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