src/jalview/gui/AlignFrame.java

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