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