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().getSequenceSelection().length < 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   @Override
3791   public void sortEValueMenuItem_actionPerformed(ActionEvent e)
3792   {
3793     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3794     AlignmentSorter.sortByEValue(viewport.getAlignment());
3795     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3796             viewport.getAlignment()));
3797     alignPanel.paintAlignment(true, false);
3798
3799   }
3800
3801   @Override
3802   public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
3803   {
3804     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3805     AlignmentSorter.sortByBitScore(viewport.getAlignment());
3806     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3807             viewport.getAlignment()));
3808     alignPanel.paintAlignment(true, false);
3809
3810   }
3811
3812   /**
3813    * DOCUMENT ME!
3814    *
3815    * @param e
3816    *          DOCUMENT ME!
3817    */
3818   @Override
3819   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3820   {
3821     new RedundancyPanel(alignPanel, this);
3822   }
3823
3824   /**
3825    * DOCUMENT ME!
3826    *
3827    * @param e
3828    *          DOCUMENT ME!
3829    */
3830   @Override
3831   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3832   {
3833     if ((viewport.getSelectionGroup() == null)
3834             || (viewport.getSelectionGroup().getSize() < 2))
3835     {
3836       JvOptionPane.showInternalMessageDialog(this,
3837               MessageManager.getString(
3838                       "label.you_must_select_least_two_sequences"),
3839               MessageManager.getString("label.invalid_selection"),
3840               JvOptionPane.WARNING_MESSAGE);
3841     }
3842     else
3843     {
3844       JInternalFrame frame = new JInternalFrame();
3845       frame.setContentPane(new PairwiseAlignPanel(viewport));
3846       Desktop.addInternalFrame(frame,
3847               MessageManager.getString("action.pairwise_alignment"), 600,
3848               500);
3849     }
3850   }
3851
3852   @Override
3853   public void autoCalculate_actionPerformed(ActionEvent e)
3854   {
3855     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3856     if (viewport.autoCalculateConsensus)
3857     {
3858       viewport.firePropertyChange("alignment", null,
3859               viewport.getAlignment().getSequences());
3860     }
3861   }
3862
3863   @Override
3864   public void sortByTreeOption_actionPerformed(ActionEvent e)
3865   {
3866     viewport.sortByTree = sortByTree.isSelected();
3867   }
3868
3869   @Override
3870   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3871   {
3872     viewport.followSelection = listenToViewSelections.isSelected();
3873   }
3874
3875   /**
3876    * Constructs a tree panel and adds it to the desktop
3877    *
3878    * @param type
3879    *          tree type (NJ or AV)
3880    * @param modelName
3881    *          name of score model used to compute the tree
3882    * @param options
3883    *          parameters for the distance or similarity calculation
3884    */
3885   void newTreePanel(String type, String modelName,
3886           SimilarityParamsI options)
3887   {
3888     String frameTitle = "";
3889     TreePanel tp;
3890
3891     boolean onSelection = false;
3892     if (viewport.getSelectionGroup() != null
3893             && viewport.getSelectionGroup().getSize() > 0)
3894     {
3895       SequenceGroup sg = viewport.getSelectionGroup();
3896
3897       /* Decide if the selection is a column region */
3898       for (SequenceI _s : sg.getSequences())
3899       {
3900         if (_s.getLength() < sg.getEndRes())
3901         {
3902           JvOptionPane.showMessageDialog(Desktop.desktop,
3903                   MessageManager.getString(
3904                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3905                   MessageManager.getString(
3906                           "label.sequences_selection_not_aligned"),
3907                   JvOptionPane.WARNING_MESSAGE);
3908
3909           return;
3910         }
3911       }
3912       onSelection = true;
3913     }
3914     else
3915     {
3916       if (viewport.getAlignment().getHeight() < 2)
3917       {
3918         return;
3919       }
3920     }
3921
3922     tp = new TreePanel(alignPanel, type, modelName, options);
3923     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3924
3925     frameTitle += " from ";
3926
3927     if (viewport.getViewName() != null)
3928     {
3929       frameTitle += viewport.getViewName() + " of ";
3930     }
3931
3932     frameTitle += this.title;
3933
3934     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3935   }
3936
3937   /**
3938    * DOCUMENT ME!
3939    *
3940    * @param title
3941    *          DOCUMENT ME!
3942    * @param order
3943    *          DOCUMENT ME!
3944    */
3945   public void addSortByOrderMenuItem(String title,
3946           final AlignmentOrder order)
3947   {
3948     final JMenuItem item = new JMenuItem(MessageManager
3949             .formatMessage("action.by_title_param", new Object[]
3950             { title }));
3951     sort.add(item);
3952     item.addActionListener(new java.awt.event.ActionListener()
3953     {
3954       @Override
3955       public void actionPerformed(ActionEvent e)
3956       {
3957         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3958
3959         // TODO: JBPNote - have to map order entries to curent SequenceI
3960         // pointers
3961         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3962
3963         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3964                 viewport.getAlignment()));
3965
3966         alignPanel.paintAlignment(true, false);
3967       }
3968     });
3969   }
3970
3971   /**
3972    * Add a new sort by annotation score menu item
3973    *
3974    * @param sort
3975    *          the menu to add the option to
3976    * @param scoreLabel
3977    *          the label used to retrieve scores for each sequence on the
3978    *          alignment
3979    */
3980   public void addSortByAnnotScoreMenuItem(JMenu sort,
3981           final String scoreLabel)
3982   {
3983     final JMenuItem item = new JMenuItem(scoreLabel);
3984     sort.add(item);
3985     item.addActionListener(new java.awt.event.ActionListener()
3986     {
3987       @Override
3988       public void actionPerformed(ActionEvent e)
3989       {
3990         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3991         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3992                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3993         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3994                 viewport.getAlignment()));
3995         alignPanel.paintAlignment(true, false);
3996       }
3997     });
3998   }
3999
4000   /**
4001    * last hash for alignment's annotation array - used to minimise cost of
4002    * rebuild.
4003    */
4004   protected int _annotationScoreVectorHash;
4005
4006   /**
4007    * search the alignment and rebuild the sort by annotation score submenu the
4008    * last alignment annotation vector hash is stored to minimize cost of
4009    * rebuilding in subsequence calls.
4010    *
4011    */
4012   @Override
4013   public void buildSortByAnnotationScoresMenu()
4014   {
4015     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4016     {
4017       return;
4018     }
4019
4020     if (viewport.getAlignment().getAlignmentAnnotation()
4021             .hashCode() == _annotationScoreVectorHash)
4022     {
4023       return;
4024     }
4025
4026     sortByAnnotScore.removeAll();
4027     Set<String> scoreSorts = new HashSet<>();
4028     for (SequenceI sqa : viewport.getAlignment().getSequences())
4029     {
4030       AlignmentAnnotation[] anns = sqa.getAnnotation();
4031       for (int i = 0; anns != null && i < anns.length; i++)
4032       {
4033         AlignmentAnnotation aa = anns[i];
4034         if (aa != null && aa.hasScore() && aa.sequenceRef != null)
4035         {
4036           scoreSorts.add(aa.label);
4037         }
4038       }
4039     }
4040     for (String label : scoreSorts)
4041     {
4042       addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
4043     }
4044     sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
4045
4046     _annotationScoreVectorHash = viewport.getAlignment()
4047             .getAlignmentAnnotation().hashCode();
4048   }
4049
4050   /**
4051    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4052    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4053    * call. Listeners are added to remove the menu item when the treePanel is
4054    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4055    * modified.
4056    */
4057   @Override
4058   public void buildTreeSortMenu()
4059   {
4060     sortByTreeMenu.removeAll();
4061
4062     List<Component> comps = PaintRefresher.components
4063             .get(viewport.getSequenceSetId());
4064     List<TreePanel> treePanels = new ArrayList<>();
4065     for (Component comp : comps)
4066     {
4067       if (comp instanceof TreePanel)
4068       {
4069         treePanels.add((TreePanel) comp);
4070       }
4071     }
4072
4073     if (treePanels.size() < 1)
4074     {
4075       sortByTreeMenu.setVisible(false);
4076       return;
4077     }
4078
4079     sortByTreeMenu.setVisible(true);
4080
4081     for (final TreePanel tp : treePanels)
4082     {
4083       final JMenuItem item = new JMenuItem(tp.getTitle());
4084       item.addActionListener(new java.awt.event.ActionListener()
4085       {
4086         @Override
4087         public void actionPerformed(ActionEvent e)
4088         {
4089           tp.sortByTree_actionPerformed();
4090           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4091
4092         }
4093       });
4094
4095       sortByTreeMenu.add(item);
4096     }
4097   }
4098
4099   public boolean sortBy(AlignmentOrder alorder, String undoname)
4100   {
4101     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4102     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4103     if (undoname != null)
4104     {
4105       addHistoryItem(new OrderCommand(undoname, oldOrder,
4106               viewport.getAlignment()));
4107     }
4108     alignPanel.paintAlignment(true, false);
4109     return true;
4110   }
4111
4112   /**
4113    * Work out whether the whole set of sequences or just the selected set will
4114    * be submitted for multiple alignment.
4115    *
4116    */
4117   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4118   {
4119     // Now, check we have enough sequences
4120     AlignmentView msa = null;
4121
4122     if ((viewport.getSelectionGroup() != null)
4123             && (viewport.getSelectionGroup().getSize() > 1))
4124     {
4125       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4126       // some common interface!
4127       /*
4128        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4129        * SequenceI[sz = seqs.getSize(false)];
4130        *
4131        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4132        * seqs.getSequenceAt(i); }
4133        */
4134       msa = viewport.getAlignmentView(true);
4135     }
4136     else if (viewport.getSelectionGroup() != null
4137             && viewport.getSelectionGroup().getSize() == 1)
4138     {
4139       int option = JvOptionPane.showConfirmDialog(this,
4140               MessageManager.getString("warn.oneseq_msainput_selection"),
4141               MessageManager.getString("label.invalid_selection"),
4142               JvOptionPane.OK_CANCEL_OPTION);
4143       if (option == JvOptionPane.OK_OPTION)
4144       {
4145         msa = viewport.getAlignmentView(false);
4146       }
4147     }
4148     else
4149     {
4150       msa = viewport.getAlignmentView(false);
4151     }
4152     return msa;
4153   }
4154
4155   /**
4156    * Decides what is submitted to a secondary structure prediction service: the
4157    * first sequence in the alignment, or in the current selection, or, if the
4158    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4159    * region or the whole alignment. (where the first sequence in the set is the
4160    * one that the prediction will be for).
4161    */
4162   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4163   {
4164     AlignmentView seqs = null;
4165
4166     if ((viewport.getSelectionGroup() != null)
4167             && (viewport.getSelectionGroup().getSize() > 0))
4168     {
4169       seqs = viewport.getAlignmentView(true);
4170     }
4171     else
4172     {
4173       seqs = viewport.getAlignmentView(false);
4174     }
4175     // limit sequences - JBPNote in future - could spawn multiple prediction
4176     // jobs
4177     // TODO: viewport.getAlignment().isAligned is a global state - the local
4178     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4179     if (!viewport.getAlignment().isAligned(false))
4180     {
4181       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4182       // TODO: if seqs.getSequences().length>1 then should really have warned
4183       // user!
4184
4185     }
4186     return seqs;
4187   }
4188
4189   /**
4190    * DOCUMENT ME!
4191    *
4192    * @param e
4193    *          DOCUMENT ME!
4194    */
4195   @Override
4196   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4197   {
4198     // Pick the tree file
4199     JalviewFileChooser chooser = new JalviewFileChooser(
4200             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4201     chooser.setFileView(new JalviewFileView());
4202     chooser.setDialogTitle(
4203             MessageManager.getString("label.select_newick_like_tree_file"));
4204     chooser.setToolTipText(
4205             MessageManager.getString("label.load_tree_file"));
4206
4207     int value = chooser.showOpenDialog(null);
4208
4209     if (value == JalviewFileChooser.APPROVE_OPTION)
4210     {
4211       String filePath = chooser.getSelectedFile().getPath();
4212       Cache.setProperty("LAST_DIRECTORY", filePath);
4213       NewickFile fin = null;
4214       try
4215       {
4216         fin = new NewickFile(filePath, DataSourceType.FILE);
4217         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4218       } catch (Exception ex)
4219       {
4220         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4221                 MessageManager.getString("label.problem_reading_tree_file"),
4222                 JvOptionPane.WARNING_MESSAGE);
4223         ex.printStackTrace();
4224       }
4225       if (fin != null && fin.hasWarningMessage())
4226       {
4227         JvOptionPane.showMessageDialog(Desktop.desktop,
4228                 fin.getWarningMessage(),
4229                 MessageManager
4230                         .getString("label.possible_problem_with_tree_file"),
4231                 JvOptionPane.WARNING_MESSAGE);
4232       }
4233     }
4234   }
4235
4236   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4237   {
4238     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4239   }
4240
4241   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4242           int h, int x, int y)
4243   {
4244     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4245   }
4246
4247   /**
4248    * Add a treeviewer for the tree extracted from a Newick file object to the
4249    * current alignment view
4250    *
4251    * @param nf
4252    *          the tree
4253    * @param title
4254    *          tree viewer title
4255    * @param input
4256    *          Associated alignment input data (or null)
4257    * @param w
4258    *          width
4259    * @param h
4260    *          height
4261    * @param x
4262    *          position
4263    * @param y
4264    *          position
4265    * @return TreePanel handle
4266    */
4267   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4268           AlignmentView input, int w, int h, int x, int y)
4269   {
4270     TreePanel tp = null;
4271
4272     try
4273     {
4274       nf.parse();
4275
4276       if (nf.getTree() != null)
4277       {
4278         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4279
4280         tp.setSize(w, h);
4281
4282         if (x > 0 && y > 0)
4283         {
4284           tp.setLocation(x, y);
4285         }
4286
4287         Desktop.addInternalFrame(tp, treeTitle, w, h);
4288       }
4289     } catch (Exception ex)
4290     {
4291       ex.printStackTrace();
4292     }
4293
4294     return tp;
4295   }
4296
4297   private boolean buildingMenu = false;
4298
4299   /**
4300    * Generates menu items and listener event actions for web service clients
4301    *
4302    */
4303   public void BuildWebServiceMenu()
4304   {
4305     while (buildingMenu)
4306     {
4307       try
4308       {
4309         System.err.println("Waiting for building menu to finish.");
4310         Thread.sleep(10);
4311       } catch (Exception e)
4312       {
4313       }
4314     }
4315     final AlignFrame me = this;
4316     buildingMenu = true;
4317     new Thread(new Runnable()
4318     {
4319       @Override
4320       public void run()
4321       {
4322         final List<JMenuItem> legacyItems = new ArrayList<>();
4323         try
4324         {
4325           // System.err.println("Building ws menu again "
4326           // + Thread.currentThread());
4327           // TODO: add support for context dependent disabling of services based
4328           // on
4329           // alignment and current selection
4330           // TODO: add additional serviceHandle parameter to specify abstract
4331           // handler
4332           // class independently of AbstractName
4333           // TODO: add in rediscovery GUI function to restart discoverer
4334           // TODO: group services by location as well as function and/or
4335           // introduce
4336           // object broker mechanism.
4337           final Vector<JMenu> wsmenu = new Vector<>();
4338           final IProgressIndicator af = me;
4339
4340           /*
4341            * do not i18n these strings - they are hard-coded in class
4342            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4343            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4344            */
4345           final JMenu msawsmenu = new JMenu("Alignment");
4346           final JMenu secstrmenu = new JMenu(
4347                   "Secondary Structure Prediction");
4348           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4349           final JMenu analymenu = new JMenu("Analysis");
4350           final JMenu dismenu = new JMenu("Protein Disorder");
4351           // JAL-940 - only show secondary structure prediction services from
4352           // the legacy server
4353           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4354               // &&
4355           Discoverer.services != null && (Discoverer.services.size() > 0))
4356           {
4357             // TODO: refactor to allow list of AbstractName/Handler bindings to
4358             // be
4359             // stored or retrieved from elsewhere
4360             // No MSAWS used any more:
4361             // Vector msaws = null; // (Vector)
4362             // Discoverer.services.get("MsaWS");
4363             Vector secstrpr = (Vector) Discoverer.services
4364                     .get("SecStrPred");
4365             if (secstrpr != null)
4366             {
4367               // Add any secondary structure prediction services
4368               for (int i = 0, j = secstrpr.size(); i < j; i++)
4369               {
4370                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4371                         .get(i);
4372                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4373                         .getServiceClient(sh);
4374                 int p = secstrmenu.getItemCount();
4375                 impl.attachWSMenuEntry(secstrmenu, me);
4376                 int q = secstrmenu.getItemCount();
4377                 for (int litm = p; litm < q; litm++)
4378                 {
4379                   legacyItems.add(secstrmenu.getItem(litm));
4380                 }
4381               }
4382             }
4383           }
4384
4385           // Add all submenus in the order they should appear on the web
4386           // services menu
4387           wsmenu.add(msawsmenu);
4388           wsmenu.add(secstrmenu);
4389           wsmenu.add(dismenu);
4390           wsmenu.add(analymenu);
4391           // No search services yet
4392           // wsmenu.add(seqsrchmenu);
4393
4394           javax.swing.SwingUtilities.invokeLater(new Runnable()
4395           {
4396             @Override
4397             public void run()
4398             {
4399               try
4400               {
4401                 webService.removeAll();
4402                 // first, add discovered services onto the webservices menu
4403                 if (wsmenu.size() > 0)
4404                 {
4405                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4406                   {
4407                     webService.add(wsmenu.get(i));
4408                   }
4409                 }
4410                 else
4411                 {
4412                   webService.add(me.webServiceNoServices);
4413                 }
4414                 // TODO: move into separate menu builder class.
4415                 boolean new_sspred = false;
4416                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4417                 {
4418                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4419                   if (jws2servs != null)
4420                   {
4421                     if (jws2servs.hasServices())
4422                     {
4423                       jws2servs.attachWSMenuEntry(webService, me);
4424                       for (Jws2Instance sv : jws2servs.getServices())
4425                       {
4426                         if (sv.getName().toLowerCase().contains("jpred"))
4427                         {
4428                           for (JMenuItem jmi : legacyItems)
4429                           {
4430                             jmi.setVisible(false);
4431                           }
4432                         }
4433                       }
4434
4435                     }
4436                     if (jws2servs.isRunning())
4437                     {
4438                       JMenuItem tm = new JMenuItem(
4439                               "Still discovering JABA Services");
4440                       tm.setEnabled(false);
4441                       webService.add(tm);
4442                     }
4443                   }
4444                 }
4445                 build_urlServiceMenu(me.webService);
4446
4447                 // TODO Mateusz - follow pattern for adding web service
4448                 // JMenuItems for slivka-based services
4449
4450                 build_fetchdbmenu(webService);
4451                 for (JMenu item : wsmenu)
4452                 {
4453                   if (item.getItemCount() == 0)
4454                   {
4455                     item.setEnabled(false);
4456                   }
4457                   else
4458                   {
4459                     item.setEnabled(true);
4460                   }
4461                 }
4462               } catch (Exception e)
4463               {
4464                 Cache.log.debug(
4465                         "Exception during web service menu building process.",
4466                         e);
4467               }
4468             }
4469           });
4470         } catch (Exception e)
4471         {
4472         }
4473         buildingMenu = false;
4474       }
4475     }).start();
4476
4477   }
4478
4479   /**
4480    * construct any groupURL type service menu entries.
4481    *
4482    * @param webService
4483    */
4484   private void build_urlServiceMenu(JMenu webService)
4485   {
4486     // TODO: remove this code when 2.7 is released
4487     // DEBUG - alignmentView
4488     /*
4489      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4490      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4491      *
4492      * @Override public void actionPerformed(ActionEvent e) {
4493      * jalview.datamodel.AlignmentView
4494      * .testSelectionViews(af.viewport.getAlignment(),
4495      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4496      *
4497      * }); webService.add(testAlView);
4498      */
4499     // TODO: refactor to RestClient discoverer and merge menu entries for
4500     // rest-style services with other types of analysis/calculation service
4501     // SHmmr test client - still being implemented.
4502     // DEBUG - alignmentView
4503
4504     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4505             .getRestClients())
4506     {
4507       client.attachWSMenuEntry(
4508               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4509               this);
4510     }
4511   }
4512
4513   /**
4514    * Searches the alignment sequences for xRefs and builds the Show
4515    * Cross-References menu (formerly called Show Products), with database
4516    * sources for which cross-references are found (protein sources for a
4517    * nucleotide alignment and vice versa)
4518    *
4519    * @return true if Show Cross-references menu should be enabled
4520    */
4521   public boolean canShowProducts()
4522   {
4523     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4524     AlignmentI dataset = viewport.getAlignment().getDataset();
4525
4526     showProducts.removeAll();
4527     final boolean dna = viewport.getAlignment().isNucleotide();
4528
4529     if (seqs == null || seqs.length == 0)
4530     {
4531       // nothing to see here.
4532       return false;
4533     }
4534
4535     boolean showp = false;
4536     try
4537     {
4538       List<String> ptypes = new CrossRef(seqs, dataset)
4539               .findXrefSourcesForSequences(dna);
4540
4541       for (final String source : ptypes)
4542       {
4543         showp = true;
4544         final AlignFrame af = this;
4545         JMenuItem xtype = new JMenuItem(source);
4546         xtype.addActionListener(new ActionListener()
4547         {
4548           @Override
4549           public void actionPerformed(ActionEvent e)
4550           {
4551             showProductsFor(af.viewport.getSequenceSelection(), dna,
4552                     source);
4553           }
4554         });
4555         showProducts.add(xtype);
4556       }
4557       showProducts.setVisible(showp);
4558       showProducts.setEnabled(showp);
4559     } catch (Exception e)
4560     {
4561       Cache.log.warn(
4562               "canShowProducts threw an exception - please report to help@jalview.org",
4563               e);
4564       return false;
4565     }
4566     return showp;
4567   }
4568
4569   /**
4570    * Finds and displays cross-references for the selected sequences (protein
4571    * products for nucleotide sequences, dna coding sequences for peptides).
4572    *
4573    * @param sel
4574    *          the sequences to show cross-references for
4575    * @param dna
4576    *          true if from a nucleotide alignment (so showing proteins)
4577    * @param source
4578    *          the database to show cross-references for
4579    */
4580   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4581           final String source)
4582   {
4583     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4584             .start();
4585   }
4586
4587   /**
4588    * Construct and display a new frame containing the translation of this
4589    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4590    */
4591   @Override
4592   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4593   {
4594     AlignmentI al = null;
4595     try
4596     {
4597       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4598
4599       al = dna.translateCdna(codeTable);
4600     } catch (Exception ex)
4601     {
4602       jalview.bin.Cache.log.error(
4603               "Exception during translation. Please report this !", ex);
4604       final String msg = MessageManager.getString(
4605               "label.error_when_translating_sequences_submit_bug_report");
4606       final String errorTitle = MessageManager
4607               .getString("label.implementation_error")
4608               + MessageManager.getString("label.translation_failed");
4609       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4610               JvOptionPane.ERROR_MESSAGE);
4611       return;
4612     }
4613     if (al == null || al.getHeight() == 0)
4614     {
4615       final String msg = MessageManager.getString(
4616               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4617       final String errorTitle = MessageManager
4618               .getString("label.translation_failed");
4619       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4620               JvOptionPane.WARNING_MESSAGE);
4621     }
4622     else
4623     {
4624       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4625       af.setFileFormat(this.currentFileFormat);
4626       final String newTitle = MessageManager
4627               .formatMessage("label.translation_of_params", new Object[]
4628               { this.getTitle(), codeTable.getId() });
4629       af.setTitle(newTitle);
4630       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4631       {
4632         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4633         viewport.openSplitFrame(af, new Alignment(seqs));
4634       }
4635       else
4636       {
4637         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4638                 DEFAULT_HEIGHT);
4639       }
4640     }
4641   }
4642
4643   /**
4644    * Set the file format
4645    *
4646    * @param format
4647    */
4648   public void setFileFormat(FileFormatI format)
4649   {
4650     this.currentFileFormat = format;
4651   }
4652
4653   /**
4654    * Try to load a features file onto the alignment.
4655    *
4656    * @param file
4657    *          contents or path to retrieve file
4658    * @param sourceType
4659    *          access mode of file (see jalview.io.AlignFile)
4660    * @return true if features file was parsed correctly.
4661    */
4662   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4663   {
4664     return avc.parseFeaturesFile(file, sourceType,
4665             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4666
4667   }
4668
4669   @Override
4670   public void refreshFeatureUI(boolean enableIfNecessary)
4671   {
4672     // note - currently this is only still here rather than in the controller
4673     // because of the featureSettings hard reference that is yet to be
4674     // abstracted
4675     if (enableIfNecessary)
4676     {
4677       viewport.setShowSequenceFeatures(true);
4678       showSeqFeatures.setSelected(true);
4679     }
4680
4681   }
4682
4683   @Override
4684   public void dragEnter(DropTargetDragEvent evt)
4685   {
4686   }
4687
4688   @Override
4689   public void dragExit(DropTargetEvent evt)
4690   {
4691   }
4692
4693   @Override
4694   public void dragOver(DropTargetDragEvent evt)
4695   {
4696   }
4697
4698   @Override
4699   public void dropActionChanged(DropTargetDragEvent evt)
4700   {
4701   }
4702
4703   @Override
4704   public void drop(DropTargetDropEvent evt)
4705   {
4706     // JAL-1552 - acceptDrop required before getTransferable call for
4707     // Java's Transferable for native dnd
4708     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4709     Transferable t = evt.getTransferable();
4710     final AlignFrame thisaf = this;
4711     final List<String> files = new ArrayList<>();
4712     List<DataSourceType> protocols = new ArrayList<>();
4713
4714     try
4715     {
4716       Desktop.transferFromDropTarget(files, protocols, evt, t);
4717     } catch (Exception e)
4718     {
4719       e.printStackTrace();
4720     }
4721     if (files != null)
4722     {
4723       new Thread(new Runnable()
4724       {
4725         @Override
4726         public void run()
4727         {
4728           try
4729           {
4730             // check to see if any of these files have names matching sequences
4731             // in
4732             // the alignment
4733             SequenceIdMatcher idm = new SequenceIdMatcher(
4734                     viewport.getAlignment().getSequencesArray());
4735             /**
4736              * Object[] { String,SequenceI}
4737              */
4738             ArrayList<Object[]> filesmatched = new ArrayList<>();
4739             ArrayList<String> filesnotmatched = new ArrayList<>();
4740             for (int i = 0; i < files.size(); i++)
4741             {
4742               String file = files.get(i).toString();
4743               String pdbfn = "";
4744               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4745               if (protocol == DataSourceType.FILE)
4746               {
4747                 File fl = new File(file);
4748                 pdbfn = fl.getName();
4749               }
4750               else if (protocol == DataSourceType.URL)
4751               {
4752                 URL url = new URL(file);
4753                 pdbfn = url.getFile();
4754               }
4755               if (pdbfn.length() > 0)
4756               {
4757                 // attempt to find a match in the alignment
4758                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4759                 int l = 0, c = pdbfn.indexOf(".");
4760                 while (mtch == null && c != -1)
4761                 {
4762                   do
4763                   {
4764                     l = c;
4765                   } while ((c = pdbfn.indexOf(".", l)) > l);
4766                   if (l > -1)
4767                   {
4768                     pdbfn = pdbfn.substring(0, l);
4769                   }
4770                   mtch = idm.findAllIdMatches(pdbfn);
4771                 }
4772                 if (mtch != null)
4773                 {
4774                   FileFormatI type = null;
4775                   try
4776                   {
4777                     type = new IdentifyFile().identify(file, protocol);
4778                   } catch (Exception ex)
4779                   {
4780                     type = null;
4781                   }
4782                   if (type != null && type.isStructureFile())
4783                   {
4784                     filesmatched.add(new Object[] { file, protocol, mtch });
4785                     continue;
4786                   }
4787                 }
4788                 // File wasn't named like one of the sequences or wasn't a PDB
4789                 // file.
4790                 filesnotmatched.add(file);
4791               }
4792             }
4793             int assocfiles = 0;
4794             if (filesmatched.size() > 0)
4795             {
4796               boolean autoAssociate = Cache
4797                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4798               if (!autoAssociate)
4799               {
4800                 String msg = MessageManager.formatMessage(
4801                         "label.automatically_associate_structure_files_with_sequences_same_name",
4802                         new Object[]
4803                         { Integer.valueOf(filesmatched.size())
4804                                 .toString() });
4805                 String ttl = MessageManager.getString(
4806                         "label.automatically_associate_structure_files_by_name");
4807                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4808                         ttl, JvOptionPane.YES_NO_OPTION);
4809                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4810               }
4811               if (autoAssociate)
4812               {
4813                 for (Object[] fm : filesmatched)
4814                 {
4815                   // try and associate
4816                   // TODO: may want to set a standard ID naming formalism for
4817                   // associating PDB files which have no IDs.
4818                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4819                   {
4820                     PDBEntry pe = new AssociatePdbFileWithSeq()
4821                             .associatePdbWithSeq((String) fm[0],
4822                                     (DataSourceType) fm[1], toassoc, false,
4823                                     Desktop.instance);
4824                     if (pe != null)
4825                     {
4826                       System.err.println("Associated file : "
4827                               + ((String) fm[0]) + " with "
4828                               + toassoc.getDisplayId(true));
4829                       assocfiles++;
4830                     }
4831                   }
4832                   // TODO: do we need to update overview ? only if features are
4833                   // shown I guess
4834                   alignPanel.paintAlignment(true, false);
4835                 }
4836               }
4837               else
4838               {
4839                 /*
4840                  * add declined structures as sequences
4841                  */
4842                 for (Object[] o : filesmatched)
4843                 {
4844                   filesnotmatched.add((String) o[0]);
4845                 }
4846               }
4847             }
4848             if (filesnotmatched.size() > 0)
4849             {
4850               if (assocfiles > 0 && (Cache.getDefault(
4851                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4852                       || JvOptionPane.showConfirmDialog(thisaf,
4853                               "<html>" + MessageManager.formatMessage(
4854                                       "label.ignore_unmatched_dropped_files_info",
4855                                       new Object[]
4856                                       { Integer.valueOf(
4857                                               filesnotmatched.size())
4858                                               .toString() })
4859                                       + "</html>",
4860                               MessageManager.getString(
4861                                       "label.ignore_unmatched_dropped_files"),
4862                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4863               {
4864                 return;
4865               }
4866               for (String fn : filesnotmatched)
4867               {
4868                 loadJalviewDataFile(fn, null, null, null);
4869               }
4870
4871             }
4872           } catch (Exception ex)
4873           {
4874             ex.printStackTrace();
4875           }
4876         }
4877       }).start();
4878     }
4879   }
4880
4881   /**
4882    * Attempt to load a "dropped" file or URL string, by testing in turn for
4883    * <ul>
4884    * <li>an Annotation file</li>
4885    * <li>a JNet file</li>
4886    * <li>a features file</li>
4887    * <li>else try to interpret as an alignment file</li>
4888    * </ul>
4889    *
4890    * @param file
4891    *          either a filename or a URL string.
4892    * @throws InterruptedException
4893    * @throws IOException
4894    */
4895   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4896           FileFormatI format, SequenceI assocSeq)
4897   {
4898     try
4899     {
4900       if (sourceType == null)
4901       {
4902         sourceType = FormatAdapter.checkProtocol(file);
4903       }
4904       // if the file isn't identified, or not positively identified as some
4905       // other filetype (PFAM is default unidentified alignment file type) then
4906       // try to parse as annotation.
4907       boolean isAnnotation = (format == null
4908               || FileFormat.Pfam.equals(format))
4909                       ? new AnnotationFile().annotateAlignmentView(viewport,
4910                               file, sourceType)
4911                       : false;
4912
4913       if (!isAnnotation)
4914       {
4915         // first see if its a T-COFFEE score file
4916         TCoffeeScoreFile tcf = null;
4917         try
4918         {
4919           tcf = new TCoffeeScoreFile(file, sourceType);
4920           if (tcf.isValid())
4921           {
4922             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4923             {
4924               buildColourMenu();
4925               changeColour(
4926                       new TCoffeeColourScheme(viewport.getAlignment()));
4927               isAnnotation = true;
4928               statusBar.setText(MessageManager.getString(
4929                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4930             }
4931             else
4932             {
4933               // some problem - if no warning its probable that the ID matching
4934               // process didn't work
4935               JvOptionPane.showMessageDialog(Desktop.desktop,
4936                       tcf.getWarningMessage() == null
4937                               ? MessageManager.getString(
4938                                       "label.check_file_matches_sequence_ids_alignment")
4939                               : tcf.getWarningMessage(),
4940                       MessageManager.getString(
4941                               "label.problem_reading_tcoffee_score_file"),
4942                       JvOptionPane.WARNING_MESSAGE);
4943             }
4944           }
4945           else
4946           {
4947             tcf = null;
4948           }
4949         } catch (Exception x)
4950         {
4951           Cache.log.debug(
4952                   "Exception when processing data source as T-COFFEE score file",
4953                   x);
4954           tcf = null;
4955         }
4956         if (tcf == null)
4957         {
4958           // try to see if its a JNet 'concise' style annotation file *before*
4959           // we
4960           // try to parse it as a features file
4961           if (format == null)
4962           {
4963             format = new IdentifyFile().identify(file, sourceType);
4964           }
4965           if (FileFormat.ScoreMatrix == format)
4966           {
4967             ScoreMatrixFile sm = new ScoreMatrixFile(
4968                     new FileParse(file, sourceType));
4969             sm.parse();
4970             // todo: i18n this message
4971             statusBar.setText(MessageManager.formatMessage(
4972                     "label.successfully_loaded_matrix",
4973                     sm.getMatrixName()));
4974           }
4975           else if (FileFormat.Jnet.equals(format))
4976           {
4977             JPredFile predictions = new JPredFile(file, sourceType);
4978             new JnetAnnotationMaker();
4979             JnetAnnotationMaker.add_annotation(predictions,
4980                     viewport.getAlignment(), 0, false);
4981             viewport.getAlignment().setupJPredAlignment();
4982             isAnnotation = true;
4983           }
4984           // else if (IdentifyFile.FeaturesFile.equals(format))
4985           else if (FileFormat.Features.equals(format))
4986           {
4987             if (parseFeaturesFile(file, sourceType))
4988             {
4989               alignPanel.paintAlignment(true, true);
4990             }
4991           }
4992           else
4993           {
4994             new FileLoader().LoadFile(viewport, file, sourceType, format);
4995           }
4996         }
4997       }
4998       if (isAnnotation)
4999       {
5000         alignPanel.adjustAnnotationHeight();
5001         viewport.updateSequenceIdColours();
5002         buildSortByAnnotationScoresMenu();
5003         alignPanel.paintAlignment(true, true);
5004       }
5005     } catch (Exception ex)
5006     {
5007       ex.printStackTrace();
5008     } catch (OutOfMemoryError oom)
5009     {
5010       try
5011       {
5012         System.gc();
5013       } catch (Exception x)
5014       {
5015       }
5016       new OOMWarning(
5017               "loading data "
5018                       + (sourceType != null
5019                               ? (sourceType == DataSourceType.PASTE
5020                                       ? "from clipboard."
5021                                       : "using " + sourceType + " from "
5022                                               + file)
5023                               : ".")
5024                       + (format != null
5025                               ? "(parsing as '" + format + "' file)"
5026                               : ""),
5027               oom, Desktop.desktop);
5028     }
5029   }
5030
5031   /**
5032    * Method invoked by the ChangeListener on the tabbed pane, in other words
5033    * when a different tabbed pane is selected by the user or programmatically.
5034    */
5035   @Override
5036   public void tabSelectionChanged(int index)
5037   {
5038     if (index > -1)
5039     {
5040       alignPanel = alignPanels.get(index);
5041       viewport = alignPanel.av;
5042       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5043       setMenusFromViewport(viewport);
5044     }
5045
5046     /*
5047      * 'focus' any colour slider that is open to the selected viewport
5048      */
5049     if (viewport.getConservationSelected())
5050     {
5051       SliderPanel.setConservationSlider(alignPanel,
5052               viewport.getResidueShading(), alignPanel.getViewName());
5053     }
5054     else
5055     {
5056       SliderPanel.hideConservationSlider();
5057     }
5058     if (viewport.getAbovePIDThreshold())
5059     {
5060       SliderPanel.setPIDSliderSource(alignPanel,
5061               viewport.getResidueShading(), alignPanel.getViewName());
5062     }
5063     else
5064     {
5065       SliderPanel.hidePIDSlider();
5066     }
5067
5068     /*
5069      * If there is a frame linked to this one in a SplitPane, switch it to the
5070      * same view tab index. No infinite recursion of calls should happen, since
5071      * tabSelectionChanged() should not get invoked on setting the selected
5072      * index to an unchanged value. Guard against setting an invalid index
5073      * before the new view peer tab has been created.
5074      */
5075     final AlignViewportI peer = viewport.getCodingComplement();
5076     if (peer != null)
5077     {
5078       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5079               .getAlignPanel().alignFrame;
5080       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5081       {
5082         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5083       }
5084     }
5085   }
5086
5087   /**
5088    * On right mouse click on view tab, prompt for and set new view name.
5089    */
5090   @Override
5091   public void tabbedPane_mousePressed(MouseEvent e)
5092   {
5093     if (e.isPopupTrigger())
5094     {
5095       String msg = MessageManager.getString("label.enter_view_name");
5096       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5097               JvOptionPane.QUESTION_MESSAGE);
5098
5099       if (reply != null)
5100       {
5101         viewport.setViewName(reply);
5102         // TODO warn if reply is in getExistingViewNames()?
5103         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5104       }
5105     }
5106   }
5107
5108   public AlignViewport getCurrentView()
5109   {
5110     return viewport;
5111   }
5112
5113   /**
5114    * Open the dialog for regex description parsing.
5115    */
5116   @Override
5117   protected void extractScores_actionPerformed(ActionEvent e)
5118   {
5119     ParseProperties pp = new jalview.analysis.ParseProperties(
5120             viewport.getAlignment());
5121     // TODO: verify regex and introduce GUI dialog for version 2.5
5122     // if (pp.getScoresFromDescription("col", "score column ",
5123     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5124     // true)>0)
5125     if (pp.getScoresFromDescription("description column",
5126             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5127     {
5128       buildSortByAnnotationScoresMenu();
5129     }
5130   }
5131
5132   /*
5133    * (non-Javadoc)
5134    *
5135    * @see
5136    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5137    * )
5138    */
5139   @Override
5140   protected void showDbRefs_actionPerformed(ActionEvent e)
5141   {
5142     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5143   }
5144
5145   /*
5146    * (non-Javadoc)
5147    *
5148    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5149    * ActionEvent)
5150    */
5151   @Override
5152   protected void showNpFeats_actionPerformed(ActionEvent e)
5153   {
5154     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5155   }
5156
5157   /**
5158    * find the viewport amongst the tabs in this alignment frame and close that
5159    * tab
5160    *
5161    * @param av
5162    */
5163   public boolean closeView(AlignViewportI av)
5164   {
5165     if (viewport == av)
5166     {
5167       this.closeMenuItem_actionPerformed(false);
5168       return true;
5169     }
5170     Component[] comp = tabbedPane.getComponents();
5171     for (int i = 0; comp != null && i < comp.length; i++)
5172     {
5173       if (comp[i] instanceof AlignmentPanel)
5174       {
5175         if (((AlignmentPanel) comp[i]).av == av)
5176         {
5177           // close the view.
5178           closeView((AlignmentPanel) comp[i]);
5179           return true;
5180         }
5181       }
5182     }
5183     return false;
5184   }
5185
5186   protected void build_fetchdbmenu(JMenu webService)
5187   {
5188     // Temporary hack - DBRef Fetcher always top level ws entry.
5189     // TODO We probably want to store a sequence database checklist in
5190     // preferences and have checkboxes.. rather than individual sources selected
5191     // here
5192     final JMenu rfetch = new JMenu(
5193             MessageManager.getString("action.fetch_db_references"));
5194     rfetch.setToolTipText(MessageManager.getString(
5195             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5196     webService.add(rfetch);
5197
5198     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5199             MessageManager.getString("option.trim_retrieved_seqs"));
5200     trimrs.setToolTipText(
5201             MessageManager.getString("label.trim_retrieved_sequences"));
5202     trimrs.setSelected(
5203             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5204     trimrs.addActionListener(new ActionListener()
5205     {
5206       @Override
5207       public void actionPerformed(ActionEvent e)
5208       {
5209         trimrs.setSelected(trimrs.isSelected());
5210         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5211                 Boolean.valueOf(trimrs.isSelected()).toString());
5212       };
5213     });
5214     rfetch.add(trimrs);
5215     JMenuItem fetchr = new JMenuItem(
5216             MessageManager.getString("label.standard_databases"));
5217     fetchr.setToolTipText(
5218             MessageManager.getString("label.fetch_embl_uniprot"));
5219     fetchr.addActionListener(new ActionListener()
5220     {
5221
5222       @Override
5223       public void actionPerformed(ActionEvent e)
5224       {
5225         new Thread(new Runnable()
5226         {
5227           @Override
5228           public void run()
5229           {
5230             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5231                     .getAlignment().isNucleotide();
5232             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5233                     alignPanel.av.getSequenceSelection(),
5234                     alignPanel.alignFrame, null,
5235                     alignPanel.alignFrame.featureSettings, isNucleotide);
5236             dbRefFetcher.addListener(new FetchFinishedListenerI()
5237             {
5238               @Override
5239               public void finished()
5240               {
5241
5242                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5243                         .getFeatureSettingsModels())
5244                 {
5245
5246                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5247                 }
5248                 AlignFrame.this.setMenusForViewport();
5249               }
5250             });
5251             dbRefFetcher.fetchDBRefs(false);
5252           }
5253         }).start();
5254
5255       }
5256
5257     });
5258     rfetch.add(fetchr);
5259     final AlignFrame me = this;
5260     new Thread(new Runnable()
5261     {
5262       @Override
5263       public void run()
5264       {
5265         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5266                 .getSequenceFetcherSingleton(me);
5267         javax.swing.SwingUtilities.invokeLater(new Runnable()
5268         {
5269           @Override
5270           public void run()
5271           {
5272             String[] dbclasses = sf.getOrderedSupportedSources();
5273             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5274             // jalview.util.QuickSort.sort(otherdb, otherdb);
5275             List<DbSourceProxy> otherdb;
5276             JMenu dfetch = new JMenu();
5277             JMenu ifetch = new JMenu();
5278             JMenuItem fetchr = null;
5279             int comp = 0, icomp = 0, mcomp = 15;
5280             String mname = null;
5281             int dbi = 0;
5282             for (String dbclass : dbclasses)
5283             {
5284               otherdb = sf.getSourceProxy(dbclass);
5285               // add a single entry for this class, or submenu allowing 'fetch
5286               // all' or pick one
5287               if (otherdb == null || otherdb.size() < 1)
5288               {
5289                 continue;
5290               }
5291               // List<DbSourceProxy> dbs=otherdb;
5292               // otherdb=new ArrayList<DbSourceProxy>();
5293               // for (DbSourceProxy db:dbs)
5294               // {
5295               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5296               // }
5297               if (mname == null)
5298               {
5299                 mname = "From " + dbclass;
5300               }
5301               if (otherdb.size() == 1)
5302               {
5303                 final DbSourceProxy[] dassource = otherdb
5304                         .toArray(new DbSourceProxy[0]);
5305                 DbSourceProxy src = otherdb.get(0);
5306                 fetchr = new JMenuItem(src.getDbSource());
5307                 fetchr.addActionListener(new ActionListener()
5308                 {
5309
5310                   @Override
5311                   public void actionPerformed(ActionEvent e)
5312                   {
5313                     new Thread(new Runnable()
5314                     {
5315
5316                       @Override
5317                       public void run()
5318                       {
5319                         boolean isNucleotide = alignPanel.alignFrame
5320                                 .getViewport().getAlignment()
5321                                 .isNucleotide();
5322                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5323                                 alignPanel.av.getSequenceSelection(),
5324                                 alignPanel.alignFrame, dassource,
5325                                 alignPanel.alignFrame.featureSettings,
5326                                 isNucleotide);
5327                         dbRefFetcher
5328                                 .addListener(new FetchFinishedListenerI()
5329                                 {
5330                                   @Override
5331                                   public void finished()
5332                                   {
5333                                     FeatureSettingsModelI srcSettings = dassource[0]
5334                                             .getFeatureColourScheme();
5335                                     alignPanel.av.mergeFeaturesStyle(
5336                                             srcSettings);
5337                                     AlignFrame.this.setMenusForViewport();
5338                                   }
5339                                 });
5340                         dbRefFetcher.fetchDBRefs(false);
5341                       }
5342                     }).start();
5343                   }
5344
5345                 });
5346                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5347                         MessageManager.formatMessage(
5348                                 "label.fetch_retrieve_from", new Object[]
5349                                 { src.getDbName() })));
5350                 dfetch.add(fetchr);
5351                 comp++;
5352               }
5353               else
5354               {
5355                 final DbSourceProxy[] dassource = otherdb
5356                         .toArray(new DbSourceProxy[0]);
5357                 // fetch all entry
5358                 DbSourceProxy src = otherdb.get(0);
5359                 fetchr = new JMenuItem(MessageManager
5360                         .formatMessage("label.fetch_all_param", new Object[]
5361                         { src.getDbSource() }));
5362                 fetchr.addActionListener(new ActionListener()
5363                 {
5364                   @Override
5365                   public void actionPerformed(ActionEvent e)
5366                   {
5367                     new Thread(new Runnable()
5368                     {
5369
5370                       @Override
5371                       public void run()
5372                       {
5373                         boolean isNucleotide = alignPanel.alignFrame
5374                                 .getViewport().getAlignment()
5375                                 .isNucleotide();
5376                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5377                                 alignPanel.av.getSequenceSelection(),
5378                                 alignPanel.alignFrame, dassource,
5379                                 alignPanel.alignFrame.featureSettings,
5380                                 isNucleotide);
5381                         dbRefFetcher
5382                                 .addListener(new FetchFinishedListenerI()
5383                                 {
5384                                   @Override
5385                                   public void finished()
5386                                   {
5387                                     AlignFrame.this.setMenusForViewport();
5388                                   }
5389                                 });
5390                         dbRefFetcher.fetchDBRefs(false);
5391                       }
5392                     }).start();
5393                   }
5394                 });
5395
5396                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5397                         MessageManager.formatMessage(
5398                                 "label.fetch_retrieve_from_all_sources",
5399                                 new Object[]
5400                                 { Integer.valueOf(otherdb.size())
5401                                         .toString(),
5402                                     src.getDbSource(), src.getDbName() })));
5403                 dfetch.add(fetchr);
5404                 comp++;
5405                 // and then build the rest of the individual menus
5406                 ifetch = new JMenu(MessageManager.formatMessage(
5407                         "label.source_from_db_source", new Object[]
5408                         { src.getDbSource() }));
5409                 icomp = 0;
5410                 String imname = null;
5411                 int i = 0;
5412                 for (DbSourceProxy sproxy : otherdb)
5413                 {
5414                   String dbname = sproxy.getDbName();
5415                   String sname = dbname.length() > 5
5416                           ? dbname.substring(0, 5) + "..."
5417                           : dbname;
5418                   String msname = dbname.length() > 10
5419                           ? dbname.substring(0, 10) + "..."
5420                           : dbname;
5421                   if (imname == null)
5422                   {
5423                     imname = MessageManager
5424                             .formatMessage("label.from_msname", new Object[]
5425                             { sname });
5426                   }
5427                   fetchr = new JMenuItem(msname);
5428                   final DbSourceProxy[] dassrc = { sproxy };
5429                   fetchr.addActionListener(new ActionListener()
5430                   {
5431
5432                     @Override
5433                     public void actionPerformed(ActionEvent e)
5434                     {
5435                       new Thread(new Runnable()
5436                       {
5437
5438                         @Override
5439                         public void run()
5440                         {
5441                           boolean isNucleotide = alignPanel.alignFrame
5442                                   .getViewport().getAlignment()
5443                                   .isNucleotide();
5444                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5445                                   alignPanel.av.getSequenceSelection(),
5446                                   alignPanel.alignFrame, dassrc,
5447                                   alignPanel.alignFrame.featureSettings,
5448                                   isNucleotide);
5449                           dbRefFetcher
5450                                   .addListener(new FetchFinishedListenerI()
5451                                   {
5452                                     @Override
5453                                     public void finished()
5454                                     {
5455                                       AlignFrame.this.setMenusForViewport();
5456                                     }
5457                                   });
5458                           dbRefFetcher.fetchDBRefs(false);
5459                         }
5460                       }).start();
5461                     }
5462
5463                   });
5464                   fetchr.setToolTipText(
5465                           "<html>" + MessageManager.formatMessage(
5466                                   "label.fetch_retrieve_from", new Object[]
5467                                   { dbname }));
5468                   ifetch.add(fetchr);
5469                   ++i;
5470                   if (++icomp >= mcomp || i == (otherdb.size()))
5471                   {
5472                     ifetch.setText(MessageManager.formatMessage(
5473                             "label.source_to_target", imname, sname));
5474                     dfetch.add(ifetch);
5475                     ifetch = new JMenu();
5476                     imname = null;
5477                     icomp = 0;
5478                     comp++;
5479                   }
5480                 }
5481               }
5482               ++dbi;
5483               if (comp >= mcomp || dbi >= (dbclasses.length))
5484               {
5485                 dfetch.setText(MessageManager.formatMessage(
5486                         "label.source_to_target", mname, dbclass));
5487                 rfetch.add(dfetch);
5488                 dfetch = new JMenu();
5489                 mname = null;
5490                 comp = 0;
5491               }
5492             }
5493           }
5494         });
5495       }
5496     }).start();
5497
5498   }
5499
5500   /**
5501    * Left justify the whole alignment.
5502    */
5503   @Override
5504   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5505   {
5506     AlignmentI al = viewport.getAlignment();
5507     al.justify(false);
5508     viewport.firePropertyChange("alignment", null, al);
5509   }
5510
5511   /**
5512    * Right justify the whole alignment.
5513    */
5514   @Override
5515   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5516   {
5517     AlignmentI al = viewport.getAlignment();
5518     al.justify(true);
5519     viewport.firePropertyChange("alignment", null, al);
5520   }
5521
5522   @Override
5523   public void setShowSeqFeatures(boolean b)
5524   {
5525     showSeqFeatures.setSelected(b);
5526     viewport.setShowSequenceFeatures(b);
5527   }
5528
5529   /*
5530    * (non-Javadoc)
5531    *
5532    * @see
5533    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5534    * awt.event.ActionEvent)
5535    */
5536   @Override
5537   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5538   {
5539     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5540     alignPanel.paintAlignment(false, false);
5541   }
5542
5543   /*
5544    * (non-Javadoc)
5545    *
5546    * @see
5547    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5548    * .ActionEvent)
5549    */
5550   @Override
5551   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5552   {
5553     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5554     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5555
5556   }
5557
5558   /*
5559    * (non-Javadoc)
5560    *
5561    * @see
5562    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5563    * .event.ActionEvent)
5564    */
5565   @Override
5566   protected void showGroupConservation_actionPerformed(ActionEvent e)
5567   {
5568     viewport.setShowGroupConservation(showGroupConservation.getState());
5569     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5570   }
5571
5572   /*
5573    * (non-Javadoc)
5574    *
5575    * @see
5576    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5577    * .event.ActionEvent)
5578    */
5579   @Override
5580   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5581   {
5582     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5583     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5584   }
5585
5586   /*
5587    * (non-Javadoc)
5588    *
5589    * @see
5590    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5591    * .event.ActionEvent)
5592    */
5593   @Override
5594   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5595   {
5596     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5597     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5598   }
5599
5600   @Override
5601   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5602   {
5603     showSequenceLogo.setState(true);
5604     viewport.setShowSequenceLogo(true);
5605     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5606     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5607   }
5608
5609   @Override
5610   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5611   {
5612     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5613   }
5614
5615   /*
5616    * (non-Javadoc)
5617    *
5618    * @see
5619    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5620    * .event.ActionEvent)
5621    */
5622   @Override
5623   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5624   {
5625     if (avc.makeGroupsFromSelection())
5626     {
5627       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5628       alignPanel.updateAnnotation();
5629       alignPanel.paintAlignment(true,
5630               viewport.needToUpdateStructureViews());
5631     }
5632   }
5633
5634   public void clearAlignmentSeqRep()
5635   {
5636     // TODO refactor alignmentseqrep to controller
5637     if (viewport.getAlignment().hasSeqrep())
5638     {
5639       viewport.getAlignment().setSeqrep(null);
5640       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5641       alignPanel.updateAnnotation();
5642       alignPanel.paintAlignment(true, true);
5643     }
5644   }
5645
5646   @Override
5647   protected void createGroup_actionPerformed(ActionEvent e)
5648   {
5649     if (avc.createGroup())
5650     {
5651       if (applyAutoAnnotationSettings.isSelected())
5652       {
5653         alignPanel.updateAnnotation(true, false);
5654       }
5655       alignPanel.alignmentChanged();
5656     }
5657   }
5658
5659   @Override
5660   protected void unGroup_actionPerformed(ActionEvent e)
5661   {
5662     if (avc.unGroup())
5663     {
5664       alignPanel.alignmentChanged();
5665     }
5666   }
5667
5668   /**
5669    * make the given alignmentPanel the currently selected tab
5670    *
5671    * @param alignmentPanel
5672    */
5673   public void setDisplayedView(AlignmentPanel alignmentPanel)
5674   {
5675     if (!viewport.getSequenceSetId()
5676             .equals(alignmentPanel.av.getSequenceSetId()))
5677     {
5678       throw new Error(MessageManager.getString(
5679               "error.implementation_error_cannot_show_view_alignment_frame"));
5680     }
5681     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5682             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5683     {
5684       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5685     }
5686   }
5687
5688   /**
5689    * Action on selection of menu options to Show or Hide annotations.
5690    *
5691    * @param visible
5692    * @param forSequences
5693    *          update sequence-related annotations
5694    * @param forAlignment
5695    *          update non-sequence-related annotations
5696    */
5697   @Override
5698   protected void setAnnotationsVisibility(boolean visible,
5699           boolean forSequences, boolean forAlignment)
5700   {
5701     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5702             .getAlignmentAnnotation();
5703     if (anns == null)
5704     {
5705       return;
5706     }
5707     for (AlignmentAnnotation aa : anns)
5708     {
5709       /*
5710        * don't display non-positional annotations on an alignment
5711        */
5712       if (aa.annotations == null)
5713       {
5714         continue;
5715       }
5716       boolean apply = (aa.sequenceRef == null && forAlignment)
5717               || (aa.sequenceRef != null && forSequences);
5718       if (apply)
5719       {
5720         aa.visible = visible;
5721       }
5722     }
5723     alignPanel.validateAnnotationDimensions(true);
5724     alignPanel.alignmentChanged();
5725   }
5726
5727   /**
5728    * Store selected annotation sort order for the view and repaint.
5729    */
5730   @Override
5731   protected void sortAnnotations_actionPerformed()
5732   {
5733     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5734     this.alignPanel.av
5735             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5736     alignPanel.paintAlignment(false, false);
5737   }
5738
5739   /**
5740    *
5741    * @return alignment panels in this alignment frame
5742    */
5743   public List<? extends AlignmentViewPanel> getAlignPanels()
5744   {
5745     // alignPanels is never null
5746     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5747     return alignPanels;
5748   }
5749
5750   /**
5751    * Open a new alignment window, with the cDNA associated with this (protein)
5752    * alignment, aligned as is the protein.
5753    */
5754   protected void viewAsCdna_actionPerformed()
5755   {
5756     // TODO no longer a menu action - refactor as required
5757     final AlignmentI alignment = getViewport().getAlignment();
5758     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5759     if (mappings == null)
5760     {
5761       return;
5762     }
5763     List<SequenceI> cdnaSeqs = new ArrayList<>();
5764     for (SequenceI aaSeq : alignment.getSequences())
5765     {
5766       for (AlignedCodonFrame acf : mappings)
5767       {
5768         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5769         if (dnaSeq != null)
5770         {
5771           /*
5772            * There is a cDNA mapping for this protein sequence - add to new
5773            * alignment. It will share the same dataset sequence as other mapped
5774            * cDNA (no new mappings need to be created).
5775            */
5776           final Sequence newSeq = new Sequence(dnaSeq);
5777           newSeq.setDatasetSequence(dnaSeq);
5778           cdnaSeqs.add(newSeq);
5779         }
5780       }
5781     }
5782     if (cdnaSeqs.size() == 0)
5783     {
5784       // show a warning dialog no mapped cDNA
5785       return;
5786     }
5787     AlignmentI cdna = new Alignment(
5788             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5789     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5790             AlignFrame.DEFAULT_HEIGHT);
5791     cdna.alignAs(alignment);
5792     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5793             + this.title;
5794     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5795             AlignFrame.DEFAULT_HEIGHT);
5796   }
5797
5798   /**
5799    * Set visibility of dna/protein complement view (available when shown in a
5800    * split frame).
5801    *
5802    * @param show
5803    */
5804   @Override
5805   protected void showComplement_actionPerformed(boolean show)
5806   {
5807     SplitContainerI sf = getSplitViewContainer();
5808     if (sf != null)
5809     {
5810       sf.setComplementVisible(this, show);
5811     }
5812   }
5813
5814   /**
5815    * Generate the reverse (optionally complemented) of the selected sequences,
5816    * and add them to the alignment
5817    */
5818   @Override
5819   protected void showReverse_actionPerformed(boolean complement)
5820   {
5821     AlignmentI al = null;
5822     try
5823     {
5824       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5825       al = dna.reverseCdna(complement);
5826       viewport.addAlignment(al, "");
5827       addHistoryItem(new EditCommand(
5828               MessageManager.getString("label.add_sequences"), Action.PASTE,
5829               al.getSequencesArray(), 0, al.getWidth(),
5830               viewport.getAlignment()));
5831     } catch (Exception ex)
5832     {
5833       System.err.println(ex.getMessage());
5834       return;
5835     }
5836   }
5837
5838   /**
5839    * Try to run a script in the Groovy console, having first ensured that this
5840    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5841    * be targeted at this alignment.
5842    */
5843   @Override
5844   protected void runGroovy_actionPerformed()
5845   {
5846     Jalview.setCurrentAlignFrame(this);
5847     groovy.ui.Console console = Desktop.getGroovyConsole();
5848     if (console != null)
5849     {
5850       try
5851       {
5852         console.runScript();
5853       } catch (Exception ex)
5854       {
5855         System.err.println((ex.toString()));
5856         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5857                 MessageManager.getString("label.couldnt_run_groovy_script"),
5858                 MessageManager.getString("label.groovy_support_failed"),
5859                 JvOptionPane.ERROR_MESSAGE);
5860       }
5861     }
5862     else
5863     {
5864       System.err.println("Can't run Groovy script as console not found");
5865     }
5866   }
5867
5868   /**
5869    * Hides columns containing (or not containing) a specified feature, provided
5870    * that would not leave all columns hidden
5871    *
5872    * @param featureType
5873    * @param columnsContaining
5874    * @return
5875    */
5876   public boolean hideFeatureColumns(String featureType,
5877           boolean columnsContaining)
5878   {
5879     boolean notForHiding = avc.markColumnsContainingFeatures(
5880             columnsContaining, false, false, featureType);
5881     if (notForHiding)
5882     {
5883       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5884               false, featureType))
5885       {
5886         getViewport().hideSelectedColumns();
5887         return true;
5888       }
5889     }
5890     return false;
5891   }
5892
5893   @Override
5894   protected void selectHighlightedColumns_actionPerformed(
5895           ActionEvent actionEvent)
5896   {
5897     // include key modifier check in case user selects from menu
5898     avc.markHighlightedColumns(
5899             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5900             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5901                     | ActionEvent.CTRL_MASK)) != 0);
5902   }
5903
5904   /**
5905    * Rebuilds the Colour menu, including any user-defined colours which have
5906    * been loaded either on startup or during the session
5907    */
5908   public void buildColourMenu()
5909   {
5910     colourMenu.removeAll();
5911
5912     colourMenu.add(applyToAllGroups);
5913     colourMenu.add(textColour);
5914     colourMenu.addSeparator();
5915
5916     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5917             viewport.getAlignment(), false);
5918
5919     colourMenu.add(annotationColour);
5920     bg.add(annotationColour);
5921     colourMenu.addSeparator();
5922     colourMenu.add(conservationMenuItem);
5923     colourMenu.add(modifyConservation);
5924     colourMenu.add(abovePIDThreshold);
5925     colourMenu.add(modifyPID);
5926
5927     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5928     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5929   }
5930
5931   /**
5932    * Open a dialog (if not already open) that allows the user to select and
5933    * calculate PCA or Tree analysis
5934    */
5935   protected void openTreePcaDialog()
5936   {
5937     if (alignPanel.getCalculationDialog() == null)
5938     {
5939       new CalculationChooser(AlignFrame.this);
5940     }
5941   }
5942
5943   /**
5944    * Sets the status of the HMMER menu
5945    */
5946   public void updateHMMERStatus()
5947   {
5948     hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5949   }
5950
5951   @Override
5952   protected void loadVcf_actionPerformed()
5953   {
5954     JalviewFileChooser chooser = new JalviewFileChooser(
5955             Cache.getProperty("LAST_DIRECTORY"));
5956     chooser.setFileView(new JalviewFileView());
5957     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5958     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5959
5960     int value = chooser.showOpenDialog(null);
5961
5962     if (value == JalviewFileChooser.APPROVE_OPTION)
5963     {
5964       String choice = chooser.getSelectedFile().getPath();
5965       Cache.setProperty("LAST_DIRECTORY", choice);
5966       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5967       new VCFLoader(choice).loadVCF(seqs, this);
5968     }
5969
5970   }
5971 }
5972
5973 class PrintThread extends Thread
5974 {
5975   AlignmentPanel ap;
5976
5977   public PrintThread(AlignmentPanel ap)
5978   {
5979     this.ap = ap;
5980   }
5981
5982   static PageFormat pf;
5983
5984   @Override
5985   public void run()
5986   {
5987     PrinterJob printJob = PrinterJob.getPrinterJob();
5988
5989     if (pf != null)
5990     {
5991       printJob.setPrintable(ap, pf);
5992     }
5993     else
5994     {
5995       printJob.setPrintable(ap);
5996     }
5997
5998     if (printJob.printDialog())
5999     {
6000       try
6001       {
6002         printJob.print();
6003       } catch (Exception PrintException)
6004       {
6005         PrintException.printStackTrace();
6006       }
6007     }
6008   }
6009 }