file_in_format", new Object[]
1440               { fileName, format }));
1441
1442     }
1443     else
1444     {
1445       AlignmentExportData exportData = getAlignmentForExport(format,
1446               viewport, null);
1447       if (exportData.getSettings().isCancelled())
1448       {
1449         return false;
1450       }
1451       FormatAdapter f = new FormatAdapter(alignPanel,
1452               exportData.getSettings());
1453       String output = f.formatSequences(format, exportData.getAlignment(), // class
1454                                                                            // cast
1455                                                                            // exceptions
1456                                                                            // will
1457               // occur in the distant future
1458               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1459               f.getCacheSuffixDefault(format),
1460               viewport.getAlignment().getHiddenColumns());
1461
1462       if (output == null)
1463       {
1464         success = false;
1465       }
1466       else
1467       {
1468         // create backupfiles object and get new temp filename destination
1469         BackupFiles backupfiles = new BackupFiles(file);
1470
1471         try
1472         {
1473           PrintWriter out = new PrintWriter(
1474                   new FileWriter(backupfiles.getTempFilePath()));
1475
1476           out.print(output);
1477           out.close();
1478           this.setTitle(file);
1479           statusBar.setText(MessageManager.formatMessage(
1480                   "label.successfully_saved_to_file_in_format", new Object[]
1481                   { fileName, format.getName() }));
1482         } catch (Exception ex)
1483         {
1484           success = false;
1485           ex.printStackTrace();
1486         }
1487
1488         backupfiles.setWriteSuccess(success);
1489         // do the backup file roll and rename the temp file to actual file
1490         success = backupfiles.rollBackupsAndRenameTempFile();
1491
1492       }
1493     }
1494
1495     if (!success)
1496     {
1497       JvOptionPane.showInternalMessageDialog(this, MessageManager
1498               .formatMessage("label.couldnt_save_file", new Object[]
1499               { fileName }),
1500               MessageManager.getString("label.error_saving_file"),
1501               JvOptionPane.WARNING_MESSAGE);
1502     }
1503
1504     return success;
1505   }
1506
1507   private void warningMessage(String warning, String title)
1508   {
1509     if (new jalview.util.Platform().isHeadless())
1510     {
1511       System.err.println("Warning: " + title + "\nWarning: " + warning);
1512
1513     }
1514     else
1515     {
1516       JvOptionPane.showInternalMessageDialog(this, warning, title,
1517               JvOptionPane.WARNING_MESSAGE);
1518     }
1519     return;
1520   }
1521
1522   /**
1523    * DOCUMENT ME!
1524    *
1525    * @param e
1526    *          DOCUMENT ME!
1527    */
1528   @Override
1529   protected void outputText_actionPerformed(ActionEvent e)
1530   {
1531     FileFormatI fileFormat = FileFormats.getInstance()
1532             .forName(e.getActionCommand());
1533     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1534             viewport, null);
1535     if (exportData.getSettings().isCancelled())
1536     {
1537       return;
1538     }
1539     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1540     cap.setForInput(null);
1541     try
1542     {
1543       FileFormatI format = fileFormat;
1544       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1545               .formatSequences(format, exportData.getAlignment(),
1546                       exportData.getOmitHidden(),
1547                       exportData.getStartEndPostions(),
1548                       viewport.getAlignment().getHiddenColumns()));
1549       Desktop.addInternalFrame(cap, MessageManager
1550               .formatMessage("label.alignment_output_command", new Object[]
1551               { e.getActionCommand() }), 600, 500);
1552     } catch (OutOfMemoryError oom)
1553     {
1554       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1555               oom);
1556       cap.dispose();
1557     }
1558
1559   }
1560
1561   public static AlignmentExportData getAlignmentForExport(
1562           FileFormatI format, AlignViewportI viewport,
1563           AlignExportSettingI exportSettings)
1564   {
1565     AlignmentI alignmentToExport = null;
1566     AlignExportSettingI settings = exportSettings;
1567     String[] omitHidden = null;
1568
1569     HiddenSequences hiddenSeqs = viewport.getAlignment()
1570             .getHiddenSequences();
1571
1572     alignmentToExport = viewport.getAlignment();
1573
1574     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1575     if (settings == null)
1576     {
1577       settings = new AlignExportSettings(hasHiddenSeqs,
1578               viewport.hasHiddenColumns(), format);
1579     }
1580     // settings.isExportAnnotations();
1581
1582     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1583     {
1584       omitHidden = viewport.getViewAsString(false,
1585               settings.isExportHiddenSequences());
1586     }
1587
1588     int[] alignmentStartEnd = new int[2];
1589     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1590     {
1591       alignmentToExport = hiddenSeqs.getFullAlignment();
1592     }
1593     else
1594     {
1595       alignmentToExport = viewport.getAlignment();
1596     }
1597     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1598             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1599     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1600             omitHidden, alignmentStartEnd, settings);
1601     return ed;
1602   }
1603
1604   /**
1605    * DOCUMENT ME!
1606    *
1607    * @param e
1608    *          DOCUMENT ME!
1609    */
1610   @Override
1611   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1612   {
1613     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1614     htmlSVG.exportHTML(null);
1615   }
1616
1617   @Override
1618   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1619   {
1620     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1621     bjs.exportHTML(null);
1622   }
1623
1624   public void createImageMap(File file, String image)
1625   {
1626     alignPanel.makePNGImageMap(file, image);
1627   }
1628
1629   /**
1630    * DOCUMENT ME!
1631    *
1632    * @param e
1633    *          DOCUMENT ME!
1634    */
1635   @Override
1636   public void createPNG(File f)
1637   {
1638     alignPanel.makePNG(f);
1639   }
1640
1641   /**
1642    * DOCUMENT ME!
1643    *
1644    * @param e
1645    *          DOCUMENT ME!
1646    */
1647   @Override
1648   public void createEPS(File f)
1649   {
1650     alignPanel.makeEPS(f);
1651   }
1652
1653   @Override
1654   public void createSVG(File f)
1655   {
1656     alignPanel.makeSVG(f);
1657   }
1658
1659   @Override
1660   public void pageSetup_actionPerformed(ActionEvent e)
1661   {
1662     PrinterJob printJob = PrinterJob.getPrinterJob();
1663     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1664   }
1665
1666   /**
1667    * DOCUMENT ME!
1668    *
1669    * @param e
1670    *          DOCUMENT ME!
1671    */
1672   @Override
1673   public void printMenuItem_actionPerformed(ActionEvent e)
1674   {
1675     // Putting in a thread avoids Swing painting problems
1676     PrintThread thread = new PrintThread(alignPanel);
1677     thread.start();
1678   }
1679
1680   @Override
1681   public void exportFeatures_actionPerformed(ActionEvent e)
1682   {
1683     new AnnotationExporter(alignPanel).exportFeatures();
1684   }
1685
1686   @Override
1687   public void exportAnnotations_actionPerformed(ActionEvent e)
1688   {
1689     new AnnotationExporter(alignPanel).exportAnnotations();
1690   }
1691
1692   @Override
1693   public void associatedData_actionPerformed(ActionEvent e)
1694           throws IOException, InterruptedException
1695   {
1696     // Pick the tree file
1697     JalviewFileChooser chooser = new JalviewFileChooser(
1698             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1699     chooser.setFileView(new JalviewFileView());
1700     chooser.setDialogTitle(
1701             MessageManager.getString("label.load_jalview_annotations"));
1702     chooser.setToolTipText(
1703             MessageManager.getString("label.load_jalview_annotations"));
1704
1705     int value = chooser.showOpenDialog(null);
1706
1707     if (value == JalviewFileChooser.APPROVE_OPTION)
1708     {
1709       String choice = chooser.getSelectedFile().getPath();
1710       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1711       loadJalviewDataFile(choice, null, null, null);
1712     }
1713
1714   }
1715
1716   /**
1717    * Close the current view or all views in the alignment frame. If the frame
1718    * only contains one view then the alignment will be removed from memory.
1719    *
1720    * @param closeAllTabs
1721    */
1722   @Override
1723   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1724   {
1725     if (alignPanels != null && alignPanels.size() < 2)
1726     {
1727       closeAllTabs = true;
1728     }
1729
1730     try
1731     {
1732       if (alignPanels != null)
1733       {
1734         if (closeAllTabs)
1735         {
1736           if (this.isClosed())
1737           {
1738             // really close all the windows - otherwise wait till
1739             // setClosed(true) is called
1740             for (int i = 0; i < alignPanels.size(); i++)
1741             {
1742               AlignmentPanel ap = alignPanels.get(i);
1743               ap.closePanel();
1744             }
1745           }
1746         }
1747         else
1748         {
1749           closeView(alignPanel);
1750         }
1751       }
1752
1753       if (closeAllTabs)
1754       {
1755         /*
1756          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1757          * be called recursively, with the frame now in 'closed' state
1758          */
1759         this.setClosed(true);
1760       }
1761     } catch (Exception ex)
1762     {
1763       ex.printStackTrace();
1764     }
1765   }
1766
1767   /**
1768    * Close the specified panel and close up tabs appropriately.
1769    *
1770    * @param panelToClose
1771    */
1772   public void closeView(AlignmentPanel panelToClose)
1773   {
1774     int index = tabbedPane.getSelectedIndex();
1775     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1776     alignPanels.remove(panelToClose);
1777     panelToClose.closePanel();
1778     panelToClose = null;
1779
1780     tabbedPane.removeTabAt(closedindex);
1781     tabbedPane.validate();
1782
1783     if (index > closedindex || index == tabbedPane.getTabCount())
1784     {
1785       // modify currently selected tab index if necessary.
1786       index--;
1787     }
1788
1789     this.tabSelectionChanged(index);
1790   }
1791
1792   /**
1793    * DOCUMENT ME!
1794    */
1795   void updateEditMenuBar()
1796   {
1797
1798     if (viewport.getHistoryList().size() > 0)
1799     {
1800       undoMenuItem.setEnabled(true);
1801       CommandI command = viewport.getHistoryList().peek();
1802       undoMenuItem.setText(MessageManager
1803               .formatMessage("label.undo_command", new Object[]
1804               { command.getDescription() }));
1805     }
1806     else
1807     {
1808       undoMenuItem.setEnabled(false);
1809       undoMenuItem.setText(MessageManager.getString("action.undo"));
1810     }
1811
1812     if (viewport.getRedoList().size() > 0)
1813     {
1814       redoMenuItem.setEnabled(true);
1815
1816       CommandI command = viewport.getRedoList().peek();
1817       redoMenuItem.setText(MessageManager
1818               .formatMessage("label.redo_command", new Object[]
1819               { command.getDescription() }));
1820     }
1821     else
1822     {
1823       redoMenuItem.setEnabled(false);
1824       redoMenuItem.setText(MessageManager.getString("action.redo"));
1825     }
1826   }
1827
1828   @Override
1829   public void addHistoryItem(CommandI command)
1830   {
1831     if (command.getSize() > 0)
1832     {
1833       viewport.addToHistoryList(command);
1834       viewport.clearRedoList();
1835       updateEditMenuBar();
1836       viewport.updateHiddenColumns();
1837       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1838       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1839       // viewport.getColumnSelection()
1840       // .getHiddenColumns().size() > 0);
1841     }
1842   }
1843
1844   /**
1845    *
1846    * @return alignment objects for all views
1847    */
1848   AlignmentI[] getViewAlignments()
1849   {
1850     if (alignPanels != null)
1851     {
1852       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1853       int i = 0;
1854       for (AlignmentPanel ap : alignPanels)
1855       {
1856         als[i++] = ap.av.getAlignment();
1857       }
1858       return als;
1859     }
1860     if (viewport != null)
1861     {
1862       return new AlignmentI[] { viewport.getAlignment() };
1863     }
1864     return null;
1865   }
1866
1867   /**
1868    * DOCUMENT ME!
1869    *
1870    * @param e
1871    *          DOCUMENT ME!
1872    */
1873   @Override
1874   protected void undoMenuItem_actionPerformed(ActionEvent e)
1875   {
1876     if (viewport.getHistoryList().isEmpty())
1877     {
1878       return;
1879     }
1880     CommandI command = viewport.getHistoryList().pop();
1881     viewport.addToRedoList(command);
1882     command.undoCommand(getViewAlignments());
1883
1884     AlignmentViewport originalSource = getOriginatingSource(command);
1885     updateEditMenuBar();
1886
1887     if (originalSource != null)
1888     {
1889       if (originalSource != viewport)
1890       {
1891         Cache.log.warn(
1892                 "Implementation worry: mismatch of viewport origin for undo");
1893       }
1894       originalSource.updateHiddenColumns();
1895       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1896       // null
1897       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1898       // viewport.getColumnSelection()
1899       // .getHiddenColumns().size() > 0);
1900       originalSource.firePropertyChange("alignment", null,
1901               originalSource.getAlignment().getSequences());
1902     }
1903   }
1904
1905   /**
1906    * DOCUMENT ME!
1907    *
1908    * @param e
1909    *          DOCUMENT ME!
1910    */
1911   @Override
1912   protected void redoMenuItem_actionPerformed(ActionEvent e)
1913   {
1914     if (viewport.getRedoList().size() < 1)
1915     {
1916       return;
1917     }
1918
1919     CommandI command = viewport.getRedoList().pop();
1920     viewport.addToHistoryList(command);
1921     command.doCommand(getViewAlignments());
1922
1923     AlignmentViewport originalSource = getOriginatingSource(command);
1924     updateEditMenuBar();
1925
1926     if (originalSource != null)
1927     {
1928
1929       if (originalSource != viewport)
1930       {
1931         Cache.log.warn(
1932                 "Implementation worry: mismatch of viewport origin for redo");
1933       }
1934       originalSource.updateHiddenColumns();
1935       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1936       // null
1937       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1938       // viewport.getColumnSelection()
1939       // .getHiddenColumns().size() > 0);
1940       originalSource.firePropertyChange("alignment", null,
1941               originalSource.getAlignment().getSequences());
1942     }
1943   }
1944
1945   AlignmentViewport getOriginatingSource(CommandI command)
1946   {
1947     AlignmentViewport originalSource = null;
1948     // For sequence removal and addition, we need to fire
1949     // the property change event FROM the viewport where the
1950     // original alignment was altered
1951     AlignmentI al = null;
1952     if (command instanceof EditCommand)
1953     {
1954       EditCommand editCommand = (EditCommand) command;
1955       al = editCommand.getAlignment();
1956       List<Component> comps = PaintRefresher.components
1957               .get(viewport.getSequenceSetId());
1958
1959       for (Component comp : comps)
1960       {
1961         if (comp instanceof AlignmentPanel)
1962         {
1963           if (al == ((AlignmentPanel) comp).av.getAlignment())
1964           {
1965             originalSource = ((AlignmentPanel) comp).av;
1966             break;
1967           }
1968         }
1969       }
1970     }
1971
1972     if (originalSource == null)
1973     {
1974       // The original view is closed, we must validate
1975       // the current view against the closed view first
1976       if (al != null)
1977       {
1978         PaintRefresher.validateSequences(al, viewport.getAlignment());
1979       }
1980
1981       originalSource = viewport;
1982     }
1983
1984     return originalSource;
1985   }
1986
1987   /**
1988    * DOCUMENT ME!
1989    *
1990    * @param up
1991    *          DOCUMENT ME!
1992    */
1993   public void moveSelectedSequences(boolean up)
1994   {
1995     SequenceGroup sg = viewport.getSelectionGroup();
1996
1997     if (sg == null)
1998     {
1999       return;
2000     }
2001     viewport.getAlignment().moveSelectedSequencesByOne(sg,
2002             viewport.getHiddenRepSequences(), up);
2003     alignPanel.paintAlignment(true, false);
2004   }
2005
2006   synchronized void slideSequences(boolean right, int size)
2007   {
2008     List<SequenceI> sg = new ArrayList<>();
2009     if (viewport.cursorMode)
2010     {
2011       sg.add(viewport.getAlignment()
2012               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
2013     }
2014     else if (viewport.getSelectionGroup() != null
2015             && viewport.getSelectionGroup().getSize() != viewport
2016                     .getAlignment().getHeight())
2017     {
2018       sg = viewport.getSelectionGroup()
2019               .getSequences(viewport.getHiddenRepSequences());
2020     }
2021
2022     if (sg.size() < 1)
2023     {
2024       return;
2025     }
2026
2027     List<SequenceI> invertGroup = new ArrayList<>();
2028
2029     for (SequenceI seq : viewport.getAlignment().getSequences())
2030     {
2031       if (!sg.contains(seq))
2032       {
2033         invertGroup.add(seq);
2034       }
2035     }
2036
2037     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
2038
2039     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
2040     for (int i = 0; i < invertGroup.size(); i++)
2041     {
2042       seqs2[i] = invertGroup.get(i);
2043     }
2044
2045     SlideSequencesCommand ssc;
2046     if (right)
2047     {
2048       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2049               viewport.getGapCharacter());
2050     }
2051     else
2052     {
2053       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2054               viewport.getGapCharacter());
2055     }
2056
2057     int groupAdjustment = 0;
2058     if (ssc.getGapsInsertedBegin() && right)
2059     {
2060       if (viewport.cursorMode)
2061       {
2062         alignPanel.getSeqPanel().moveCursor(size, 0);
2063       }
2064       else
2065       {
2066         groupAdjustment = size;
2067       }
2068     }
2069     else if (!ssc.getGapsInsertedBegin() && !right)
2070     {
2071       if (viewport.cursorMode)
2072       {
2073         alignPanel.getSeqPanel().moveCursor(-size, 0);
2074       }
2075       else
2076       {
2077         groupAdjustment = -size;
2078       }
2079     }
2080
2081     if (groupAdjustment != 0)
2082     {
2083       viewport.getSelectionGroup().setStartRes(
2084               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2085       viewport.getSelectionGroup().setEndRes(
2086               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2087     }
2088
2089     /*
2090      * just extend the last slide command if compatible; but not if in
2091      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2092      */
2093     boolean appendHistoryItem = false;
2094     Deque<CommandI> historyList = viewport.getHistoryList();
2095     boolean inSplitFrame = getSplitViewContainer() != null;
2096     if (!inSplitFrame && historyList != null && historyList.size() > 0
2097             && historyList.peek() instanceof SlideSequencesCommand)
2098     {
2099       appendHistoryItem = ssc.appendSlideCommand(
2100               (SlideSequencesCommand) historyList.peek());
2101     }
2102
2103     if (!appendHistoryItem)
2104     {
2105       addHistoryItem(ssc);
2106     }
2107
2108     repaint();
2109   }
2110
2111   /**
2112    * DOCUMENT ME!
2113    *
2114    * @param e
2115    *          DOCUMENT ME!
2116    */
2117   @Override
2118   protected void copy_actionPerformed(ActionEvent e)
2119   {
2120     if (viewport.getSelectionGroup() == null)
2121     {
2122       return;
2123     }
2124     // TODO: preserve the ordering of displayed alignment annotation in any
2125     // internal paste (particularly sequence associated annotation)
2126     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2127     String[] omitHidden = null;
2128
2129     if (viewport.hasHiddenColumns())
2130     {
2131       omitHidden = viewport.getViewAsString(true);
2132     }
2133
2134     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2135             seqs, omitHidden, null);
2136
2137     StringSelection ss = new StringSelection(output);
2138
2139     try
2140     {
2141       jalview.gui.Desktop.internalCopy = true;
2142       // Its really worth setting the clipboard contents
2143       // to empty before setting the large StringSelection!!
2144       Toolkit.getDefaultToolkit().getSystemClipboard()
2145               .setContents(new StringSelection(""), null);
2146
2147       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2148               Desktop.instance);
2149     } catch (OutOfMemoryError er)
2150     {
2151       new OOMWarning("copying region", er);
2152       return;
2153     }
2154
2155     HiddenColumns hiddenColumns = null;
2156     if (viewport.hasHiddenColumns())
2157     {
2158       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2159       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2160
2161       // create new HiddenColumns object with copy of hidden regions
2162       // between startRes and endRes, offset by startRes
2163       hiddenColumns = new HiddenColumns(
2164               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2165               hiddenCutoff, hiddenOffset);
2166     }
2167
2168     Desktop.jalviewClipboard = new Object[] { seqs,
2169         viewport.getAlignment().getDataset(), hiddenColumns };
2170     statusBar.setText(MessageManager.formatMessage(
2171             "label.copied_sequences_to_clipboard", new Object[]
2172             { Integer.valueOf(seqs.length).toString() }));
2173   }
2174
2175   /**
2176    * DOCUMENT ME!
2177    *
2178    * @param e
2179    *          DOCUMENT ME!
2180    * @throws InterruptedException
2181    * @throws IOException
2182    */
2183   @Override
2184   protected void pasteNew_actionPerformed(ActionEvent e)
2185           throws IOException, InterruptedException
2186   {
2187     paste(true);
2188   }
2189
2190   /**
2191    * DOCUMENT ME!
2192    *
2193    * @param e
2194    *          DOCUMENT ME!
2195    * @throws InterruptedException
2196    * @throws IOException
2197    */
2198   @Override
2199   protected void pasteThis_actionPerformed(ActionEvent e)
2200           throws IOException, InterruptedException
2201   {
2202     paste(false);
2203   }
2204
2205   /**
2206    * Paste contents of Jalview clipboard
2207    *
2208    * @param newAlignment
2209    *          true to paste to a new alignment, otherwise add to this.
2210    * @throws InterruptedException
2211    * @throws IOException
2212    */
2213   void paste(boolean newAlignment) throws IOException, InterruptedException
2214   {
2215     boolean externalPaste = true;
2216     try
2217     {
2218       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2219       Transferable contents = c.getContents(this);
2220
2221       if (contents == null)
2222       {
2223         return;
2224       }
2225
2226       String str;
2227       FileFormatI format;
2228       try
2229       {
2230         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2231         if (str.length() < 1)
2232         {
2233           return;
2234         }
2235
2236         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2237
2238       } catch (OutOfMemoryError er)
2239       {
2240         new OOMWarning("Out of memory pasting sequences!!", er);
2241         return;
2242       }
2243
2244       SequenceI[] sequences;
2245       boolean annotationAdded = false;
2246       AlignmentI alignment = null;
2247
2248       if (Desktop.jalviewClipboard != null)
2249       {
2250         // The clipboard was filled from within Jalview, we must use the
2251         // sequences
2252         // And dataset from the copied alignment
2253         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2254         // be doubly sure that we create *new* sequence objects.
2255         sequences = new SequenceI[newseq.length];
2256         for (int i = 0; i < newseq.length; i++)
2257         {
2258           sequences[i] = new Sequence(newseq[i]);
2259         }
2260         alignment = new Alignment(sequences);
2261         externalPaste = false;
2262       }
2263       else
2264       {
2265         // parse the clipboard as an alignment.
2266         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2267                 format);
2268         sequences = alignment.getSequencesArray();
2269       }
2270
2271       int alwidth = 0;
2272       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2273       int fgroup = -1;
2274
2275       if (newAlignment)
2276       {
2277
2278         if (Desktop.jalviewClipboard != null)
2279         {
2280           // dataset is inherited
2281           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2282         }
2283         else
2284         {
2285           // new dataset is constructed
2286           alignment.setDataset(null);
2287         }
2288         alwidth = alignment.getWidth() + 1;
2289       }
2290       else
2291       {
2292         AlignmentI pastedal = alignment; // preserve pasted alignment object
2293         // Add pasted sequences and dataset into existing alignment.
2294         alignment = viewport.getAlignment();
2295         alwidth = alignment.getWidth() + 1;
2296         // decide if we need to import sequences from an existing dataset
2297         boolean importDs = Desktop.jalviewClipboard != null
2298                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2299         // importDs==true instructs us to copy over new dataset sequences from
2300         // an existing alignment
2301         Vector newDs = (importDs) ? new Vector() : null; // used to create
2302         // minimum dataset set
2303
2304         for (int i = 0; i < sequences.length; i++)
2305         {
2306           if (importDs)
2307           {
2308             newDs.addElement(null);
2309           }
2310           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2311           // paste
2312           if (importDs && ds != null)
2313           {
2314             if (!newDs.contains(ds))
2315             {
2316               newDs.setElementAt(ds, i);
2317               ds = new Sequence(ds);
2318               // update with new dataset sequence
2319               sequences[i].setDatasetSequence(ds);
2320             }
2321             else
2322             {
2323               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2324             }
2325           }
2326           else
2327           {
2328             // copy and derive new dataset sequence
2329             sequences[i] = sequences[i].deriveSequence();
2330             alignment.getDataset()
2331                     .addSequence(sequences[i].getDatasetSequence());
2332             // TODO: avoid creation of duplicate dataset sequences with a
2333             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2334           }
2335           alignment.addSequence(sequences[i]); // merges dataset
2336         }
2337         if (newDs != null)
2338         {
2339           newDs.clear(); // tidy up
2340         }
2341         if (alignment.getAlignmentAnnotation() != null)
2342         {
2343           for (AlignmentAnnotation alan : alignment
2344                   .getAlignmentAnnotation())
2345           {
2346             if (alan.graphGroup > fgroup)
2347             {
2348               fgroup = alan.graphGroup;
2349             }
2350           }
2351         }
2352         if (pastedal.getAlignmentAnnotation() != null)
2353         {
2354           // Add any annotation attached to alignment.
2355           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2356           for (int i = 0; i < alann.length; i++)
2357           {
2358             annotationAdded = true;
2359             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2360             {
2361               AlignmentAnnotation newann = new AlignmentAnnotation(
2362                       alann[i]);
2363               if (newann.graphGroup > -1)
2364               {
2365                 if (newGraphGroups.size() <= newann.graphGroup
2366                         || newGraphGroups.get(newann.graphGroup) == null)
2367                 {
2368                   for (int q = newGraphGroups
2369                           .size(); q <= newann.graphGroup; q++)
2370                   {
2371                     newGraphGroups.add(q, null);
2372                   }
2373                   newGraphGroups.set(newann.graphGroup,
2374                           Integer.valueOf(++fgroup));
2375                 }
2376                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2377                         .intValue();
2378               }
2379
2380               newann.padAnnotation(alwidth);
2381               alignment.addAnnotation(newann);
2382             }
2383           }
2384         }
2385       }
2386       if (!newAlignment)
2387       {
2388         // /////
2389         // ADD HISTORY ITEM
2390         //
2391         addHistoryItem(new EditCommand(
2392                 MessageManager.getString("label.add_sequences"),
2393                 Action.PASTE, sequences, 0, alignment.getWidth(),
2394                 alignment));
2395       }
2396       // Add any annotations attached to sequences
2397       for (int i = 0; i < sequences.length; i++)
2398       {
2399         if (sequences[i].getAnnotation() != null)
2400         {
2401           AlignmentAnnotation newann;
2402           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2403           {
2404             annotationAdded = true;
2405             newann = sequences[i].getAnnotation()[a];
2406             newann.adjustForAlignment();
2407             newann.padAnnotation(alwidth);
2408             if (newann.graphGroup > -1)
2409             {
2410               if (newann.graphGroup > -1)
2411               {
2412                 if (newGraphGroups.size() <= newann.graphGroup
2413                         || newGraphGroups.get(newann.graphGroup) == null)
2414                 {
2415                   for (int q = newGraphGroups
2416                           .size(); q <= newann.graphGroup; q++)
2417                   {
2418                     newGraphGroups.add(q, null);
2419                   }
2420                   newGraphGroups.set(newann.graphGroup,
2421                           Integer.valueOf(++fgroup));
2422                 }
2423                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2424                         .intValue();
2425               }
2426             }
2427             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2428             // was
2429             // duplicated
2430             // earlier
2431             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2432                     a);
2433           }
2434         }
2435       }
2436       if (!newAlignment)
2437       {
2438
2439         // propagate alignment changed.
2440         viewport.getRanges().setEndSeq(alignment.getHeight());
2441         if (annotationAdded)
2442         {
2443           // Duplicate sequence annotation in all views.
2444           AlignmentI[] alview = this.getViewAlignments();
2445           for (int i = 0; i < sequences.length; i++)
2446           {
2447             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2448             if (sann == null)
2449             {
2450               continue;
2451             }
2452             for (int avnum = 0; avnum < alview.length; avnum++)
2453             {
2454               if (alview[avnum] != alignment)
2455               {
2456                 // duplicate in a view other than the one with input focus
2457                 int avwidth = alview[avnum].getWidth() + 1;
2458                 // this relies on sann being preserved after we
2459                 // modify the sequence's annotation array for each duplication
2460                 for (int a = 0; a < sann.length; a++)
2461                 {
2462                   AlignmentAnnotation newann = new AlignmentAnnotation(
2463                           sann[a]);
2464                   sequences[i].addAlignmentAnnotation(newann);
2465                   newann.padAnnotation(avwidth);
2466                   alview[avnum].addAnnotation(newann); // annotation was
2467                   // duplicated earlier
2468                   // TODO JAL-1145 graphGroups are not updated for sequence
2469                   // annotation added to several views. This may cause
2470                   // strangeness
2471                   alview[avnum].setAnnotationIndex(newann, a);
2472                 }
2473               }
2474             }
2475           }
2476           buildSortByAnnotationScoresMenu();
2477         }
2478         viewport.firePropertyChange("alignment", null,
2479                 alignment.getSequences());
2480         if (alignPanels != null)
2481         {
2482           for (AlignmentPanel ap : alignPanels)
2483           {
2484             ap.validateAnnotationDimensions(false);
2485           }
2486         }
2487         else
2488         {
2489           alignPanel.validateAnnotationDimensions(false);
2490         }
2491
2492       }
2493       else
2494       {
2495         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2496                 DEFAULT_HEIGHT);
2497         String newtitle = new String("Copied sequences");
2498
2499         if (Desktop.jalviewClipboard != null
2500                 && Desktop.jalviewClipboard[2] != null)
2501         {
2502           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2503           af.viewport.setHiddenColumns(hc);
2504         }
2505
2506         // >>>This is a fix for the moment, until a better solution is
2507         // found!!<<<
2508         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2509                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2510                         .getFeatureRenderer());
2511
2512         // TODO: maintain provenance of an alignment, rather than just make the
2513         // title a concatenation of operations.
2514         if (!externalPaste)
2515         {
2516           if (title.startsWith("Copied sequences"))
2517           {
2518             newtitle = title;
2519           }
2520           else
2521           {
2522             newtitle = newtitle.concat("- from " + title);
2523           }
2524         }
2525         else
2526         {
2527           newtitle = new String("Pasted sequences");
2528         }
2529
2530         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2531                 DEFAULT_HEIGHT);
2532
2533       }
2534
2535     } catch (Exception ex)
2536     {
2537       ex.printStackTrace();
2538       System.out.println("Exception whilst pasting: " + ex);
2539       // could be anything being pasted in here
2540     }
2541   }
2542
2543   @Override
2544   protected void expand_newalign(ActionEvent e)
2545   {
2546     try
2547     {
2548       AlignmentI alignment = AlignmentUtils
2549               .expandContext(getViewport().getAlignment(), -1);
2550       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2551               DEFAULT_HEIGHT);
2552       String newtitle = new String("Flanking alignment");
2553
2554       if (Desktop.jalviewClipboard != null
2555               && Desktop.jalviewClipboard[2] != null)
2556       {
2557         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2558         af.viewport.setHiddenColumns(hc);
2559       }
2560
2561       // >>>This is a fix for the moment, until a better solution is
2562       // found!!<<<
2563       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2564               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2565                       .getFeatureRenderer());
2566
2567       // TODO: maintain provenance of an alignment, rather than just make the
2568       // title a concatenation of operations.
2569       {
2570         if (title.startsWith("Copied sequences"))
2571         {
2572           newtitle = title;
2573         }
2574         else
2575         {
2576           newtitle = newtitle.concat("- from " + title);
2577         }
2578       }
2579
2580       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2581
2582     } catch (Exception ex)
2583     {
2584       ex.printStackTrace();
2585       System.out.println("Exception whilst pasting: " + ex);
2586       // could be anything being pasted in here
2587     } catch (OutOfMemoryError oom)
2588     {
2589       new OOMWarning("Viewing flanking region of alignment", oom);
2590     }
2591   }
2592
2593   /**
2594    * DOCUMENT ME!
2595    *
2596    * @param e
2597    *          DOCUMENT ME!
2598    */
2599   @Override
2600   protected void cut_actionPerformed(ActionEvent e)
2601   {
2602     copy_actionPerformed(null);
2603     delete_actionPerformed(null);
2604   }
2605
2606   /**
2607    * DOCUMENT ME!
2608    *
2609    * @param e
2610    *          DOCUMENT ME!
2611    */
2612   @Override
2613   protected void delete_actionPerformed(ActionEvent evt)
2614   {
2615
2616     SequenceGroup sg = viewport.getSelectionGroup();
2617     if (sg == null)
2618     {
2619       return;
2620     }
2621
2622     /*
2623      * If the cut affects all sequences, warn, remove highlighted columns
2624      */
2625     if (sg.getSize() == viewport.getAlignment().getHeight())
2626     {
2627       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2628               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2629       if (isEntireAlignWidth)
2630       {
2631         int confirm = JvOptionPane.showConfirmDialog(this,
2632                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2633                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2634                 JvOptionPane.OK_CANCEL_OPTION);
2635
2636         if (confirm == JvOptionPane.CANCEL_OPTION
2637                 || confirm == JvOptionPane.CLOSED_OPTION)
2638         {
2639           return;
2640         }
2641       }
2642       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2643               sg.getEndRes() + 1);
2644     }
2645     SequenceI[] cut = sg.getSequences()
2646             .toArray(new SequenceI[sg.getSize()]);
2647
2648     addHistoryItem(new EditCommand(
2649             MessageManager.getString("label.cut_sequences"), Action.CUT,
2650             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2651             viewport.getAlignment()));
2652
2653     viewport.setSelectionGroup(null);
2654     viewport.sendSelection();
2655     viewport.getAlignment().deleteGroup(sg);
2656
2657     viewport.firePropertyChange("alignment", null,
2658             viewport.getAlignment().getSequences());
2659     if (viewport.getAlignment().getHeight() < 1)
2660     {
2661       try
2662       {
2663         this.setClosed(true);
2664       } catch (Exception ex)
2665       {
2666       }
2667     }
2668   }
2669
2670   /**
2671    * DOCUMENT ME!
2672    *
2673    * @param e
2674    *          DOCUMENT ME!
2675    */
2676   @Override
2677   protected void deleteGroups_actionPerformed(ActionEvent e)
2678   {
2679     if (avc.deleteGroups())
2680     {
2681       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2682       alignPanel.updateAnnotation();
2683       alignPanel.paintAlignment(true, true);
2684     }
2685   }
2686
2687   /**
2688    * DOCUMENT ME!
2689    *
2690    * @param e
2691    *          DOCUMENT ME!
2692    */
2693   @Override
2694   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2695   {
2696     SequenceGroup sg = new SequenceGroup(
2697             viewport.getAlignment().getSequences());
2698
2699     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2700     viewport.setSelectionGroup(sg);
2701     viewport.isSelectionGroupChanged(true);
2702     viewport.sendSelection();
2703     // JAL-2034 - should delegate to
2704     // alignPanel to decide if overview needs
2705     // updating.
2706     alignPanel.paintAlignment(false, false);
2707     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2708   }
2709
2710   /**
2711    * DOCUMENT ME!
2712    *
2713    * @param e
2714    *          DOCUMENT ME!
2715    */
2716   @Override
2717   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2718   {
2719     if (viewport.cursorMode)
2720     {
2721       alignPanel.getSeqPanel().keyboardNo1 = null;
2722       alignPanel.getSeqPanel().keyboardNo2 = null;
2723     }
2724     viewport.setSelectionGroup(null);
2725     viewport.getColumnSelection().clear();
2726     viewport.setSelectionGroup(null);
2727     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2728     // JAL-2034 - should delegate to
2729     // alignPanel to decide if overview needs
2730     // updating.
2731     alignPanel.paintAlignment(false, false);
2732     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2733     viewport.sendSelection();
2734   }
2735
2736   /**
2737    * DOCUMENT ME!
2738    *
2739    * @param e
2740    *          DOCUMENT ME!
2741    */
2742   @Override
2743   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2744   {
2745     SequenceGroup sg = viewport.getSelectionGroup();
2746
2747     if (sg == null)
2748     {
2749       selectAllSequenceMenuItem_actionPerformed(null);
2750
2751       return;
2752     }
2753
2754     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2755     {
2756       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2757     }
2758     // JAL-2034 - should delegate to
2759     // alignPanel to decide if overview needs
2760     // updating.
2761
2762     alignPanel.paintAlignment(true, false);
2763     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2764     viewport.sendSelection();
2765   }
2766
2767   @Override
2768   public void invertColSel_actionPerformed(ActionEvent e)
2769   {
2770     viewport.invertColumnSelection();
2771     alignPanel.paintAlignment(true, false);
2772     viewport.sendSelection();
2773   }
2774
2775   /**
2776    * DOCUMENT ME!
2777    *
2778    * @param e
2779    *          DOCUMENT ME!
2780    */
2781   @Override
2782   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2783   {
2784     trimAlignment(true);
2785   }
2786
2787   /**
2788    * DOCUMENT ME!
2789    *
2790    * @param e
2791    *          DOCUMENT ME!
2792    */
2793   @Override
2794   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2795   {
2796     trimAlignment(false);
2797   }
2798
2799   void trimAlignment(boolean trimLeft)
2800   {
2801     ColumnSelection colSel = viewport.getColumnSelection();
2802     int column;
2803
2804     if (!colSel.isEmpty())
2805     {
2806       if (trimLeft)
2807       {
2808         column = colSel.getMin();
2809       }
2810       else
2811       {
2812         column = colSel.getMax();
2813       }
2814
2815       SequenceI[] seqs;
2816       if (viewport.getSelectionGroup() != null)
2817       {
2818         seqs = viewport.getSelectionGroup()
2819                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2820       }
2821       else
2822       {
2823         seqs = viewport.getAlignment().getSequencesArray();
2824       }
2825
2826       TrimRegionCommand trimRegion;
2827       if (trimLeft)
2828       {
2829         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2830                 column, viewport.getAlignment());
2831         viewport.getRanges().setStartRes(0);
2832       }
2833       else
2834       {
2835         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2836                 column, viewport.getAlignment());
2837       }
2838
2839       statusBar.setText(MessageManager
2840               .formatMessage("label.removed_columns", new String[]
2841               { Integer.valueOf(trimRegion.getSize()).toString() }));
2842
2843       addHistoryItem(trimRegion);
2844
2845       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2846       {
2847         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2848                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2849         {
2850           viewport.getAlignment().deleteGroup(sg);
2851         }
2852       }
2853
2854       viewport.firePropertyChange("alignment", null,
2855               viewport.getAlignment().getSequences());
2856     }
2857   }
2858
2859   /**
2860    * DOCUMENT ME!
2861    *
2862    * @param e
2863    *          DOCUMENT ME!
2864    */
2865   @Override
2866   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2867   {
2868     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2869
2870     SequenceI[] seqs;
2871     if (viewport.getSelectionGroup() != null)
2872     {
2873       seqs = viewport.getSelectionGroup()
2874               .getSequencesAsArray(viewport.getHiddenRepSequences());
2875       start = viewport.getSelectionGroup().getStartRes();
2876       end = viewport.getSelectionGroup().getEndRes();
2877     }
2878     else
2879     {
2880       seqs = viewport.getAlignment().getSequencesArray();
2881     }
2882
2883     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2884             "Remove Gapped Columns", seqs, start, end,
2885             viewport.getAlignment());
2886
2887     addHistoryItem(removeGapCols);
2888
2889     statusBar.setText(MessageManager
2890             .formatMessage("label.removed_empty_columns", new Object[]
2891             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2892
2893     // This is to maintain viewport position on first residue
2894     // of first sequence
2895     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2896     ViewportRanges ranges = viewport.getRanges();
2897     int startRes = seq.findPosition(ranges.getStartRes());
2898     // ShiftList shifts;
2899     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2900     // edit.alColumnChanges=shifts.getInverse();
2901     // if (viewport.hasHiddenColumns)
2902     // viewport.getColumnSelection().compensateForEdits(shifts);
2903     ranges.setStartRes(seq.findIndex(startRes) - 1);
2904     viewport.firePropertyChange("alignment", null,
2905             viewport.getAlignment().getSequences());
2906
2907   }
2908
2909   /**
2910    * DOCUMENT ME!
2911    *
2912    * @param e
2913    *          DOCUMENT ME!
2914    */
2915   @Override
2916   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2917   {
2918     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2919
2920     SequenceI[] seqs;
2921     if (viewport.getSelectionGroup() != null)
2922     {
2923       seqs = viewport.getSelectionGroup()
2924               .getSequencesAsArray(viewport.getHiddenRepSequences());
2925       start = viewport.getSelectionGroup().getStartRes();
2926       end = viewport.getSelectionGroup().getEndRes();
2927     }
2928     else
2929     {
2930       seqs = viewport.getAlignment().getSequencesArray();
2931     }
2932
2933     // This is to maintain viewport position on first residue
2934     // of first sequence
2935     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2936     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2937
2938     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2939             viewport.getAlignment()));
2940
2941     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2942
2943     viewport.firePropertyChange("alignment", null,
2944             viewport.getAlignment().getSequences());
2945
2946   }
2947
2948   /**
2949    * DOCUMENT ME!
2950    *
2951    * @param e
2952    *          DOCUMENT ME!
2953    */
2954   @Override
2955   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2956   {
2957     viewport.setPadGaps(padGapsMenuitem.isSelected());
2958     viewport.firePropertyChange("alignment", null,
2959             viewport.getAlignment().getSequences());
2960   }
2961
2962   /**
2963    * DOCUMENT ME!
2964    *
2965    * @param e
2966    *          DOCUMENT ME!
2967    */
2968   @Override
2969   public void findMenuItem_actionPerformed(ActionEvent e)
2970   {
2971     new Finder();
2972   }
2973
2974   /**
2975    * Create a new view of the current alignment.
2976    */
2977   @Override
2978   public void newView_actionPerformed(ActionEvent e)
2979   {
2980     newView(null, true);
2981   }
2982
2983   /**
2984    * Creates and shows a new view of the current alignment.
2985    *
2986    * @param viewTitle
2987    *          title of newly created view; if null, one will be generated
2988    * @param copyAnnotation
2989    *          if true then duplicate all annnotation, groups and settings
2990    * @return new alignment panel, already displayed.
2991    */
2992   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2993   {
2994     /*
2995      * Create a new AlignmentPanel (with its own, new Viewport)
2996      */
2997     AlignmentPanel newap = new jalview.project.Jalview2XML()
2998             .copyAlignPanel(alignPanel);
2999     if (!copyAnnotation)
3000     {
3001       /*
3002        * remove all groups and annotation except for the automatic stuff
3003        */
3004       newap.av.getAlignment().deleteAllGroups();
3005       newap.av.getAlignment().deleteAllAnnotations(false);
3006     }
3007
3008     newap.av.setGatherViewsHere(false);
3009
3010     if (viewport.getViewName() == null)
3011     {
3012       viewport.setViewName(MessageManager
3013               .getString("label.view_name_original"));
3014     }
3015
3016     /*
3017      * Views share the same edits undo and redo stacks
3018      */
3019     newap.av.setHistoryList(viewport.getHistoryList());
3020     newap.av.setRedoList(viewport.getRedoList());
3021
3022     /*
3023      * copy any visualisation settings that are not saved in the project
3024      */
3025     newap.av.setColourAppliesToAllGroups(
3026             viewport.getColourAppliesToAllGroups());
3027
3028     /*
3029      * Views share the same mappings; need to deregister any new mappings
3030      * created by copyAlignPanel, and register the new reference to the shared
3031      * mappings
3032      */
3033     newap.av.replaceMappings(viewport.getAlignment());
3034
3035     /*
3036      * start up cDNA consensus (if applicable) now mappings are in place
3037      */
3038     if (newap.av.initComplementConsensus())
3039     {
3040       newap.refresh(true); // adjust layout of annotations
3041     }
3042
3043     newap.av.setViewName(getNewViewName(viewTitle));
3044
3045     addAlignmentPanel(newap, true);
3046     newap.alignmentChanged();
3047
3048     if (alignPanels.size() == 2)
3049     {
3050       viewport.setGatherViewsHere(true);
3051     }
3052     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3053     return newap;
3054   }
3055
3056   /**
3057    * Make a new name for the view, ensuring it is unique within the current
3058    * sequenceSetId. (This used to be essential for Jalview Project archives, but
3059    * these now use viewId. Unique view names are still desirable for usability.)
3060    *
3061    * @param viewTitle
3062    * @return
3063    */
3064   protected String getNewViewName(String viewTitle)
3065   {
3066     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3067     boolean addFirstIndex = false;
3068     if (viewTitle == null || viewTitle.trim().length() == 0)
3069     {
3070       viewTitle = MessageManager.getString("action.view");
3071       addFirstIndex = true;
3072     }
3073     else
3074     {
3075       index = 1;// we count from 1 if given a specific name
3076     }
3077     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3078
3079     List<Component> comps = PaintRefresher.components
3080             .get(viewport.getSequenceSetId());
3081
3082     List<String> existingNames = getExistingViewNames(comps);
3083
3084     while (existingNames.contains(newViewName))
3085     {
3086       newViewName = viewTitle + " " + (++index);
3087     }
3088     return newViewName;
3089   }
3090
3091   /**
3092    * Returns a list of distinct view names found in the given list of
3093    * components. View names are held on the viewport of an AlignmentPanel.
3094    *
3095    * @param comps
3096    * @return
3097    */
3098   protected List<String> getExistingViewNames(List<Component> comps)
3099   {
3100     List<String> existingNames = new ArrayList<>();
3101     for (Component comp : comps)
3102     {
3103       if (comp instanceof AlignmentPanel)
3104       {
3105         AlignmentPanel ap = (AlignmentPanel) comp;
3106         if (!existingNames.contains(ap.av.getViewName()))
3107         {
3108           existingNames.add(ap.av.getViewName());
3109         }
3110       }
3111     }
3112     return existingNames;
3113   }
3114
3115   /**
3116    * Explode tabbed views into separate windows.
3117    */
3118   @Override
3119   public void expandViews_actionPerformed(ActionEvent e)
3120   {
3121     Desktop.explodeViews(this);
3122   }
3123
3124   /**
3125    * Gather views in separate windows back into a tabbed presentation.
3126    */
3127   @Override
3128   public void gatherViews_actionPerformed(ActionEvent e)
3129   {
3130     Desktop.instance.gatherViews(this);
3131   }
3132
3133   /**
3134    * DOCUMENT ME!
3135    *
3136    * @param e
3137    *          DOCUMENT ME!
3138    */
3139   @Override
3140   public void font_actionPerformed(ActionEvent e)
3141   {
3142     new FontChooser(alignPanel);
3143   }
3144
3145   /**
3146    * DOCUMENT ME!
3147    *
3148    * @param e
3149    *          DOCUMENT ME!
3150    */
3151   @Override
3152   protected void seqLimit_actionPerformed(ActionEvent e)
3153   {
3154     viewport.setShowJVSuffix(seqLimits.isSelected());
3155
3156     alignPanel.getIdPanel().getIdCanvas()
3157             .setPreferredSize(alignPanel.calculateIdWidth());
3158     alignPanel.paintAlignment(true, false);
3159   }
3160
3161   @Override
3162   public void idRightAlign_actionPerformed(ActionEvent e)
3163   {
3164     viewport.setRightAlignIds(idRightAlign.isSelected());
3165     alignPanel.paintAlignment(false, false);
3166   }
3167
3168   @Override
3169   public void centreColumnLabels_actionPerformed(ActionEvent e)
3170   {
3171     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3172     alignPanel.paintAlignment(false, false);
3173   }
3174
3175   /*
3176    * (non-Javadoc)
3177    *
3178    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3179    */
3180   @Override
3181   protected void followHighlight_actionPerformed()
3182   {
3183     /*
3184      * Set the 'follow' flag on the Viewport (and scroll to position if now
3185      * true).
3186      */
3187     final boolean state = this.followHighlightMenuItem.getState();
3188     viewport.setFollowHighlight(state);
3189     if (state)
3190     {
3191       alignPanel.scrollToPosition(viewport.getSearchResults());
3192     }
3193   }
3194
3195   /**
3196    * DOCUMENT ME!
3197    *
3198    * @param e
3199    *          DOCUMENT ME!
3200    */
3201   @Override
3202   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3203   {
3204     viewport.setColourText(colourTextMenuItem.isSelected());
3205     alignPanel.paintAlignment(false, false);
3206   }
3207
3208   /**
3209    * DOCUMENT ME!
3210    *
3211    * @param e
3212    *          DOCUMENT ME!
3213    */
3214   @Override
3215   public void wrapMenuItem_actionPerformed(ActionEvent e)
3216   {
3217     scaleAbove.setVisible(wrapMenuItem.isSelected());
3218     scaleLeft.setVisible(wrapMenuItem.isSelected());
3219     scaleRight.setVisible(wrapMenuItem.isSelected());
3220     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3221     alignPanel.updateLayout();
3222   }
3223
3224   @Override
3225   public void showAllSeqs_actionPerformed(ActionEvent e)
3226   {
3227     viewport.showAllHiddenSeqs();
3228   }
3229
3230   @Override
3231   public void showAllColumns_actionPerformed(ActionEvent e)
3232   {
3233     viewport.showAllHiddenColumns();
3234     alignPanel.paintAlignment(true, true);
3235     viewport.sendSelection();
3236   }
3237
3238   @Override
3239   public void hideSelSequences_actionPerformed(ActionEvent e)
3240   {
3241     viewport.hideAllSelectedSeqs();
3242   }
3243
3244   /**
3245    * called by key handler and the hide all/show all menu items
3246    *
3247    * @param toggleSeqs
3248    * @param toggleCols
3249    */
3250   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3251   {
3252
3253     boolean hide = false;
3254     SequenceGroup sg = viewport.getSelectionGroup();
3255     if (!toggleSeqs && !toggleCols)
3256     {
3257       // Hide everything by the current selection - this is a hack - we do the
3258       // invert and then hide
3259       // first check that there will be visible columns after the invert.
3260       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3261               && sg.getStartRes() <= sg.getEndRes()))
3262       {
3263         // now invert the sequence set, if required - empty selection implies
3264         // that no hiding is required.
3265         if (sg != null)
3266         {
3267           invertSequenceMenuItem_actionPerformed(null);
3268           sg = viewport.getSelectionGroup();
3269           toggleSeqs = true;
3270
3271         }
3272         viewport.expandColSelection(sg, true);
3273         // finally invert the column selection and get the new sequence
3274         // selection.
3275         invertColSel_actionPerformed(null);
3276         toggleCols = true;
3277       }
3278     }
3279
3280     if (toggleSeqs)
3281     {
3282       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3283       {
3284         hideSelSequences_actionPerformed(null);
3285         hide = true;
3286       }
3287       else if (!(toggleCols && viewport.hasSelectedColumns()))
3288       {
3289         showAllSeqs_actionPerformed(null);
3290       }
3291     }
3292
3293     if (toggleCols)
3294     {
3295       if (viewport.hasSelectedColumns())
3296       {
3297         hideSelColumns_actionPerformed(null);
3298         if (!toggleSeqs)
3299         {
3300           viewport.setSelectionGroup(sg);
3301         }
3302       }
3303       else if (!hide)
3304       {
3305         showAllColumns_actionPerformed(null);
3306       }
3307     }
3308   }
3309
3310   /*
3311    * (non-Javadoc)
3312    *
3313    * @see
3314    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3315    * event.ActionEvent)
3316    */
3317   @Override
3318   public void hideAllButSelection_actionPerformed(ActionEvent e)
3319   {
3320     toggleHiddenRegions(false, false);
3321     viewport.sendSelection();
3322   }
3323
3324   /*
3325    * (non-Javadoc)
3326    *
3327    * @see
3328    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3329    * .ActionEvent)
3330    */
3331   @Override
3332   public void hideAllSelection_actionPerformed(ActionEvent e)
3333   {
3334     SequenceGroup sg = viewport.getSelectionGroup();
3335     viewport.expandColSelection(sg, false);
3336     viewport.hideAllSelectedSeqs();
3337     viewport.hideSelectedColumns();
3338     alignPanel.updateLayout();
3339     alignPanel.paintAlignment(true, true);
3340     viewport.sendSelection();
3341   }
3342
3343   /*
3344    * (non-Javadoc)
3345    *
3346    * @see
3347    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3348    * ActionEvent)
3349    */
3350   @Override
3351   public void showAllhidden_actionPerformed(ActionEvent e)
3352   {
3353     viewport.showAllHiddenColumns();
3354     viewport.showAllHiddenSeqs();
3355     alignPanel.paintAlignment(true, true);
3356     viewport.sendSelection();
3357   }
3358
3359   @Override
3360   public void hideSelColumns_actionPerformed(ActionEvent e)
3361   {
3362     viewport.hideSelectedColumns();
3363     alignPanel.updateLayout();
3364     alignPanel.paintAlignment(true, true);
3365     viewport.sendSelection();
3366   }
3367
3368   @Override
3369   public void hiddenMarkers_actionPerformed(ActionEvent e)
3370   {
3371     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3372     repaint();
3373   }
3374
3375   /**
3376    * DOCUMENT ME!
3377    *
3378    * @param e
3379    *          DOCUMENT ME!
3380    */
3381   @Override
3382   protected void scaleAbove_actionPerformed(ActionEvent e)
3383   {
3384     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3385     alignPanel.updateLayout();
3386     alignPanel.paintAlignment(true, false);
3387   }
3388
3389   /**
3390    * DOCUMENT ME!
3391    *
3392    * @param e
3393    *          DOCUMENT ME!
3394    */
3395   @Override
3396   protected void scaleLeft_actionPerformed(ActionEvent e)
3397   {
3398     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3399     alignPanel.updateLayout();
3400     alignPanel.paintAlignment(true, false);
3401   }
3402
3403   /**
3404    * DOCUMENT ME!
3405    *
3406    * @param e
3407    *          DOCUMENT ME!
3408    */
3409   @Override
3410   protected void scaleRight_actionPerformed(ActionEvent e)
3411   {
3412     viewport.setScaleRightWrapped(scaleRight.isSelected());
3413     alignPanel.updateLayout();
3414     alignPanel.paintAlignment(true, false);
3415   }
3416
3417   /**
3418    * DOCUMENT ME!
3419    *
3420    * @param e
3421    *          DOCUMENT ME!
3422    */
3423   @Override
3424   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3425   {
3426     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3427     alignPanel.paintAlignment(false, false);
3428   }
3429
3430   /**
3431    * DOCUMENT ME!
3432    *
3433    * @param e
3434    *          DOCUMENT ME!
3435    */
3436   @Override
3437   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3438   {
3439     viewport.setShowText(viewTextMenuItem.isSelected());
3440     alignPanel.paintAlignment(false, false);
3441   }
3442
3443   /**
3444    * DOCUMENT ME!
3445    *
3446    * @param e
3447    *          DOCUMENT ME!
3448    */
3449   @Override
3450   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3451   {
3452     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3453     alignPanel.paintAlignment(false, false);
3454   }
3455
3456   public FeatureSettings featureSettings;
3457
3458   @Override
3459   public FeatureSettingsControllerI getFeatureSettingsUI()
3460   {
3461     return featureSettings;
3462   }
3463
3464   @Override
3465   public void featureSettings_actionPerformed(ActionEvent e)
3466   {
3467     if (featureSettings != null)
3468     {
3469       featureSettings.close();
3470       featureSettings = null;
3471     }
3472     if (!showSeqFeatures.isSelected())
3473     {
3474       // make sure features are actually displayed
3475       showSeqFeatures.setSelected(true);
3476       showSeqFeatures_actionPerformed(null);
3477     }
3478     featureSettings = new FeatureSettings(this);
3479   }
3480
3481   /**
3482    * Set or clear 'Show Sequence Features'
3483    *
3484    * @param evt
3485    *          DOCUMENT ME!
3486    */
3487   @Override
3488   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3489   {
3490     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3491     alignPanel.paintAlignment(true, true);
3492   }
3493
3494   /**
3495    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3496    * the annotations panel as a whole.
3497    *
3498    * The options to show/hide all annotations should be enabled when the panel
3499    * is shown, and disabled when the panel is hidden.
3500    *
3501    * @param e
3502    */
3503   @Override
3504   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3505   {
3506     final boolean setVisible = annotationPanelMenuItem.isSelected();
3507     viewport.setShowAnnotation(setVisible);
3508     this.showAllSeqAnnotations.setEnabled(setVisible);
3509     this.hideAllSeqAnnotations.setEnabled(setVisible);
3510     this.showAllAlAnnotations.setEnabled(setVisible);
3511     this.hideAllAlAnnotations.setEnabled(setVisible);
3512     alignPanel.updateLayout();
3513   }
3514
3515   @Override
3516   public void alignmentProperties()
3517   {
3518     JEditorPane editPane = new JEditorPane("text/html", "");
3519     editPane.setEditable(false);
3520     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3521             .formatAsHtml();
3522     editPane.setText(
3523             MessageManager.formatMessage("label.html_content", new Object[]
3524             { contents.toString() }));
3525     JInternalFrame frame = new JInternalFrame();
3526     frame.getContentPane().add(new JScrollPane(editPane));
3527
3528     Desktop.addInternalFrame(frame, MessageManager
3529             .formatMessage("label.alignment_properties", new Object[]
3530             { getTitle() }), 500, 400);
3531   }
3532
3533   /**
3534    * DOCUMENT ME!
3535    *
3536    * @param e
3537    *          DOCUMENT ME!
3538    */
3539   @Override
3540   public void overviewMenuItem_actionPerformed(ActionEvent e)
3541   {
3542     if (alignPanel.overviewPanel != null)
3543     {
3544       return;
3545     }
3546
3547     JInternalFrame frame = new JInternalFrame();
3548     final OverviewPanel overview = new OverviewPanel(alignPanel);
3549     frame.setContentPane(overview);
3550     Desktop.addInternalFrame(frame, MessageManager
3551             .formatMessage("label.overview_params", new Object[]
3552             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3553             true, true);
3554     frame.pack();
3555     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3556     frame.addInternalFrameListener(
3557             new javax.swing.event.InternalFrameAdapter()
3558             {
3559               @Override
3560               public void internalFrameClosed(
3561                       javax.swing.event.InternalFrameEvent evt)
3562               {
3563                 overview.dispose();
3564                 alignPanel.setOverviewPanel(null);
3565               };
3566             });
3567     if (getKeyListeners().length > 0)
3568     {
3569       frame.addKeyListener(getKeyListeners()[0]);
3570     }
3571
3572     alignPanel.setOverviewPanel(overview);
3573   }
3574
3575   @Override
3576   public void textColour_actionPerformed()
3577   {
3578     new TextColourChooser().chooseColour(alignPanel, null);
3579   }
3580
3581   /*
3582    * public void covariationColour_actionPerformed() {
3583    * changeColour(new
3584    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3585    * ()[0])); }
3586    */
3587   @Override
3588   public void annotationColour_actionPerformed()
3589   {
3590     new AnnotationColourChooser(viewport, alignPanel);
3591   }
3592
3593   @Override
3594   public void annotationColumn_actionPerformed(ActionEvent e)
3595   {
3596     new AnnotationColumnChooser(viewport, alignPanel);
3597   }
3598
3599   /**
3600    * Action on the user checking or unchecking the option to apply the selected
3601    * colour scheme to all groups. If unchecked, groups may have their own
3602    * independent colour schemes.
3603    *
3604    * @param selected
3605    */
3606   @Override
3607   public void applyToAllGroups_actionPerformed(boolean selected)
3608   {
3609     viewport.setColourAppliesToAllGroups(selected);
3610   }
3611
3612   /**
3613    * Action on user selecting a colour from the colour menu
3614    *
3615    * @param name
3616    *          the name (not the menu item label!) of the colour scheme
3617    */
3618   @Override
3619   public void changeColour_actionPerformed(String name)
3620   {
3621     /*
3622      * 'User Defined' opens a panel to configure or load a
3623      * user-defined colour scheme
3624      */
3625     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3626     {
3627       new UserDefinedColours(alignPanel);
3628       return;
3629     }
3630
3631     /*
3632      * otherwise set the chosen colour scheme (or null for 'None')
3633      */
3634     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3635             viewport,
3636             viewport.getAlignment(), viewport.getHiddenRepSequences());
3637     changeColour(cs);
3638   }
3639
3640   /**
3641    * Actions on setting or changing the alignment colour scheme
3642    *
3643    * @param cs
3644    */
3645   @Override
3646   public void changeColour(ColourSchemeI cs)
3647   {
3648     // TODO: pull up to controller method
3649     ColourMenuHelper.setColourSelected(colourMenu, cs);
3650
3651     viewport.setGlobalColourScheme(cs);
3652
3653     alignPanel.paintAlignment(true, true);
3654   }
3655
3656   /**
3657    * Show the PID threshold slider panel
3658    */
3659   @Override
3660   protected void modifyPID_actionPerformed()
3661   {
3662     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3663             alignPanel.getViewName());
3664     SliderPanel.showPIDSlider();
3665   }
3666
3667   /**
3668    * Show the Conservation slider panel
3669    */
3670   @Override
3671   protected void modifyConservation_actionPerformed()
3672   {
3673     SliderPanel.setConservationSlider(alignPanel,
3674             viewport.getResidueShading(), alignPanel.getViewName());
3675     SliderPanel.showConservationSlider();
3676   }
3677
3678   /**
3679    * Action on selecting or deselecting (Colour) By Conservation
3680    */
3681   @Override
3682   public void conservationMenuItem_actionPerformed(boolean selected)
3683   {
3684     modifyConservation.setEnabled(selected);
3685     viewport.setConservationSelected(selected);
3686     viewport.getResidueShading().setConservationApplied(selected);
3687
3688     changeColour(viewport.getGlobalColourScheme());
3689     if (selected)
3690     {
3691       modifyConservation_actionPerformed();
3692     }
3693     else
3694     {
3695       SliderPanel.hideConservationSlider();
3696     }
3697   }
3698
3699   /**
3700    * Action on selecting or deselecting (Colour) Above PID Threshold
3701    */
3702   @Override
3703   public void abovePIDThreshold_actionPerformed(boolean selected)
3704   {
3705     modifyPID.setEnabled(selected);
3706     viewport.setAbovePIDThreshold(selected);
3707     if (!selected)
3708     {
3709       viewport.getResidueShading().setThreshold(0,
3710               viewport.isIgnoreGapsConsensus());
3711     }
3712
3713     changeColour(viewport.getGlobalColourScheme());
3714     if (selected)
3715     {
3716       modifyPID_actionPerformed();
3717     }
3718     else
3719     {
3720       SliderPanel.hidePIDSlider();
3721     }
3722   }
3723
3724   /**
3725    * DOCUMENT ME!
3726    *
3727    * @param e
3728    *          DOCUMENT ME!
3729    */
3730   @Override
3731   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3732   {
3733     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3734     AlignmentSorter.sortByPID(viewport.getAlignment(),
3735             viewport.getAlignment().getSequenceAt(0));
3736     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3737             viewport.getAlignment()));
3738     alignPanel.paintAlignment(true, false);
3739   }
3740
3741   /**
3742    * DOCUMENT ME!
3743    *
3744    * @param e
3745    *          DOCUMENT ME!
3746    */
3747   @Override
3748   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3749   {
3750     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751     AlignmentSorter.sortByID(viewport.getAlignment());
3752     addHistoryItem(
3753             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3754     alignPanel.paintAlignment(true, false);
3755   }
3756
3757   /**
3758    * DOCUMENT ME!
3759    *
3760    * @param e
3761    *          DOCUMENT ME!
3762    */
3763   @Override
3764   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3765   {
3766     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3767     AlignmentSorter.sortByLength(viewport.getAlignment());
3768     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3769             viewport.getAlignment()));
3770     alignPanel.paintAlignment(true, false);
3771   }
3772
3773   /**
3774    * DOCUMENT ME!
3775    *
3776    * @param e
3777    *          DOCUMENT ME!
3778    */
3779   @Override
3780   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3781   {
3782     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3783     AlignmentSorter.sortByGroup(viewport.getAlignment());
3784     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3785             viewport.getAlignment()));
3786
3787     alignPanel.paintAlignment(true, false);
3788   }
3789
3790   /**
3791    * DOCUMENT ME!
3792    *
3793    * @param e
3794    *          DOCUMENT ME!
3795    */
3796   @Override
3797   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3798   {
3799     new RedundancyPanel(alignPanel, this);
3800   }
3801
3802   /**
3803    * DOCUMENT ME!
3804    *
3805    * @param e
3806    *          DOCUMENT ME!
3807    */
3808   @Override
3809   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3810   {
3811     if ((viewport.getSelectionGroup() == null)
3812             || (viewport.getSelectionGroup().getSize() < 2))
3813     {
3814       JvOptionPane.showInternalMessageDialog(this,
3815               MessageManager.getString(
3816                       "label.you_must_select_least_two_sequences"),
3817               MessageManager.getString("label.invalid_selection"),
3818               JvOptionPane.WARNING_MESSAGE);
3819     }
3820     else
3821     {
3822       JInternalFrame frame = new JInternalFrame();
3823       frame.setContentPane(new PairwiseAlignPanel(viewport));
3824       Desktop.addInternalFrame(frame,
3825               MessageManager.getString("action.pairwise_alignment"), 600,
3826               500);
3827     }
3828   }
3829
3830   @Override
3831   public void autoCalculate_actionPerformed(ActionEvent e)
3832   {
3833     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3834     if (viewport.autoCalculateConsensus)
3835     {
3836       viewport.firePropertyChange("alignment", null,
3837               viewport.getAlignment().getSequences());
3838     }
3839   }
3840
3841   @Override
3842   public void sortByTreeOption_actionPerformed(ActionEvent e)
3843   {
3844     viewport.sortByTree = sortByTree.isSelected();
3845   }
3846
3847   @Override
3848   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3849   {
3850     viewport.followSelection = listenToViewSelections.isSelected();
3851   }
3852
3853   /**
3854    * Constructs a tree panel and adds it to the desktop
3855    *
3856    * @param type
3857    *          tree type (NJ or AV)
3858    * @param modelName
3859    *          name of score model used to compute the tree
3860    * @param options
3861    *          parameters for the distance or similarity calculation
3862    */
3863   void newTreePanel(String type, String modelName,
3864           SimilarityParamsI options)
3865   {
3866     String frameTitle = "";
3867     TreePanel tp;
3868
3869     boolean onSelection = false;
3870     if (viewport.getSelectionGroup() != null
3871             && viewport.getSelectionGroup().getSize() > 0)
3872     {
3873       SequenceGroup sg = viewport.getSelectionGroup();
3874
3875       /* Decide if the selection is a column region */
3876       for (SequenceI _s : sg.getSequences())
3877       {
3878         if (_s.getLength() < sg.getEndRes())
3879         {
3880           JvOptionPane.showMessageDialog(Desktop.desktop,
3881                   MessageManager.getString(
3882                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3883                   MessageManager.getString(
3884                           "label.sequences_selection_not_aligned"),
3885                   JvOptionPane.WARNING_MESSAGE);
3886
3887           return;
3888         }
3889       }
3890       onSelection = true;
3891     }
3892     else
3893     {
3894       if (viewport.getAlignment().getHeight() < 2)
3895       {
3896         return;
3897       }
3898     }
3899
3900     tp = new TreePanel(alignPanel, type, modelName, options);
3901     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3902
3903     frameTitle += " from ";
3904
3905     if (viewport.getViewName() != null)
3906     {
3907       frameTitle += viewport.getViewName() + " of ";
3908     }
3909
3910     frameTitle += this.title;
3911
3912     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3913   }
3914
3915   /**
3916    * DOCUMENT ME!
3917    *
3918    * @param title
3919    *          DOCUMENT ME!
3920    * @param order
3921    *          DOCUMENT ME!
3922    */
3923   public void addSortByOrderMenuItem(String title,
3924           final AlignmentOrder order)
3925   {
3926     final JMenuItem item = new JMenuItem(MessageManager
3927             .formatMessage("action.by_title_param", new Object[]
3928             { title }));
3929     sort.add(item);
3930     item.addActionListener(new java.awt.event.ActionListener()
3931     {
3932       @Override
3933       public void actionPerformed(ActionEvent e)
3934       {
3935         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3936
3937         // TODO: JBPNote - have to map order entries to curent SequenceI
3938         // pointers
3939         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3940
3941         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3942                 viewport.getAlignment()));
3943
3944         alignPanel.paintAlignment(true, false);
3945       }
3946     });
3947   }
3948
3949   /**
3950    * Add a new sort by annotation score menu item
3951    *
3952    * @param sort
3953    *          the menu to add the option to
3954    * @param scoreLabel
3955    *          the label used to retrieve scores for each sequence on the
3956    *          alignment
3957    */
3958   public void addSortByAnnotScoreMenuItem(JMenu sort,
3959           final String scoreLabel)
3960   {
3961     final JMenuItem item = new JMenuItem(scoreLabel);
3962     sort.add(item);
3963     item.addActionListener(new java.awt.event.ActionListener()
3964     {
3965       @Override
3966       public void actionPerformed(ActionEvent e)
3967       {
3968         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3969         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3970                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3971         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3972                 viewport.getAlignment()));
3973         alignPanel.paintAlignment(true, false);
3974       }
3975     });
3976   }
3977
3978   /**
3979    * last hash for alignment's annotation array - used to minimise cost of
3980    * rebuild.
3981    */
3982   protected int _annotationScoreVectorHash;
3983
3984   /**
3985    * search the alignment and rebuild the sort by annotation score submenu the
3986    * last alignment annotation vector hash is stored to minimize cost of
3987    * rebuilding in subsequence calls.
3988    *
3989    */
3990   @Override
3991   public void buildSortByAnnotationScoresMenu()
3992   {
3993     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3994     {
3995       return;
3996     }
3997
3998     if (viewport.getAlignment().getAlignmentAnnotation()
3999             .hashCode() == _annotationScoreVectorHash)
4000     {
4001       return;
4002     }
4003
4004     sortByAnnotScore.removeAll();
4005     Set<String> scoreSorts = new HashSet<>();
4006     for (SequenceI sqa : viewport.getAlignment().getSequences())
4007     {
4008       AlignmentAnnotation[] anns = sqa.getAnnotation();
4009       for (int i = 0; anns != null && i < anns.length; i++)
4010       {
4011         AlignmentAnnotation aa = anns[i];
4012         if (aa != null && aa.hasScore() && aa.sequenceRef != null)
4013         {
4014           scoreSorts.add(aa.label);
4015         }
4016       }
4017     }
4018     for (String label : scoreSorts)
4019     {
4020       addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
4021     }
4022     sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
4023
4024     _annotationScoreVectorHash = viewport.getAlignment()
4025             .getAlignmentAnnotation().hashCode();
4026   }
4027
4028   /**
4029    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4030    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4031    * call. Listeners are added to remove the menu item when the treePanel is
4032    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4033    * modified.
4034    */
4035   @Override
4036   public void buildTreeSortMenu()
4037   {
4038     sortByTreeMenu.removeAll();
4039
4040     List<Component> comps = PaintRefresher.components
4041             .get(viewport.getSequenceSetId());
4042     List<TreePanel> treePanels = new ArrayList<>();
4043     for (Component comp : comps)
4044     {
4045       if (comp instanceof TreePanel)
4046       {
4047         treePanels.add((TreePanel) comp);
4048       }
4049     }
4050
4051     if (treePanels.size() < 1)
4052     {
4053       sortByTreeMenu.setVisible(false);
4054       return;
4055     }
4056
4057     sortByTreeMenu.setVisible(true);
4058
4059     for (final TreePanel tp : treePanels)
4060     {
4061       final JMenuItem item = new JMenuItem(tp.getTitle());
4062       item.addActionListener(new java.awt.event.ActionListener()
4063       {
4064         @Override
4065         public void actionPerformed(ActionEvent e)
4066         {
4067           tp.sortByTree_actionPerformed();
4068           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4069
4070         }
4071       });
4072
4073       sortByTreeMenu.add(item);
4074     }
4075   }
4076
4077   public boolean sortBy(AlignmentOrder alorder, String undoname)
4078   {
4079     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4080     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4081     if (undoname != null)
4082     {
4083       addHistoryItem(new OrderCommand(undoname, oldOrder,
4084               viewport.getAlignment()));
4085     }
4086     alignPanel.paintAlignment(true, false);
4087     return true;
4088   }
4089
4090   /**
4091    * Work out whether the whole set of sequences or just the selected set will
4092    * be submitted for multiple alignment.
4093    *
4094    */
4095   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4096   {
4097     // Now, check we have enough sequences
4098     AlignmentView msa = null;
4099
4100     if ((viewport.getSelectionGroup() != null)
4101             && (viewport.getSelectionGroup().getSize() > 1))
4102     {
4103       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4104       // some common interface!
4105       /*
4106        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4107        * SequenceI[sz = seqs.getSize(false)];
4108        *
4109        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4110        * seqs.getSequenceAt(i); }
4111        */
4112       msa = viewport.getAlignmentView(true);
4113     }
4114     else if (viewport.getSelectionGroup() != null
4115             && viewport.getSelectionGroup().getSize() == 1)
4116     {
4117       int option = JvOptionPane.showConfirmDialog(this,
4118               MessageManager.getString("warn.oneseq_msainput_selection"),
4119               MessageManager.getString("label.invalid_selection"),
4120               JvOptionPane.OK_CANCEL_OPTION);
4121       if (option == JvOptionPane.OK_OPTION)
4122       {
4123         msa = viewport.getAlignmentView(false);
4124       }
4125     }
4126     else
4127     {
4128       msa = viewport.getAlignmentView(false);
4129     }
4130     return msa;
4131   }
4132
4133   /**
4134    * Decides what is submitted to a secondary structure prediction service: the
4135    * first sequence in the alignment, or in the current selection, or, if the
4136    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4137    * region or the whole alignment. (where the first sequence in the set is the
4138    * one that the prediction will be for).
4139    */
4140   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4141   {
4142     AlignmentView seqs = null;
4143
4144     if ((viewport.getSelectionGroup() != null)
4145             && (viewport.getSelectionGroup().getSize() > 0))
4146     {
4147       seqs = viewport.getAlignmentView(true);
4148     }
4149     else
4150     {
4151       seqs = viewport.getAlignmentView(false);
4152     }
4153     // limit sequences - JBPNote in future - could spawn multiple prediction
4154     // jobs
4155     // TODO: viewport.getAlignment().isAligned is a global state - the local
4156     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4157     if (!viewport.getAlignment().isAligned(false))
4158     {
4159       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4160       // TODO: if seqs.getSequences().length>1 then should really have warned
4161       // user!
4162
4163     }
4164     return seqs;
4165   }
4166
4167   /**
4168    * DOCUMENT ME!
4169    *
4170    * @param e
4171    *          DOCUMENT ME!
4172    */
4173   @Override
4174   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4175   {
4176     // Pick the tree file
4177     JalviewFileChooser chooser = new JalviewFileChooser(
4178             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4179     chooser.setFileView(new JalviewFileView());
4180     chooser.setDialogTitle(
4181             MessageManager.getString("label.select_newick_like_tree_file"));
4182     chooser.setToolTipText(
4183             MessageManager.getString("label.load_tree_file"));
4184
4185     int value = chooser.showOpenDialog(null);
4186
4187     if (value == JalviewFileChooser.APPROVE_OPTION)
4188     {
4189       String filePath = chooser.getSelectedFile().getPath();
4190       Cache.setProperty("LAST_DIRECTORY", filePath);
4191       NewickFile fin = null;
4192       try
4193       {
4194         fin = new NewickFile(filePath, DataSourceType.FILE);
4195         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4196       } catch (Exception ex)
4197       {
4198         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4199                 MessageManager.getString("label.problem_reading_tree_file"),
4200                 JvOptionPane.WARNING_MESSAGE);
4201         ex.printStackTrace();
4202       }
4203       if (fin != null && fin.hasWarningMessage())
4204       {
4205         JvOptionPane.showMessageDialog(Desktop.desktop,
4206                 fin.getWarningMessage(),
4207                 MessageManager
4208                         .getString("label.possible_problem_with_tree_file"),
4209                 JvOptionPane.WARNING_MESSAGE);
4210       }
4211     }
4212   }
4213
4214   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4215   {
4216     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4217   }
4218
4219   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4220           int h, int x, int y)
4221   {
4222     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4223   }
4224
4225   /**
4226    * Add a treeviewer for the tree extracted from a Newick file object to the
4227    * current alignment view
4228    *
4229    * @param nf
4230    *          the tree
4231    * @param title
4232    *          tree viewer title
4233    * @param input
4234    *          Associated alignment input data (or null)
4235    * @param w
4236    *          width
4237    * @param h
4238    *          height
4239    * @param x
4240    *          position
4241    * @param y
4242    *          position
4243    * @return TreePanel handle
4244    */
4245   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4246           AlignmentView input, int w, int h, int x, int y)
4247   {
4248     TreePanel tp = null;
4249
4250     try
4251     {
4252       nf.parse();
4253
4254       if (nf.getTree() != null)
4255       {
4256         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4257
4258         tp.setSize(w, h);
4259
4260         if (x > 0 && y > 0)
4261         {
4262           tp.setLocation(x, y);
4263         }
4264
4265         Desktop.addInternalFrame(tp, treeTitle, w, h);
4266       }
4267     } catch (Exception ex)
4268     {
4269       ex.printStackTrace();
4270     }
4271
4272     return tp;
4273   }
4274
4275   private boolean buildingMenu = false;
4276
4277   /**
4278    * Generates menu items and listener event actions for web service clients
4279    *
4280    */
4281   public void BuildWebServiceMenu()
4282   {
4283     while (buildingMenu)
4284     {
4285       try
4286       {
4287         System.err.println("Waiting for building menu to finish.");
4288         Thread.sleep(10);
4289       } catch (Exception e)
4290       {
4291       }
4292     }
4293     final AlignFrame me = this;
4294     buildingMenu = true;
4295     new Thread(new Runnable()
4296     {
4297       @Override
4298       public void run()
4299       {
4300         final List<JMenuItem> legacyItems = new ArrayList<>();
4301         try
4302         {
4303           // System.err.println("Building ws menu again "
4304           // + Thread.currentThread());
4305           // TODO: add support for context dependent disabling of services based
4306           // on
4307           // alignment and current selection
4308           // TODO: add additional serviceHandle parameter to specify abstract
4309           // handler
4310           // class independently of AbstractName
4311           // TODO: add in rediscovery GUI function to restart discoverer
4312           // TODO: group services by location as well as function and/or
4313           // introduce
4314           // object broker mechanism.
4315           final Vector<JMenu> wsmenu = new Vector<>();
4316           final IProgressIndicator af = me;
4317
4318           /*
4319            * do not i18n these strings - they are hard-coded in class
4320            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4321            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4322            */
4323           final JMenu msawsmenu = new JMenu("Alignment");
4324           final JMenu secstrmenu = new JMenu(
4325                   "Secondary Structure Prediction");
4326           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4327           final JMenu analymenu = new JMenu("Analysis");
4328           final JMenu dismenu = new JMenu("Protein Disorder");
4329           // JAL-940 - only show secondary structure prediction services from
4330           // the legacy server
4331           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4332               // &&
4333           Discoverer.services != null && (Discoverer.services.size() > 0))
4334           {
4335             // TODO: refactor to allow list of AbstractName/Handler bindings to
4336             // be
4337             // stored or retrieved from elsewhere
4338             // No MSAWS used any more:
4339             // Vector msaws = null; // (Vector)
4340             // Discoverer.services.get("MsaWS");
4341             Vector secstrpr = (Vector) Discoverer.services
4342                     .get("SecStrPred");
4343             if (secstrpr != null)
4344             {
4345               // Add any secondary structure prediction services
4346               for (int i = 0, j = secstrpr.size(); i < j; i++)
4347               {
4348                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4349                         .get(i);
4350                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4351                         .getServiceClient(sh);
4352                 int p = secstrmenu.getItemCount();
4353                 impl.attachWSMenuEntry(secstrmenu, me);
4354                 int q = secstrmenu.getItemCount();
4355                 for (int litm = p; litm < q; litm++)
4356                 {
4357                   legacyItems.add(secstrmenu.getItem(litm));
4358                 }
4359               }
4360             }
4361           }
4362
4363           // Add all submenus in the order they should appear on the web
4364           // services menu
4365           wsmenu.add(msawsmenu);
4366           wsmenu.add(secstrmenu);
4367           wsmenu.add(dismenu);
4368           wsmenu.add(analymenu);
4369           // No search services yet
4370           // wsmenu.add(seqsrchmenu);
4371
4372           javax.swing.SwingUtilities.invokeLater(new Runnable()
4373           {
4374             @Override
4375             public void run()
4376             {
4377               try
4378               {
4379                 webService.removeAll();
4380                 // first, add discovered services onto the webservices menu
4381                 if (wsmenu.size() > 0)
4382                 {
4383                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4384                   {
4385                     webService.add(wsmenu.get(i));
4386                   }
4387                 }
4388                 else
4389                 {
4390                   webService.add(me.webServiceNoServices);
4391                 }
4392                 // TODO: move into separate menu builder class.
4393                 boolean new_sspred = false;
4394                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4395                 {
4396                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4397                   if (jws2servs != null)
4398                   {
4399                     if (jws2servs.hasServices())
4400                     {
4401                       jws2servs.attachWSMenuEntry(webService, me);
4402                       for (Jws2Instance sv : jws2servs.getServices())
4403                       {
4404                         if (sv.getName().toLowerCase().contains("jpred"))
4405                         {
4406                           for (JMenuItem jmi : legacyItems)
4407                           {
4408                             jmi.setVisible(false);
4409                           }
4410                         }
4411                       }
4412
4413                     }
4414                     if (jws2servs.isRunning())
4415                     {
4416                       JMenuItem tm = new JMenuItem(
4417                               "Still discovering JABA Services");
4418                       tm.setEnabled(false);
4419                       webService.add(tm);
4420                     }
4421                   }
4422                 }
4423                 build_urlServiceMenu(me.webService);
4424
4425                 // TODO Mateusz - follow pattern for adding web service
4426                 // JMenuItems for slivka-based services
4427
4428                 build_fetchdbmenu(webService);
4429                 for (JMenu item : wsmenu)
4430                 {
4431                   if (item.getItemCount() == 0)
4432                   {
4433                     item.setEnabled(false);
4434                   }
4435                   else
4436                   {
4437                     item.setEnabled(true);
4438                   }
4439                 }
4440               } catch (Exception e)
4441               {
4442                 Cache.log.debug(
4443                         "Exception during web service menu building process.",
4444                         e);
4445               }
4446             }
4447           });
4448         } catch (Exception e)
4449         {
4450         }
4451         buildingMenu = false;
4452       }
4453     }).start();
4454
4455   }
4456
4457   /**
4458    * construct any groupURL type service menu entries.
4459    *
4460    * @param webService
4461    */
4462   private void build_urlServiceMenu(JMenu webService)
4463   {
4464     // TODO: remove this code when 2.7 is released
4465     // DEBUG - alignmentView
4466     /*
4467      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4468      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4469      *
4470      * @Override public void actionPerformed(ActionEvent e) {
4471      * jalview.datamodel.AlignmentView
4472      * .testSelectionViews(af.viewport.getAlignment(),
4473      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4474      *
4475      * }); webService.add(testAlView);
4476      */
4477     // TODO: refactor to RestClient discoverer and merge menu entries for
4478     // rest-style services with other types of analysis/calculation service
4479     // SHmmr test client - still being implemented.
4480     // DEBUG - alignmentView
4481
4482     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4483             .getRestClients())
4484     {
4485       client.attachWSMenuEntry(
4486               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4487               this);
4488     }
4489   }
4490
4491   /**
4492    * Searches the alignment sequences for xRefs and builds the Show
4493    * Cross-References menu (formerly called Show Products), with database
4494    * sources for which cross-references are found (protein sources for a
4495    * nucleotide alignment and vice versa)
4496    *
4497    * @return true if Show Cross-references menu should be enabled
4498    */
4499   public boolean canShowProducts()
4500   {
4501     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4502     AlignmentI dataset = viewport.getAlignment().getDataset();
4503
4504     showProducts.removeAll();
4505     final boolean dna = viewport.getAlignment().isNucleotide();
4506
4507     if (seqs == null || seqs.length == 0)
4508     {
4509       // nothing to see here.
4510       return false;
4511     }
4512
4513     boolean showp = false;
4514     try
4515     {
4516       List<String> ptypes = new CrossRef(seqs, dataset)
4517               .findXrefSourcesForSequences(dna);
4518
4519       for (final String source : ptypes)
4520       {
4521         showp = true;
4522         final AlignFrame af = this;
4523         JMenuItem xtype = new JMenuItem(source);
4524         xtype.addActionListener(new ActionListener()
4525         {
4526           @Override
4527           public void actionPerformed(ActionEvent e)
4528           {
4529             showProductsFor(af.viewport.getSequenceSelection(), dna,
4530                     source);
4531           }
4532         });
4533         showProducts.add(xtype);
4534       }
4535       showProducts.setVisible(showp);
4536       showProducts.setEnabled(showp);
4537     } catch (Exception e)
4538     {
4539       Cache.log.warn(
4540               "canShowProducts threw an exception - please report to help@jalview.org",
4541               e);
4542       return false;
4543     }
4544     return showp;
4545   }
4546
4547   /**
4548    * Finds and displays cross-references for the selected sequences (protein
4549    * products for nucleotide sequences, dna coding sequences for peptides).
4550    *
4551    * @param sel
4552    *          the sequences to show cross-references for
4553    * @param dna
4554    *          true if from a nucleotide alignment (so showing proteins)
4555    * @param source
4556    *          the database to show cross-references for
4557    */
4558   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4559           final String source)
4560   {
4561     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4562             .start();
4563   }
4564
4565   /**
4566    * Construct and display a new frame containing the translation of this
4567    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4568    */
4569   @Override
4570   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4571   {
4572     AlignmentI al = null;
4573     try
4574     {
4575       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4576
4577       al = dna.translateCdna(codeTable);
4578     } catch (Exception ex)
4579     {
4580       jalview.bin.Cache.log.error(
4581               "Exception during translation. Please report this !", ex);
4582       final String msg = MessageManager.getString(
4583               "label.error_when_translating_sequences_submit_bug_report");
4584       final String errorTitle = MessageManager
4585               .getString("label.implementation_error")
4586               + MessageManager.getString("label.translation_failed");
4587       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4588               JvOptionPane.ERROR_MESSAGE);
4589       return;
4590     }
4591     if (al == null || al.getHeight() == 0)
4592     {
4593       final String msg = MessageManager.getString(
4594               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4595       final String errorTitle = MessageManager
4596               .getString("label.translation_failed");
4597       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4598               JvOptionPane.WARNING_MESSAGE);
4599     }
4600     else
4601     {
4602       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4603       af.setFileFormat(this.currentFileFormat);
4604       final String newTitle = MessageManager
4605               .formatMessage("label.translation_of_params", new Object[]
4606               { this.getTitle(), codeTable.getId() });
4607       af.setTitle(newTitle);
4608       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4609       {
4610         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4611         viewport.openSplitFrame(af, new Alignment(seqs));
4612       }
4613       else
4614       {
4615         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4616                 DEFAULT_HEIGHT);
4617       }
4618     }
4619   }
4620
4621   /**
4622    * Set the file format
4623    *
4624    * @param format
4625    */
4626   public void setFileFormat(FileFormatI format)
4627   {
4628     this.currentFileFormat = format;
4629   }
4630
4631   /**
4632    * Try to load a features file onto the alignment.
4633    *
4634    * @param file
4635    *          contents or path to retrieve file
4636    * @param sourceType
4637    *          access mode of file (see jalview.io.AlignFile)
4638    * @return true if features file was parsed correctly.
4639    */
4640   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4641   {
4642     return avc.parseFeaturesFile(file, sourceType,
4643             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4644
4645   }
4646
4647   @Override
4648   public void refreshFeatureUI(boolean enableIfNecessary)
4649   {
4650     // note - currently this is only still here rather than in the controller
4651     // because of the featureSettings hard reference that is yet to be
4652     // abstracted
4653     if (enableIfNecessary)
4654     {
4655       viewport.setShowSequenceFeatures(true);
4656       showSeqFeatures.setSelected(true);
4657     }
4658
4659   }
4660
4661   @Override
4662   public void dragEnter(DropTargetDragEvent evt)
4663   {
4664   }
4665
4666   @Override
4667   public void dragExit(DropTargetEvent evt)
4668   {
4669   }
4670
4671   @Override
4672   public void dragOver(DropTargetDragEvent evt)
4673   {
4674   }
4675
4676   @Override
4677   public void dropActionChanged(DropTargetDragEvent evt)
4678   {
4679   }
4680
4681   @Override
4682   public void drop(DropTargetDropEvent evt)
4683   {
4684     // JAL-1552 - acceptDrop required before getTransferable call for
4685     // Java's Transferable for native dnd
4686     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4687     Transferable t = evt.getTransferable();
4688     final AlignFrame thisaf = this;
4689     final List<String> files = new ArrayList<>();
4690     List<DataSourceType> protocols = new ArrayList<>();
4691
4692     try
4693     {
4694       Desktop.transferFromDropTarget(files, protocols, evt, t);
4695     } catch (Exception e)
4696     {
4697       e.printStackTrace();
4698     }
4699     if (files != null)
4700     {
4701       new Thread(new Runnable()
4702       {
4703         @Override
4704         public void run()
4705         {
4706           try
4707           {
4708             // check to see if any of these files have names matching sequences
4709             // in
4710             // the alignment
4711             SequenceIdMatcher idm = new SequenceIdMatcher(
4712                     viewport.getAlignment().getSequencesArray());
4713             /**
4714              * Object[] { String,SequenceI}
4715              */
4716             ArrayList<Object[]> filesmatched = new ArrayList<>();
4717             ArrayList<String> filesnotmatched = new ArrayList<>();
4718             for (int i = 0; i < files.size(); i++)
4719             {
4720               String file = files.get(i).toString();
4721               String pdbfn = "";
4722               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4723               if (protocol == DataSourceType.FILE)
4724               {
4725                 File fl = new File(file);
4726                 pdbfn = fl.getName();
4727               }
4728               else if (protocol == DataSourceType.URL)
4729               {
4730                 URL url = new URL(file);
4731                 pdbfn = url.getFile();
4732               }
4733               if (pdbfn.length() > 0)
4734               {
4735                 // attempt to find a match in the alignment
4736                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4737                 int l = 0, c = pdbfn.indexOf(".");
4738                 while (mtch == null && c != -1)
4739                 {
4740                   do
4741                   {
4742                     l = c;
4743                   } while ((c = pdbfn.indexOf(".", l)) > l);
4744                   if (l > -1)
4745                   {
4746                     pdbfn = pdbfn.substring(0, l);
4747                   }
4748                   mtch = idm.findAllIdMatches(pdbfn);
4749                 }
4750                 if (mtch != null)
4751                 {
4752                   FileFormatI type = null;
4753                   try
4754                   {
4755                     type = new IdentifyFile().identify(file, protocol);
4756                   } catch (Exception ex)
4757                   {
4758                     type = null;
4759                   }
4760                   if (type != null && type.isStructureFile())
4761                   {
4762                     filesmatched.add(new Object[] { file, protocol, mtch });
4763                     continue;
4764                   }
4765                 }
4766                 // File wasn't named like one of the sequences or wasn't a PDB
4767                 // file.
4768                 filesnotmatched.add(file);
4769               }
4770             }
4771             int assocfiles = 0;
4772             if (filesmatched.size() > 0)
4773             {
4774               boolean autoAssociate = Cache
4775                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4776               if (!autoAssociate)
4777               {
4778                 String msg = MessageManager.formatMessage(
4779                         "label.automatically_associate_structure_files_with_sequences_same_name",
4780                         new Object[]
4781                         { Integer.valueOf(filesmatched.size())
4782                                 .toString() });
4783                 String ttl = MessageManager.getString(
4784                         "label.automatically_associate_structure_files_by_name");
4785                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4786                         ttl, JvOptionPane.YES_NO_OPTION);
4787                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4788               }
4789               if (autoAssociate)
4790               {
4791                 for (Object[] fm : filesmatched)
4792                 {
4793                   // try and associate
4794                   // TODO: may want to set a standard ID naming formalism for
4795                   // associating PDB files which have no IDs.
4796                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4797                   {
4798                     PDBEntry pe = new AssociatePdbFileWithSeq()
4799                             .associatePdbWithSeq((String) fm[0],
4800                                     (DataSourceType) fm[1], toassoc, false,
4801                                     Desktop.instance);
4802                     if (pe != null)
4803                     {
4804                       System.err.println("Associated file : "
4805                               + ((String) fm[0]) + " with "
4806                               + toassoc.getDisplayId(true));
4807                       assocfiles++;
4808                     }
4809                   }
4810                   // TODO: do we need to update overview ? only if features are
4811                   // shown I guess
4812                   alignPanel.paintAlignment(true, false);
4813                 }
4814               }
4815               else
4816               {
4817                 /*
4818                  * add declined structures as sequences
4819                  */
4820                 for (Object[] o : filesmatched)
4821                 {
4822                   filesnotmatched.add((String) o[0]);
4823                 }
4824               }
4825             }
4826             if (filesnotmatched.size() > 0)
4827             {
4828               if (assocfiles > 0 && (Cache.getDefault(
4829                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4830                       || JvOptionPane.showConfirmDialog(thisaf,
4831                               "<html>" + MessageManager.formatMessage(
4832                                       "label.ignore_unmatched_dropped_files_info",
4833                                       new Object[]
4834                                       { Integer.valueOf(
4835                                               filesnotmatched.size())
4836                                               .toString() })
4837                                       + "</html>",
4838                               MessageManager.getString(
4839                                       "label.ignore_unmatched_dropped_files"),
4840                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4841               {
4842                 return;
4843               }
4844               for (String fn : filesnotmatched)
4845               {
4846                 loadJalviewDataFile(fn, null, null, null);
4847               }
4848
4849             }
4850           } catch (Exception ex)
4851           {
4852             ex.printStackTrace();
4853           }
4854         }
4855       }).start();
4856     }
4857   }
4858
4859   /**
4860    * Attempt to load a "dropped" file or URL string, by testing in turn for
4861    * <ul>
4862    * <li>an Annotation file</li>
4863    * <li>a JNet file</li>
4864    * <li>a features file</li>
4865    * <li>else try to interpret as an alignment file</li>
4866    * </ul>
4867    *
4868    * @param file
4869    *          either a filename or a URL string.
4870    * @throws InterruptedException
4871    * @throws IOException
4872    */
4873   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4874           FileFormatI format, SequenceI assocSeq)
4875   {
4876     try
4877     {
4878       if (sourceType == null)
4879       {
4880         sourceType = FormatAdapter.checkProtocol(file);
4881       }
4882       // if the file isn't identified, or not positively identified as some
4883       // other filetype (PFAM is default unidentified alignment file type) then
4884       // try to parse as annotation.
4885       boolean isAnnotation = (format == null
4886               || FileFormat.Pfam.equals(format))
4887                       ? new AnnotationFile().annotateAlignmentView(viewport,
4888                               file, sourceType)
4889                       : false;
4890
4891       if (!isAnnotation)
4892       {
4893         // first see if its a T-COFFEE score file
4894         TCoffeeScoreFile tcf = null;
4895         try
4896         {
4897           tcf = new TCoffeeScoreFile(file, sourceType);
4898           if (tcf.isValid())
4899           {
4900             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4901             {
4902               buildColourMenu();
4903               changeColour(
4904                       new TCoffeeColourScheme(viewport.getAlignment()));
4905               isAnnotation = true;
4906               statusBar.setText(MessageManager.getString(
4907                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4908             }
4909             else
4910             {
4911               // some problem - if no warning its probable that the ID matching
4912               // process didn't work
4913               JvOptionPane.showMessageDialog(Desktop.desktop,
4914                       tcf.getWarningMessage() == null
4915                               ? MessageManager.getString(
4916                                       "label.check_file_matches_sequence_ids_alignment")
4917                               : tcf.getWarningMessage(),
4918                       MessageManager.getString(
4919                               "label.problem_reading_tcoffee_score_file"),
4920                       JvOptionPane.WARNING_MESSAGE);
4921             }
4922           }
4923           else
4924           {
4925             tcf = null;
4926           }
4927         } catch (Exception x)
4928         {
4929           Cache.log.debug(
4930                   "Exception when processing data source as T-COFFEE score file",
4931                   x);
4932           tcf = null;
4933         }
4934         if (tcf == null)
4935         {
4936           // try to see if its a JNet 'concise' style annotation file *before*
4937           // we
4938           // try to parse it as a features file
4939           if (format == null)
4940           {
4941             format = new IdentifyFile().identify(file, sourceType);
4942           }
4943           if (FileFormat.ScoreMatrix == format)
4944           {
4945             ScoreMatrixFile sm = new ScoreMatrixFile(
4946                     new FileParse(file, sourceType));
4947             sm.parse();
4948             // todo: i18n this message
4949             statusBar.setText(MessageManager.formatMessage(
4950                     "label.successfully_loaded_matrix",
4951                     sm.getMatrixName()));
4952           }
4953           else if (FileFormat.Jnet.equals(format))
4954           {
4955             JPredFile predictions = new JPredFile(file, sourceType);
4956             new JnetAnnotationMaker();
4957             JnetAnnotationMaker.add_annotation(predictions,
4958                     viewport.getAlignment(), 0, false);
4959             viewport.getAlignment().setupJPredAlignment();
4960             isAnnotation = true;
4961           }
4962           // else if (IdentifyFile.FeaturesFile.equals(format))
4963           else if (FileFormat.Features.equals(format))
4964           {
4965             if (parseFeaturesFile(file, sourceType))
4966             {
4967               alignPanel.paintAlignment(true, true);
4968             }
4969           }
4970           else
4971           {
4972             new FileLoader().LoadFile(viewport, file, sourceType, format);
4973           }
4974         }
4975       }
4976       if (isAnnotation)
4977       {
4978         alignPanel.adjustAnnotationHeight();
4979         viewport.updateSequenceIdColours();
4980         buildSortByAnnotationScoresMenu();
4981         alignPanel.paintAlignment(true, true);
4982       }
4983     } catch (Exception ex)
4984     {
4985       ex.printStackTrace();
4986     } catch (OutOfMemoryError oom)
4987     {
4988       try
4989       {
4990         System.gc();
4991       } catch (Exception x)
4992       {
4993       }
4994       new OOMWarning(
4995               "loading data "
4996                       + (sourceType != null
4997                               ? (sourceType == DataSourceType.PASTE
4998                                       ? "from clipboard."
4999                                       : "using " + sourceType + " from "
5000                                               + file)
5001                               : ".")
5002                       + (format != null
5003                               ? "(parsing as '" + format + "' file)"
5004                               : ""),
5005               oom, Desktop.desktop);
5006     }
5007   }
5008
5009   /**
5010    * Method invoked by the ChangeListener on the tabbed pane, in other words
5011    * when a different tabbed pane is selected by the user or programmatically.
5012    */
5013   @Override
5014   public void tabSelectionChanged(int index)
5015   {
5016     if (index > -1)
5017     {
5018       alignPanel = alignPanels.get(index);
5019       viewport = alignPanel.av;
5020       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5021       setMenusFromViewport(viewport);
5022     }
5023
5024     /*
5025      * 'focus' any colour slider that is open to the selected viewport
5026      */
5027     if (viewport.getConservationSelected())
5028     {
5029       SliderPanel.setConservationSlider(alignPanel,
5030               viewport.getResidueShading(), alignPanel.getViewName());
5031     }
5032     else
5033     {
5034       SliderPanel.hideConservationSlider();
5035     }
5036     if (viewport.getAbovePIDThreshold())
5037     {
5038       SliderPanel.setPIDSliderSource(alignPanel,
5039               viewport.getResidueShading(), alignPanel.getViewName());
5040     }
5041     else
5042     {
5043       SliderPanel.hidePIDSlider();
5044     }
5045
5046     /*
5047      * If there is a frame linked to this one in a SplitPane, switch it to the
5048      * same view tab index. No infinite recursion of calls should happen, since
5049      * tabSelectionChanged() should not get invoked on setting the selected
5050      * index to an unchanged value. Guard against setting an invalid index
5051      * before the new view peer tab has been created.
5052      */
5053     final AlignViewportI peer = viewport.getCodingComplement();
5054     if (peer != null)
5055     {
5056       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5057               .getAlignPanel().alignFrame;
5058       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5059       {
5060         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5061       }
5062     }
5063   }
5064
5065   /**
5066    * On right mouse click on view tab, prompt for and set new view name.
5067    */
5068   @Override
5069   public void tabbedPane_mousePressed(MouseEvent e)
5070   {
5071     if (e.isPopupTrigger())
5072     {
5073       String msg = MessageManager.getString("label.enter_view_name");
5074       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5075               JvOptionPane.QUESTION_MESSAGE);
5076
5077       if (reply != null)
5078       {
5079         viewport.setViewName(reply);
5080         // TODO warn if reply is in getExistingViewNames()?
5081         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5082       }
5083     }
5084   }
5085
5086   public AlignViewport getCurrentView()
5087   {
5088     return viewport;
5089   }
5090
5091   /**
5092    * Open the dialog for regex description parsing.
5093    */
5094   @Override
5095   protected void extractScores_actionPerformed(ActionEvent e)
5096   {
5097     ParseProperties pp = new jalview.analysis.ParseProperties(
5098             viewport.getAlignment());
5099     // TODO: verify regex and introduce GUI dialog for version 2.5
5100     // if (pp.getScoresFromDescription("col", "score column ",
5101     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5102     // true)>0)
5103     if (pp.getScoresFromDescription("description column",
5104             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5105     {
5106       buildSortByAnnotationScoresMenu();
5107     }
5108   }
5109
5110   /*
5111    * (non-Javadoc)
5112    *
5113    * @see
5114    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5115    * )
5116    */
5117   @Override
5118   protected void showDbRefs_actionPerformed(ActionEvent e)
5119   {
5120     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5121   }
5122
5123   /*
5124    * (non-Javadoc)
5125    *
5126    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5127    * ActionEvent)
5128    */
5129   @Override
5130   protected void showNpFeats_actionPerformed(ActionEvent e)
5131   {
5132     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5133   }
5134
5135   /**
5136    * find the viewport amongst the tabs in this alignment frame and close that
5137    * tab
5138    *
5139    * @param av
5140    */
5141   public boolean closeView(AlignViewportI av)
5142   {
5143     if (viewport == av)
5144     {
5145       this.closeMenuItem_actionPerformed(false);
5146       return true;
5147     }
5148     Component[] comp = tabbedPane.getComponents();
5149     for (int i = 0; comp != null && i < comp.length; i++)
5150     {
5151       if (comp[i] instanceof AlignmentPanel)
5152       {
5153         if (((AlignmentPanel) comp[i]).av == av)
5154         {
5155           // close the view.
5156           closeView((AlignmentPanel) comp[i]);
5157           return true;
5158         }
5159       }
5160     }
5161     return false;
5162   }
5163
5164   protected void build_fetchdbmenu(JMenu webService)
5165   {
5166     // Temporary hack - DBRef Fetcher always top level ws entry.
5167     // TODO We probably want to store a sequence database checklist in
5168     // preferences and have checkboxes.. rather than individual sources selected
5169     // here
5170     final JMenu rfetch = new JMenu(
5171             MessageManager.getString("action.fetch_db_references"));
5172     rfetch.setToolTipText(MessageManager.getString(
5173             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5174     webService.add(rfetch);
5175
5176     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5177             MessageManager.getString("option.trim_retrieved_seqs"));
5178     trimrs.setToolTipText(
5179             MessageManager.getString("label.trim_retrieved_sequences"));
5180     trimrs.setSelected(
5181             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5182     trimrs.addActionListener(new ActionListener()
5183     {
5184       @Override
5185       public void actionPerformed(ActionEvent e)
5186       {
5187         trimrs.setSelected(trimrs.isSelected());
5188         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5189                 Boolean.valueOf(trimrs.isSelected()).toString());
5190       };
5191     });
5192     rfetch.add(trimrs);
5193     JMenuItem fetchr = new JMenuItem(
5194             MessageManager.getString("label.standard_databases"));
5195     fetchr.setToolTipText(
5196             MessageManager.getString("label.fetch_embl_uniprot"));
5197     fetchr.addActionListener(new ActionListener()
5198     {
5199
5200       @Override
5201       public void actionPerformed(ActionEvent e)
5202       {
5203         new Thread(new Runnable()
5204         {
5205           @Override
5206           public void run()
5207           {
5208             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5209                     .getAlignment().isNucleotide();
5210             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5211                     alignPanel.av.getSequenceSelection(),
5212                     alignPanel.alignFrame, null,
5213                     alignPanel.alignFrame.featureSettings, isNucleotide);
5214             dbRefFetcher.addListener(new FetchFinishedListenerI()
5215             {
5216               @Override
5217               public void finished()
5218               {
5219
5220                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5221                         .getFeatureSettingsModels())
5222                 {
5223
5224                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5225                 }
5226                 AlignFrame.this.setMenusForViewport();
5227               }
5228             });
5229             dbRefFetcher.fetchDBRefs(false);
5230           }
5231         }).start();
5232
5233       }
5234
5235     });
5236     rfetch.add(fetchr);
5237     final AlignFrame me = this;
5238     new Thread(new Runnable()
5239     {
5240       @Override
5241       public void run()
5242       {
5243         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5244                 .getSequenceFetcherSingleton(me);
5245         javax.swing.SwingUtilities.invokeLater(new Runnable()
5246         {
5247           @Override
5248           public void run()
5249           {
5250             String[] dbclasses = sf.getOrderedSupportedSources();
5251             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5252             // jalview.util.QuickSort.sort(otherdb, otherdb);
5253             List<DbSourceProxy> otherdb;
5254             JMenu dfetch = new JMenu();
5255             JMenu ifetch = new JMenu();
5256             JMenuItem fetchr = null;
5257             int comp = 0, icomp = 0, mcomp = 15;
5258             String mname = null;
5259             int dbi = 0;
5260             for (String dbclass : dbclasses)
5261             {
5262               otherdb = sf.getSourceProxy(dbclass);
5263               // add a single entry for this class, or submenu allowing 'fetch
5264               // all' or pick one
5265               if (otherdb == null || otherdb.size() < 1)
5266               {
5267                 continue;
5268               }
5269               // List<DbSourceProxy> dbs=otherdb;
5270               // otherdb=new ArrayList<DbSourceProxy>();
5271               // for (DbSourceProxy db:dbs)
5272               // {
5273               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5274               // }
5275               if (mname == null)
5276               {
5277                 mname = "From " + dbclass;
5278               }
5279               if (otherdb.size() == 1)
5280               {
5281                 final DbSourceProxy[] dassource = otherdb
5282                         .toArray(new DbSourceProxy[0]);
5283                 DbSourceProxy src = otherdb.get(0);
5284                 fetchr = new JMenuItem(src.getDbSource());
5285                 fetchr.addActionListener(new ActionListener()
5286                 {
5287
5288                   @Override
5289                   public void actionPerformed(ActionEvent e)
5290                   {
5291                     new Thread(new Runnable()
5292                     {
5293
5294                       @Override
5295                       public void run()
5296                       {
5297                         boolean isNucleotide = alignPanel.alignFrame
5298                                 .getViewport().getAlignment()
5299                                 .isNucleotide();
5300                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5301                                 alignPanel.av.getSequenceSelection(),
5302                                 alignPanel.alignFrame, dassource,
5303                                 alignPanel.alignFrame.featureSettings,
5304                                 isNucleotide);
5305                         dbRefFetcher
5306                                 .addListener(new FetchFinishedListenerI()
5307                                 {
5308                                   @Override
5309                                   public void finished()
5310                                   {
5311                                     FeatureSettingsModelI srcSettings = dassource[0]
5312                                             .getFeatureColourScheme();
5313                                     alignPanel.av.mergeFeaturesStyle(
5314                                             srcSettings);
5315                                     AlignFrame.this.setMenusForViewport();
5316                                   }
5317                                 });
5318                         dbRefFetcher.fetchDBRefs(false);
5319                       }
5320                     }).start();
5321                   }
5322
5323                 });
5324                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5325                         MessageManager.formatMessage(
5326                                 "label.fetch_retrieve_from", new Object[]
5327                                 { src.getDbName() })));
5328                 dfetch.add(fetchr);
5329                 comp++;
5330               }
5331               else
5332               {
5333                 final DbSourceProxy[] dassource = otherdb
5334                         .toArray(new DbSourceProxy[0]);
5335                 // fetch all entry
5336                 DbSourceProxy src = otherdb.get(0);
5337                 fetchr = new JMenuItem(MessageManager
5338                         .formatMessage("label.fetch_all_param", new Object[]
5339                         { src.getDbSource() }));
5340                 fetchr.addActionListener(new ActionListener()
5341                 {
5342                   @Override
5343                   public void actionPerformed(ActionEvent e)
5344                   {
5345                     new Thread(new Runnable()
5346                     {
5347
5348                       @Override
5349                       public void run()
5350                       {
5351                         boolean isNucleotide = alignPanel.alignFrame
5352                                 .getViewport().getAlignment()
5353                                 .isNucleotide();
5354                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5355                                 alignPanel.av.getSequenceSelection(),
5356                                 alignPanel.alignFrame, dassource,
5357                                 alignPanel.alignFrame.featureSettings,
5358                                 isNucleotide);
5359                         dbRefFetcher
5360                                 .addListener(new FetchFinishedListenerI()
5361                                 {
5362                                   @Override
5363                                   public void finished()
5364                                   {
5365                                     AlignFrame.this.setMenusForViewport();
5366                                   }
5367                                 });
5368                         dbRefFetcher.fetchDBRefs(false);
5369                       }
5370                     }).start();
5371                   }
5372                 });
5373
5374                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5375                         MessageManager.formatMessage(
5376                                 "label.fetch_retrieve_from_all_sources",
5377                                 new Object[]
5378                                 { Integer.valueOf(otherdb.size())
5379                                         .toString(),
5380                                     src.getDbSource(), src.getDbName() })));
5381                 dfetch.add(fetchr);
5382                 comp++;
5383                 // and then build the rest of the individual menus
5384                 ifetch = new JMenu(MessageManager.formatMessage(
5385                         "label.source_from_db_source", new Object[]
5386                         { src.getDbSource() }));
5387                 icomp = 0;
5388                 String imname = null;
5389                 int i = 0;
5390                 for (DbSourceProxy sproxy : otherdb)
5391                 {
5392                   String dbname = sproxy.getDbName();
5393                   String sname = dbname.length() > 5
5394                           ? dbname.substring(0, 5) + "..."
5395                           : dbname;
5396                   String msname = dbname.length() > 10
5397                           ? dbname.substring(0, 10) + "..."
5398                           : dbname;
5399                   if (imname == null)
5400                   {
5401                     imname = MessageManager
5402                             .formatMessage("label.from_msname", new Object[]
5403                             { sname });
5404                   }
5405                   fetchr = new JMenuItem(msname);
5406                   final DbSourceProxy[] dassrc = { sproxy };
5407                   fetchr.addActionListener(new ActionListener()
5408                   {
5409
5410                     @Override
5411                     public void actionPerformed(ActionEvent e)
5412                     {
5413                       new Thread(new Runnable()
5414                       {
5415
5416                         @Override
5417                         public void run()
5418                         {
5419                           boolean isNucleotide = alignPanel.alignFrame
5420                                   .getViewport().getAlignment()
5421                                   .isNucleotide();
5422                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5423                                   alignPanel.av.getSequenceSelection(),
5424                                   alignPanel.alignFrame, dassrc,
5425                                   alignPanel.alignFrame.featureSettings,
5426                                   isNucleotide);
5427                           dbRefFetcher
5428                                   .addListener(new FetchFinishedListenerI()
5429                                   {
5430                                     @Override
5431                                     public void finished()
5432                                     {
5433                                       AlignFrame.this.setMenusForViewport();
5434                                     }
5435                                   });
5436                           dbRefFetcher.fetchDBRefs(false);
5437                         }
5438                       }).start();
5439                     }
5440
5441                   });
5442                   fetchr.setToolTipText(
5443                           "<html>" + MessageManager.formatMessage(
5444                                   "label.fetch_retrieve_from", new Object[]
5445                                   { dbname }));
5446                   ifetch.add(fetchr);
5447                   ++i;
5448                   if (++icomp >= mcomp || i == (otherdb.size()))
5449                   {
5450                     ifetch.setText(MessageManager.formatMessage(
5451                             "label.source_to_target", imname, sname));
5452                     dfetch.add(ifetch);
5453                     ifetch = new JMenu();
5454                     imname = null;
5455                     icomp = 0;
5456                     comp++;
5457                   }
5458                 }
5459               }
5460               ++dbi;
5461               if (comp >= mcomp || dbi >= (dbclasses.length))
5462               {
5463                 dfetch.setText(MessageManager.formatMessage(
5464                         "label.source_to_target", mname, dbclass));
5465                 rfetch.add(dfetch);
5466                 dfetch = new JMenu();
5467                 mname = null;
5468                 comp = 0;
5469               }
5470             }
5471           }
5472         });
5473       }
5474     }).start();
5475
5476   }
5477
5478   /**
5479    * Left justify the whole alignment.
5480    */
5481   @Override
5482   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5483   {
5484     AlignmentI al = viewport.getAlignment();
5485     al.justify(false);
5486     viewport.firePropertyChange("alignment", null, al);
5487   }
5488
5489   /**
5490    * Right justify the whole alignment.
5491    */
5492   @Override
5493   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5494   {
5495     AlignmentI al = viewport.getAlignment();
5496     al.justify(true);
5497     viewport.firePropertyChange("alignment", null, al);
5498   }
5499
5500   @Override
5501   public void setShowSeqFeatures(boolean b)
5502   {
5503     showSeqFeatures.setSelected(b);
5504     viewport.setShowSequenceFeatures(b);
5505   }
5506
5507   /*
5508    * (non-Javadoc)
5509    *
5510    * @see
5511    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5512    * awt.event.ActionEvent)
5513    */
5514   @Override
5515   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5516   {
5517     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5518     alignPanel.paintAlignment(false, false);
5519   }
5520
5521   /*
5522    * (non-Javadoc)
5523    *
5524    * @see
5525    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5526    * .ActionEvent)
5527    */
5528   @Override
5529   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5530   {
5531     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5532     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5533
5534   }
5535
5536   /*
5537    * (non-Javadoc)
5538    *
5539    * @see
5540    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5541    * .event.ActionEvent)
5542    */
5543   @Override
5544   protected void showGroupConservation_actionPerformed(ActionEvent e)
5545   {
5546     viewport.setShowGroupConservation(showGroupConservation.getState());
5547     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5548   }
5549
5550   /*
5551    * (non-Javadoc)
5552    *
5553    * @see
5554    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5555    * .event.ActionEvent)
5556    */
5557   @Override
5558   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5559   {
5560     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5561     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5562   }
5563
5564   /*
5565    * (non-Javadoc)
5566    *
5567    * @see
5568    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5569    * .event.ActionEvent)
5570    */
5571   @Override
5572   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5573   {
5574     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5575     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5576   }
5577
5578   @Override
5579   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5580   {
5581     showSequenceLogo.setState(true);
5582     viewport.setShowSequenceLogo(true);
5583     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5584     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5585   }
5586
5587   @Override
5588   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5589   {
5590     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5591   }
5592
5593   /*
5594    * (non-Javadoc)
5595    *
5596    * @see
5597    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5598    * .event.ActionEvent)
5599    */
5600   @Override
5601   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5602   {
5603     if (avc.makeGroupsFromSelection())
5604     {
5605       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5606       alignPanel.updateAnnotation();
5607       alignPanel.paintAlignment(true,
5608               viewport.needToUpdateStructureViews());
5609     }
5610   }
5611
5612   public void clearAlignmentSeqRep()
5613   {
5614     // TODO refactor alignmentseqrep to controller
5615     if (viewport.getAlignment().hasSeqrep())
5616     {
5617       viewport.getAlignment().setSeqrep(null);
5618       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5619       alignPanel.updateAnnotation();
5620       alignPanel.paintAlignment(true, true);
5621     }
5622   }
5623
5624   @Override
5625   protected void createGroup_actionPerformed(ActionEvent e)
5626   {
5627     if (avc.createGroup())
5628     {
5629       if (applyAutoAnnotationSettings.isSelected())
5630       {
5631         alignPanel.updateAnnotation(true, false);
5632       }
5633       alignPanel.alignmentChanged();
5634     }
5635   }
5636
5637   @Override
5638   protected void unGroup_actionPerformed(ActionEvent e)
5639   {
5640     if (avc.unGroup())
5641     {
5642       alignPanel.alignmentChanged();
5643     }
5644   }
5645
5646   /**
5647    * make the given alignmentPanel the currently selected tab
5648    *
5649    * @param alignmentPanel
5650    */
5651   public void setDisplayedView(AlignmentPanel alignmentPanel)
5652   {
5653     if (!viewport.getSequenceSetId()
5654             .equals(alignmentPanel.av.getSequenceSetId()))
5655     {
5656       throw new Error(MessageManager.getString(
5657               "error.implementation_error_cannot_show_view_alignment_frame"));
5658     }
5659     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5660             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5661     {
5662       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5663     }
5664   }
5665
5666   /**
5667    * Action on selection of menu options to Show or Hide annotations.
5668    *
5669    * @param visible
5670    * @param forSequences
5671    *          update sequence-related annotations
5672    * @param forAlignment
5673    *          update non-sequence-related annotations
5674    */
5675   @Override
5676   protected void setAnnotationsVisibility(boolean visible,
5677           boolean forSequences, boolean forAlignment)
5678   {
5679     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5680             .getAlignmentAnnotation();
5681     if (anns == null)
5682     {
5683       return;
5684     }
5685     for (AlignmentAnnotation aa : anns)
5686     {
5687       /*
5688        * don't display non-positional annotations on an alignment
5689        */
5690       if (aa.annotations == null)
5691       {
5692         continue;
5693       }
5694       boolean apply = (aa.sequenceRef == null && forAlignment)
5695               || (aa.sequenceRef != null && forSequences);
5696       if (apply)
5697       {
5698         aa.visible = visible;
5699       }
5700     }
5701     alignPanel.validateAnnotationDimensions(true);
5702     alignPanel.alignmentChanged();
5703   }
5704
5705   /**
5706    * Store selected annotation sort order for the view and repaint.
5707    */
5708   @Override
5709   protected void sortAnnotations_actionPerformed()
5710   {
5711     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5712     this.alignPanel.av
5713             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5714     alignPanel.paintAlignment(false, false);
5715   }
5716
5717   /**
5718    *
5719    * @return alignment panels in this alignment frame
5720    */
5721   public List<? extends AlignmentViewPanel> getAlignPanels()
5722   {
5723     // alignPanels is never null
5724     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5725     return alignPanels;
5726   }
5727
5728   /**
5729    * Open a new alignment window, with the cDNA associated with this (protein)
5730    * alignment, aligned as is the protein.
5731    */
5732   protected void viewAsCdna_actionPerformed()
5733   {
5734     // TODO no longer a menu action - refactor as required
5735     final AlignmentI alignment = getViewport().getAlignment();
5736     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5737     if (mappings == null)
5738     {
5739       return;
5740     }
5741     List<SequenceI> cdnaSeqs = new ArrayList<>();
5742     for (SequenceI aaSeq : alignment.getSequences())
5743     {
5744       for (AlignedCodonFrame acf : mappings)
5745       {
5746         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5747         if (dnaSeq != null)
5748         {
5749           /*
5750            * There is a cDNA mapping for this protein sequence - add to new
5751            * alignment. It will share the same dataset sequence as other mapped
5752            * cDNA (no new mappings need to be created).
5753            */
5754           final Sequence newSeq = new Sequence(dnaSeq);
5755           newSeq.setDatasetSequence(dnaSeq);
5756           cdnaSeqs.add(newSeq);
5757         }
5758       }
5759     }
5760     if (cdnaSeqs.size() == 0)
5761     {
5762       // show a warning dialog no mapped cDNA
5763       return;
5764     }
5765     AlignmentI cdna = new Alignment(
5766             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5767     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5768             AlignFrame.DEFAULT_HEIGHT);
5769     cdna.alignAs(alignment);
5770     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5771             + this.title;
5772     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5773             AlignFrame.DEFAULT_HEIGHT);
5774   }
5775
5776   /**
5777    * Set visibility of dna/protein complement view (available when shown in a
5778    * split frame).
5779    *
5780    * @param show
5781    */
5782   @Override
5783   protected void showComplement_actionPerformed(boolean show)
5784   {
5785     SplitContainerI sf = getSplitViewContainer();
5786     if (sf != null)
5787     {
5788       sf.setComplementVisible(this, show);
5789     }
5790   }
5791
5792   /**
5793    * Generate the reverse (optionally complemented) of the selected sequences,
5794    * and add them to the alignment
5795    */
5796   @Override
5797   protected void showReverse_actionPerformed(boolean complement)
5798   {
5799     AlignmentI al = null;
5800     try
5801     {
5802       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5803       al = dna.reverseCdna(complement);
5804       viewport.addAlignment(al, "");
5805       addHistoryItem(new EditCommand(
5806               MessageManager.getString("label.add_sequences"), Action.PASTE,
5807               al.getSequencesArray(), 0, al.getWidth(),
5808               viewport.getAlignment()));
5809     } catch (Exception ex)
5810     {
5811       System.err.println(ex.getMessage());
5812       return;
5813     }
5814   }
5815
5816   /**
5817    * Try to run a script in the Groovy console, having first ensured that this
5818    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5819    * be targeted at this alignment.
5820    */
5821   @Override
5822   protected void runGroovy_actionPerformed()
5823   {
5824     Jalview.setCurrentAlignFrame(this);
5825     groovy.ui.Console console = Desktop.getGroovyConsole();
5826     if (console != null)
5827     {
5828       try
5829       {
5830         console.runScript();
5831       } catch (Exception ex)
5832       {
5833         System.err.println((ex.toString()));
5834         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5835                 MessageManager.getString("label.couldnt_run_groovy_script"),
5836                 MessageManager.getString("label.groovy_support_failed"),
5837                 JvOptionPane.ERROR_MESSAGE);
5838       }
5839     }
5840     else
5841     {
5842       System.err.println("Can't run Groovy script as console not found");
5843     }
5844   }
5845
5846   /**
5847    * Hides columns containing (or not containing) a specified feature, provided
5848    * that would not leave all columns hidden
5849    *
5850    * @param featureType
5851    * @param columnsContaining
5852    * @return
5853    */
5854   public boolean hideFeatureColumns(String featureType,
5855           boolean columnsContaining)
5856   {
5857     boolean notForHiding = avc.markColumnsContainingFeatures(
5858             columnsContaining, false, false, featureType);
5859     if (notForHiding)
5860     {
5861       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5862               false, featureType))
5863       {
5864         getViewport().hideSelectedColumns();
5865         return true;
5866       }
5867     }
5868     return false;
5869   }
5870
5871   @Override
5872   protected void selectHighlightedColumns_actionPerformed(
5873           ActionEvent actionEvent)
5874   {
5875     // include key modifier check in case user selects from menu
5876     avc.markHighlightedColumns(
5877             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5878             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5879                     | ActionEvent.CTRL_MASK)) != 0);
5880   }
5881
5882   /**
5883    * Rebuilds the Colour menu, including any user-defined colours which have
5884    * been loaded either on startup or during the session
5885    */
5886   public void buildColourMenu()
5887   {
5888     colourMenu.removeAll();
5889
5890     colourMenu.add(applyToAllGroups);
5891     colourMenu.add(textColour);
5892     colourMenu.addSeparator();
5893
5894     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5895             viewport.getAlignment(), false);
5896
5897     colourMenu.add(annotationColour);
5898     bg.add(annotationColour);
5899     colourMenu.addSeparator();
5900     colourMenu.add(conservationMenuItem);
5901     colourMenu.add(modifyConservation);
5902     colourMenu.add(abovePIDThreshold);
5903     colourMenu.add(modifyPID);
5904
5905     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5906     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5907   }
5908
5909   /**
5910    * Open a dialog (if not already open) that allows the user to select and
5911    * calculate PCA or Tree analysis
5912    */
5913   protected void openTreePcaDialog()
5914   {
5915     if (alignPanel.getCalculationDialog() == null)
5916     {
5917       new CalculationChooser(AlignFrame.this);
5918     }
5919   }
5920
5921   /**
5922    * Sets the status of the HMMER menu
5923    */
5924   public void updateHMMERStatus()
5925   {
5926     hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5927   }
5928
5929   @Override
5930   protected void loadVcf_actionPerformed()
5931   {
5932     JalviewFileChooser chooser = new JalviewFileChooser(
5933             Cache.getProperty("LAST_DIRECTORY"));
5934     chooser.setFileView(new JalviewFileView());
5935     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5936     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5937
5938     int value = chooser.showOpenDialog(null);
5939
5940     if (value == JalviewFileChooser.APPROVE_OPTION)
5941     {
5942       String choice = chooser.getSelectedFile().getPath();
5943       Cache.setProperty("LAST_DIRECTORY", choice);
5944       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5945       new VCFLoader(choice).loadVCF(seqs, this);
5946     }
5947
5948   }
5949 }
5950
5951 class PrintThread extends Thread
5952 {
5953   AlignmentPanel ap;
5954
5955   public PrintThread(AlignmentPanel ap)
5956   {
5957     this.ap = ap;
5958   }
5959
5960   static PageFormat pf;
5961
5962   @Override
5963   public void run()
5964   {
5965     PrinterJob printJob = PrinterJob.getPrinterJob();
5966
5967     if (pf != null)
5968     {
5969       printJob.setPrintable(ap, pf);
5970     }
5971     else
5972     {
5973       printJob.setPrintable(ap);
5974     }
5975
5976     if (printJob.printDialog())
5977     {
5978       try
5979       {
5980         printJob.print();
5981       } catch (Exception PrintException)
5982       {
5983         PrintException.printStackTrace();
5984       }
5985     }
5986   }
5987 }