src/jalview/gui/AlignFrame.java

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