src/jalview/gui/AlignFrame.java

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