src/jalview/gui/AlignFrame.java

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