src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.FeatureSettingsModelI;
  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.DBRefSource;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  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.FileLoader;
  69 import jalview.io.FormatAdapter;
  70 import jalview.io.HtmlSvgOutput;
  71 import jalview.io.IdentifyFile;
  72 import jalview.io.JalviewFileChooser;
  73 import jalview.io.JalviewFileView;
  74 import jalview.io.JnetAnnotationMaker;
  75 import jalview.io.NewickFile;
  76 import jalview.io.TCoffeeScoreFile;
  77 import jalview.jbgui.GAlignFrame;
  78 import jalview.schemes.Blosum62ColourScheme;
  79 import jalview.schemes.BuriedColourScheme;
  80 import jalview.schemes.ClustalxColourScheme;
  81 import jalview.schemes.ColourSchemeI;
  82 import jalview.schemes.ColourSchemeProperty;
  83 import jalview.schemes.HelixColourScheme;
  84 import jalview.schemes.HydrophobicColourScheme;
  85 import jalview.schemes.NucleotideColourScheme;
  86 import jalview.schemes.PIDColourScheme;
  87 import jalview.schemes.PurinePyrimidineColourScheme;
  88 import jalview.schemes.RNAHelicesColourChooser;
  89 import jalview.schemes.ResidueProperties;
  90 import jalview.schemes.StrandColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.schemes.TaylorColourScheme;
  93 import jalview.schemes.TurnColourScheme;
  94 import jalview.schemes.UserColourScheme;
  95 import jalview.schemes.ZappoColourScheme;
  96 import jalview.structure.StructureSelectionManager;
  97 import jalview.util.MessageManager;
  98 import jalview.viewmodel.AlignmentViewport;
  99 import jalview.ws.DBRefFetcher;
 100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 101 import jalview.ws.SequenceFetcher;
 102 import jalview.ws.jws1.Discoverer;
 103 import jalview.ws.jws2.Jws2Discoverer;
 104 import jalview.ws.jws2.jabaws2.Jws2Instance;
 105 import jalview.ws.seqfetcher.DbSourceProxy;
 106
 107 import java.awt.BorderLayout;
 108 import java.awt.Component;
 109 import java.awt.Rectangle;
 110 import java.awt.Toolkit;
 111 import java.awt.datatransfer.Clipboard;
 112 import java.awt.datatransfer.DataFlavor;
 113 import java.awt.datatransfer.StringSelection;
 114 import java.awt.datatransfer.Transferable;
 115 import java.awt.dnd.DnDConstants;
 116 import java.awt.dnd.DropTargetDragEvent;
 117 import java.awt.dnd.DropTargetDropEvent;
 118 import java.awt.dnd.DropTargetEvent;
 119 import java.awt.dnd.DropTargetListener;
 120 import java.awt.event.ActionEvent;
 121 import java.awt.event.ActionListener;
 122 import java.awt.event.FocusAdapter;
 123 import java.awt.event.FocusEvent;
 124 import java.awt.event.ItemEvent;
 125 import java.awt.event.ItemListener;
 126 import java.awt.event.KeyAdapter;
 127 import java.awt.event.KeyEvent;
 128 import java.awt.event.MouseAdapter;
 129 import java.awt.event.MouseEvent;
 130 import java.awt.print.PageFormat;
 131 import java.awt.print.PrinterJob;
 132 import java.beans.PropertyChangeEvent;
 133 import java.io.File;
 134 import java.lang.reflect.Method;
 135 import java.net.URL;
 136 import java.util.ArrayList;
 137 import java.util.Arrays;
 138 import java.util.Deque;
 139 import java.util.Enumeration;
 140 import java.util.Hashtable;
 141 import java.util.List;
 142 import java.util.Vector;
 143
 144 import javax.swing.JCheckBoxMenuItem;
 145 import javax.swing.JEditorPane;
 146 import javax.swing.JInternalFrame;
 147 import javax.swing.JLayeredPane;
 148 import javax.swing.JMenu;
 149 import javax.swing.JMenuItem;
 150 import javax.swing.JOptionPane;
 151 import javax.swing.JRadioButtonMenuItem;
 152 import javax.swing.JScrollPane;
 153 import javax.swing.SwingUtilities;
 154
 155 /**
 156  * DOCUMENT ME!
 157  *
 158  * @author $author$
 159  * @version $Revision$
 160  */
 161 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 162         IProgressIndicator, AlignViewControllerGuiI
 163 {
 164
 165   public static final int DEFAULT_WIDTH = 700;
 166
 167   public static final int DEFAULT_HEIGHT = 500;
 168
 169   /*
 170    * The currently displayed panel (selected tabbed view if more than one)
 171    */
 172   public AlignmentPanel alignPanel;
 173
 174   AlignViewport viewport;
 175
 176   public AlignViewControllerI avc;
 177
 178   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 179
 180   /**
 181    * Last format used to load or save alignments in this window
 182    */
 183   String currentFileFormat = null;
 184
 185   /**
 186    * Current filename for this alignment
 187    */
 188   String fileName = null;
 189
 190   /**
 191    * Creates a new AlignFrame object with specific width and height.
 192    *
 193    * @param al
 194    * @param width
 195    * @param height
 196    */
 197   public AlignFrame(AlignmentI al, int width, int height)
 198   {
 199     this(al, null, width, height);
 200   }
 201
 202   /**
 203    * Creates a new AlignFrame object with specific width, height and
 204    * sequenceSetId
 205    *
 206    * @param al
 207    * @param width
 208    * @param height
 209    * @param sequenceSetId
 210    */
 211   public AlignFrame(AlignmentI al, int width, int height,
 212           String sequenceSetId)
 213   {
 214     this(al, null, width, height, sequenceSetId);
 215   }
 216
 217   /**
 218    * Creates a new AlignFrame object with specific width, height and
 219    * sequenceSetId
 220    *
 221    * @param al
 222    * @param width
 223    * @param height
 224    * @param sequenceSetId
 225    * @param viewId
 226    */
 227   public AlignFrame(AlignmentI al, int width, int height,
 228           String sequenceSetId, String viewId)
 229   {
 230     this(al, null, width, height, sequenceSetId, viewId);
 231   }
 232
 233   /**
 234    * new alignment window with hidden columns
 235    *
 236    * @param al
 237    *          AlignmentI
 238    * @param hiddenColumns
 239    *          ColumnSelection or null
 240    * @param width
 241    *          Width of alignment frame
 242    * @param height
 243    *          height of frame.
 244    */
 245   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 246           int width, int height)
 247   {
 248     this(al, hiddenColumns, width, height, null);
 249   }
 250
 251   /**
 252    * Create alignment frame for al with hiddenColumns, a specific width and
 253    * height, and specific sequenceId
 254    *
 255    * @param al
 256    * @param hiddenColumns
 257    * @param width
 258    * @param height
 259    * @param sequenceSetId
 260    *          (may be null)
 261    */
 262   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 263           int width, int height, String sequenceSetId)
 264   {
 265     this(al, hiddenColumns, width, height, sequenceSetId, null);
 266   }
 267
 268   /**
 269    * Create alignment frame for al with hiddenColumns, a specific width and
 270    * height, and specific sequenceId
 271    *
 272    * @param al
 273    * @param hiddenColumns
 274    * @param width
 275    * @param height
 276    * @param sequenceSetId
 277    *          (may be null)
 278    * @param viewId
 279    *          (may be null)
 280    */
 281   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 282           int width, int height, String sequenceSetId, String viewId)
 283   {
 284     setSize(width, height);
 285
 286     if (al.getDataset() == null)
 287     {
 288       al.setDataset(null);
 289     }
 290
 291     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 292
 293     alignPanel = new AlignmentPanel(this, viewport);
 294
 295     addAlignmentPanel(alignPanel, true);
 296     init();
 297   }
 298
 299   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 300           ColumnSelection hiddenColumns, int width, int height)
 301   {
 302     setSize(width, height);
 303
 304     if (al.getDataset() == null)
 305     {
 306       al.setDataset(null);
 307     }
 308
 309     viewport = new AlignViewport(al, hiddenColumns);
 310
 311     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 312     {
 313       viewport.hideSequence(hiddenSeqs);
 314     }
 315     alignPanel = new AlignmentPanel(this, viewport);
 316     addAlignmentPanel(alignPanel, true);
 317     init();
 318   }
 319
 320   /**
 321    * Make a new AlignFrame from existing alignmentPanels
 322    *
 323    * @param ap
 324    *          AlignmentPanel
 325    * @param av
 326    *          AlignViewport
 327    */
 328   public AlignFrame(AlignmentPanel ap)
 329   {
 330     viewport = ap.av;
 331     alignPanel = ap;
 332     addAlignmentPanel(ap, false);
 333     init();
 334   }
 335
 336   /**
 337    * initalise the alignframe from the underlying viewport data and the
 338    * configurations
 339    */
 340   void init()
 341   {
 342     if (!Jalview.isHeadlessMode())
 343     {
 344       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 345     }
 346
 347     avc = new jalview.controller.AlignViewController(this, viewport,
 348             alignPanel);
 349     if (viewport.getAlignmentConservationAnnotation() == null)
 350     {
 351       BLOSUM62Colour.setEnabled(false);
 352       conservationMenuItem.setEnabled(false);
 353       modifyConservation.setEnabled(false);
 354       // PIDColour.setEnabled(false);
 355       // abovePIDThreshold.setEnabled(false);
 356       // modifyPID.setEnabled(false);
 357     }
 358
 359     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 360             "No sort");
 361
 362     if (sortby.equals("Id"))
 363     {
 364       sortIDMenuItem_actionPerformed(null);
 365     }
 366     else if (sortby.equals("Pairwise Identity"))
 367     {
 368       sortPairwiseMenuItem_actionPerformed(null);
 369     }
 370
 371     if (Desktop.desktop != null)
 372     {
 373       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 374       addServiceListeners();
 375       setGUINucleotide(viewport.getAlignment().isNucleotide());
 376     }
 377
 378     this.alignPanel.av
 379             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 380
 381     setMenusFromViewport(viewport);
 382     buildSortByAnnotationScoresMenu();
 383     buildTreeMenu();
 384
 385     if (viewport.getWrapAlignment())
 386     {
 387       wrapMenuItem_actionPerformed(null);
 388     }
 389
 390     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 391     {
 392       this.overviewMenuItem_actionPerformed(null);
 393     }
 394
 395     addKeyListener();
 396
 397     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 398     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 399     final String menuLabel = MessageManager
 400             .getString("label.copy_format_from");
 401     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 402             new ViewSetProvider()
 403             {
 404
 405               @Override
 406               public AlignmentPanel[] getAllAlignmentPanels()
 407               {
 408                 origview.clear();
 409                 origview.add(alignPanel);
 410                 // make an array of all alignment panels except for this one
 411                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 412                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 413                 aps.remove(AlignFrame.this.alignPanel);
 414                 return aps.toArray(new AlignmentPanel[aps.size()]);
 415               }
 416             }, selviews, new ItemListener()
 417             {
 418
 419               @Override
 420               public void itemStateChanged(ItemEvent e)
 421               {
 422                 if (origview.size() > 0)
 423                 {
 424                   final AlignmentPanel ap = origview.get(0);
 425
 426                   /*
 427                    * Copy the ViewStyle of the selected panel to 'this one'.
 428                    * Don't change value of 'scaleProteinAsCdna' unless copying
 429                    * from a SplitFrame.
 430                    */
 431                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 432                           .getViewStyle();
 433                   boolean fromSplitFrame = selviews.get(0)
 434                           .getAlignViewport().getCodingComplement() != null;
 435                   if (!fromSplitFrame)
 436                   {
 437                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 438                             .getViewStyle().isScaleProteinAsCdna());
 439                   }
 440                   ap.getAlignViewport().setViewStyle(vs);
 441
 442                   /*
 443                    * Also rescale ViewStyle of SplitFrame complement if there is
 444                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 445                    * the whole ViewStyle (allow cDNA protein to have different
 446                    * fonts)
 447                    */
 448                   AlignViewportI complement = ap.getAlignViewport()
 449                           .getCodingComplement();
 450                   if (complement != null && vs.isScaleProteinAsCdna())
 451                   {
 452                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 453                     ((SplitFrame) af.getSplitViewContainer())
 454                             .adjustLayout();
 455                     af.setMenusForViewport();
 456                   }
 457
 458                   ap.updateLayout();
 459                   ap.setSelected(true);
 460                   ap.alignFrame.setMenusForViewport();
 461
 462                 }
 463               }
 464             });
 465     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 466             .indexOf("devel") > -1
 467             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 468                     .indexOf("test") > -1)
 469     {
 470       formatMenu.add(vsel);
 471     }
 472     addFocusListener(new FocusAdapter()
 473     {
 474       @Override
 475       public void focusGained(FocusEvent e)
 476       {
 477         Desktop.setCurrentAlignFrame(AlignFrame.this);
 478       }
 479     });
 480
 481   }
 482
 483   /**
 484    * Change the filename and format for the alignment, and enable the 'reload'
 485    * button functionality.
 486    *
 487    * @param file
 488    *          valid filename
 489    * @param format
 490    *          format of file
 491    */
 492   public void setFileName(String file, String format)
 493   {
 494     fileName = file;
 495     setFileFormat(format);
 496     reload.setEnabled(true);
 497   }
 498
 499   /**
 500    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 501    * events
 502    */
 503   void addKeyListener()
 504   {
 505     addKeyListener(new KeyAdapter()
 506     {
 507       @Override
 508       public void keyPressed(KeyEvent evt)
 509       {
 510         if (viewport.cursorMode
 511                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 512                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 513                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 514                 && Character.isDigit(evt.getKeyChar()))
 515         {
 516           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 517         }
 518
 519         switch (evt.getKeyCode())
 520         {
 521
 522         case 27: // escape key
 523           deselectAllSequenceMenuItem_actionPerformed(null);
 524
 525           break;
 526
 527         case KeyEvent.VK_DOWN:
 528           if (evt.isAltDown() || !viewport.cursorMode)
 529           {
 530             moveSelectedSequences(false);
 531           }
 532           if (viewport.cursorMode)
 533           {
 534             alignPanel.getSeqPanel().moveCursor(0, 1);
 535           }
 536           break;
 537
 538         case KeyEvent.VK_UP:
 539           if (evt.isAltDown() || !viewport.cursorMode)
 540           {
 541             moveSelectedSequences(true);
 542           }
 543           if (viewport.cursorMode)
 544           {
 545             alignPanel.getSeqPanel().moveCursor(0, -1);
 546           }
 547
 548           break;
 549
 550         case KeyEvent.VK_LEFT:
 551           if (evt.isAltDown() || !viewport.cursorMode)
 552           {
 553             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 554           }
 555           else
 556           {
 557             alignPanel.getSeqPanel().moveCursor(-1, 0);
 558           }
 559
 560           break;
 561
 562         case KeyEvent.VK_RIGHT:
 563           if (evt.isAltDown() || !viewport.cursorMode)
 564           {
 565             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 566           }
 567           else
 568           {
 569             alignPanel.getSeqPanel().moveCursor(1, 0);
 570           }
 571           break;
 572
 573         case KeyEvent.VK_SPACE:
 574           if (viewport.cursorMode)
 575           {
 576             alignPanel.getSeqPanel().insertGapAtCursor(
 577                     evt.isControlDown() || evt.isShiftDown()
 578                             || evt.isAltDown());
 579           }
 580           break;
 581
 582         // case KeyEvent.VK_A:
 583         // if (viewport.cursorMode)
 584         // {
 585         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 586         // //System.out.println("A");
 587         // }
 588         // break;
 589         /*
 590          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 591          * System.out.println("closing bracket"); } break;
 592          */
 593         case KeyEvent.VK_DELETE:
 594         case KeyEvent.VK_BACK_SPACE:
 595           if (!viewport.cursorMode)
 596           {
 597             cut_actionPerformed(null);
 598           }
 599           else
 600           {
 601             alignPanel.getSeqPanel().deleteGapAtCursor(
 602                     evt.isControlDown() || evt.isShiftDown()
 603                             || evt.isAltDown());
 604           }
 605
 606           break;
 607
 608         case KeyEvent.VK_S:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().setCursorRow();
 612           }
 613           break;
 614         case KeyEvent.VK_C:
 615           if (viewport.cursorMode && !evt.isControlDown())
 616           {
 617             alignPanel.getSeqPanel().setCursorColumn();
 618           }
 619           break;
 620         case KeyEvent.VK_P:
 621           if (viewport.cursorMode)
 622           {
 623             alignPanel.getSeqPanel().setCursorPosition();
 624           }
 625           break;
 626
 627         case KeyEvent.VK_ENTER:
 628         case KeyEvent.VK_COMMA:
 629           if (viewport.cursorMode)
 630           {
 631             alignPanel.getSeqPanel().setCursorRowAndColumn();
 632           }
 633           break;
 634
 635         case KeyEvent.VK_Q:
 636           if (viewport.cursorMode)
 637           {
 638             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 639           }
 640           break;
 641         case KeyEvent.VK_M:
 642           if (viewport.cursorMode)
 643           {
 644             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 645           }
 646           break;
 647
 648         case KeyEvent.VK_F2:
 649           viewport.cursorMode = !viewport.cursorMode;
 650           statusBar.setText(MessageManager.formatMessage(
 651                   "label.keyboard_editing_mode",
 652                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 653           if (viewport.cursorMode)
 654           {
 655             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 656             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 657           }
 658           alignPanel.getSeqPanel().seqCanvas.repaint();
 659           break;
 660
 661         case KeyEvent.VK_F1:
 662           try
 663           {
 664             Help.showHelpWindow();
 665           } catch (Exception ex)
 666           {
 667             ex.printStackTrace();
 668           }
 669           break;
 670         case KeyEvent.VK_H:
 671         {
 672           boolean toggleSeqs = !evt.isControlDown();
 673           boolean toggleCols = !evt.isShiftDown();
 674           toggleHiddenRegions(toggleSeqs, toggleCols);
 675           break;
 676         }
 677         case KeyEvent.VK_PAGE_UP:
 678           if (viewport.getWrapAlignment())
 679           {
 680             alignPanel.scrollUp(true);
 681           }
 682           else
 683           {
 684             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 685                     - viewport.endSeq + viewport.startSeq);
 686           }
 687           break;
 688         case KeyEvent.VK_PAGE_DOWN:
 689           if (viewport.getWrapAlignment())
 690           {
 691             alignPanel.scrollUp(false);
 692           }
 693           else
 694           {
 695             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 696                     + viewport.endSeq - viewport.startSeq);
 697           }
 698           break;
 699         }
 700       }
 701
 702       @Override
 703       public void keyReleased(KeyEvent evt)
 704       {
 705         switch (evt.getKeyCode())
 706         {
 707         case KeyEvent.VK_LEFT:
 708           if (evt.isAltDown() || !viewport.cursorMode)
 709           {
 710             viewport.firePropertyChange("alignment", null, viewport
 711                     .getAlignment().getSequences());
 712           }
 713           break;
 714
 715         case KeyEvent.VK_RIGHT:
 716           if (evt.isAltDown() || !viewport.cursorMode)
 717           {
 718             viewport.firePropertyChange("alignment", null, viewport
 719                     .getAlignment().getSequences());
 720           }
 721           break;
 722         }
 723       }
 724     });
 725   }
 726
 727   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 728   {
 729     ap.alignFrame = this;
 730     avc = new jalview.controller.AlignViewController(this, viewport,
 731             alignPanel);
 732
 733     alignPanels.add(ap);
 734
 735     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 736
 737     int aSize = alignPanels.size();
 738
 739     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 740
 741     if (aSize == 1 && ap.av.viewName == null)
 742     {
 743       this.getContentPane().add(ap, BorderLayout.CENTER);
 744     }
 745     else
 746     {
 747       if (aSize == 2)
 748       {
 749         setInitialTabVisible();
 750       }
 751
 752       expandViews.setEnabled(true);
 753       gatherViews.setEnabled(true);
 754       tabbedPane.addTab(ap.av.viewName, ap);
 755
 756       ap.setVisible(false);
 757     }
 758
 759     if (newPanel)
 760     {
 761       if (ap.av.isPadGaps())
 762       {
 763         ap.av.getAlignment().padGaps();
 764       }
 765       ap.av.updateConservation(ap);
 766       ap.av.updateConsensus(ap);
 767       ap.av.updateStrucConsensus(ap);
 768     }
 769   }
 770
 771   public void setInitialTabVisible()
 772   {
 773     expandViews.setEnabled(true);
 774     gatherViews.setEnabled(true);
 775     tabbedPane.setVisible(true);
 776     AlignmentPanel first = alignPanels.get(0);
 777     tabbedPane.addTab(first.av.viewName, first);
 778     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 779   }
 780
 781   public AlignViewport getViewport()
 782   {
 783     return viewport;
 784   }
 785
 786   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 787   private void addServiceListeners()
 788   {
 789     final java.beans.PropertyChangeListener thisListener;
 790     Desktop.instance.addJalviewPropertyChangeListener("services",
 791             thisListener = new java.beans.PropertyChangeListener()
 792             {
 793               @Override
 794               public void propertyChange(PropertyChangeEvent evt)
 795               {
 796                 // // System.out.println("Discoverer property change.");
 797                 // if (evt.getPropertyName().equals("services"))
 798                 {
 799                   SwingUtilities.invokeLater(new Runnable()
 800                   {
 801
 802                     @Override
 803                     public void run()
 804                     {
 805                       System.err
 806                               .println("Rebuild WS Menu for service change");
 807                       BuildWebServiceMenu();
 808                     }
 809
 810                   });
 811                 }
 812               }
 813             });
 814     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 815     {
 816       @Override
 817       public void internalFrameClosed(
 818               javax.swing.event.InternalFrameEvent evt)
 819       {
 820         // System.out.println("deregistering discoverer listener");
 821         Desktop.instance.removeJalviewPropertyChangeListener("services",
 822                 thisListener);
 823         closeMenuItem_actionPerformed(true);
 824       };
 825     });
 826     // Finally, build the menu once to get current service state
 827     new Thread(new Runnable()
 828     {
 829       @Override
 830       public void run()
 831       {
 832         BuildWebServiceMenu();
 833       }
 834     }).start();
 835   }
 836
 837   /**
 838    * Configure menu items that vary according to whether the alignment is
 839    * nucleotide or protein
 840    *
 841    * @param nucleotide
 842    */
 843   public void setGUINucleotide(boolean nucleotide)
 844   {
 845     showTranslation.setVisible(nucleotide);
 846     showReverse.setVisible(nucleotide);
 847     showReverseComplement.setVisible(nucleotide);
 848     conservationMenuItem.setEnabled(!nucleotide);
 849     modifyConservation.setEnabled(!nucleotide);
 850     showGroupConservation.setEnabled(!nucleotide);
 851     rnahelicesColour.setEnabled(nucleotide);
 852     purinePyrimidineColour.setEnabled(nucleotide);
 853     showComplementMenuItem.setText(MessageManager
 854             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 855     setColourSelected(jalview.bin.Cache.getDefault(
 856             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 857                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 858   }
 859
 860   /**
 861    * set up menus for the current viewport. This may be called after any
 862    * operation that affects the data in the current view (selection changed,
 863    * etc) to update the menus to reflect the new state.
 864    */
 865   @Override
 866   public void setMenusForViewport()
 867   {
 868     setMenusFromViewport(viewport);
 869   }
 870
 871   /**
 872    * Need to call this method when tabs are selected for multiple views, or when
 873    * loading from Jalview2XML.java
 874    *
 875    * @param av
 876    *          AlignViewport
 877    */
 878   void setMenusFromViewport(AlignViewport av)
 879   {
 880     padGapsMenuitem.setSelected(av.isPadGaps());
 881     colourTextMenuItem.setSelected(av.isShowColourText());
 882     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 883     conservationMenuItem.setSelected(av.getConservationSelected());
 884     seqLimits.setSelected(av.getShowJVSuffix());
 885     idRightAlign.setSelected(av.isRightAlignIds());
 886     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 887     renderGapsMenuItem.setSelected(av.isRenderGaps());
 888     wrapMenuItem.setSelected(av.getWrapAlignment());
 889     scaleAbove.setVisible(av.getWrapAlignment());
 890     scaleLeft.setVisible(av.getWrapAlignment());
 891     scaleRight.setVisible(av.getWrapAlignment());
 892     annotationPanelMenuItem.setState(av.isShowAnnotation());
 893     /*
 894      * Show/hide annotations only enabled if annotation panel is shown
 895      */
 896     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 901     viewTextMenuItem.setSelected(av.getShowText());
 902     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 903     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 904     showGroupConservation.setSelected(av.isShowGroupConservation());
 905     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 906     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 907     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 908
 909     setColourSelected(ColourSchemeProperty.getColourName(av
 910             .getGlobalColourScheme()));
 911
 912     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 913     hiddenMarkers.setState(av.getShowHiddenMarkers());
 914     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 915     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 916     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 917     autoCalculate.setSelected(av.autoCalculateConsensus);
 918     sortByTree.setSelected(av.sortByTree);
 919     listenToViewSelections.setSelected(av.followSelection);
 920     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 921     rnahelicesColour
 922             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 923
 924     showProducts.setEnabled(canShowProducts());
 925     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 926
 927     updateEditMenuBar();
 928   }
 929
 930   /**
 931    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 932    *
 933    * @param b
 934    */
 935   public void setGroovyEnabled(boolean b)
 936   {
 937     runGroovy.setEnabled(b);
 938   }
 939
 940   private IProgressIndicator progressBar;
 941
 942   /*
 943    * (non-Javadoc)
 944    *
 945    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 946    */
 947   @Override
 948   public void setProgressBar(String message, long id)
 949   {
 950     progressBar.setProgressBar(message, id);
 951   }
 952
 953   @Override
 954   public void registerHandler(final long id,
 955           final IProgressIndicatorHandler handler)
 956   {
 957     progressBar.registerHandler(id, handler);
 958   }
 959
 960   /**
 961    *
 962    * @return true if any progress bars are still active
 963    */
 964   @Override
 965   public boolean operationInProgress()
 966   {
 967     return progressBar.operationInProgress();
 968   }
 969
 970   @Override
 971   public void setStatus(String text)
 972   {
 973     statusBar.setText(text);
 974   }
 975
 976   /*
 977    * Added so Castor Mapping file can obtain Jalview Version
 978    */
 979   public String getVersion()
 980   {
 981     return jalview.bin.Cache.getProperty("VERSION");
 982   }
 983
 984   public FeatureRenderer getFeatureRenderer()
 985   {
 986     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 987   }
 988
 989   @Override
 990   public void fetchSequence_actionPerformed(ActionEvent e)
 991   {
 992     new jalview.gui.SequenceFetcher(this);
 993   }
 994
 995   @Override
 996   public void addFromFile_actionPerformed(ActionEvent e)
 997   {
 998     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 999   }
1000
1001   @Override
1002   public void reload_actionPerformed(ActionEvent e)
1003   {
1004     if (fileName != null)
1005     {
1006       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1007       // originating file's format
1008       // TODO: work out how to recover feature settings for correct view(s) when
1009       // file is reloaded.
1010       if (currentFileFormat.equals("Jalview"))
1011       {
1012         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1013         for (int i = 0; i < frames.length; i++)
1014         {
1015           if (frames[i] instanceof AlignFrame && frames[i] != this
1016                   && ((AlignFrame) frames[i]).fileName != null
1017                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1018           {
1019             try
1020             {
1021               frames[i].setSelected(true);
1022               Desktop.instance.closeAssociatedWindows();
1023             } catch (java.beans.PropertyVetoException ex)
1024             {
1025             }
1026           }
1027
1028         }
1029         Desktop.instance.closeAssociatedWindows();
1030
1031         FileLoader loader = new FileLoader();
1032         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1033         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1034       }
1035       else
1036       {
1037         Rectangle bounds = this.getBounds();
1038
1039         FileLoader loader = new FileLoader();
1040         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1041         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042                 protocol, currentFileFormat);
1043
1044         newframe.setBounds(bounds);
1045         if (featureSettings != null && featureSettings.isShowing())
1046         {
1047           final Rectangle fspos = featureSettings.frame.getBounds();
1048           // TODO: need a 'show feature settings' function that takes bounds -
1049           // need to refactor Desktop.addFrame
1050           newframe.featureSettings_actionPerformed(null);
1051           final FeatureSettings nfs = newframe.featureSettings;
1052           SwingUtilities.invokeLater(new Runnable()
1053           {
1054             @Override
1055             public void run()
1056             {
1057               nfs.frame.setBounds(fspos);
1058             }
1059           });
1060           this.featureSettings.close();
1061           this.featureSettings = null;
1062         }
1063         this.closeMenuItem_actionPerformed(true);
1064       }
1065     }
1066   }
1067
1068   @Override
1069   public void addFromText_actionPerformed(ActionEvent e)
1070   {
1071     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1072             .getAlignPanel());
1073   }
1074
1075   @Override
1076   public void addFromURL_actionPerformed(ActionEvent e)
1077   {
1078     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1079   }
1080
1081   @Override
1082   public void save_actionPerformed(ActionEvent e)
1083   {
1084     if (fileName == null
1085             || (currentFileFormat == null || !jalview.io.FormatAdapter
1086                     .isValidIOFormat(currentFileFormat, true))
1087             || fileName.startsWith("http"))
1088     {
1089       saveAs_actionPerformed(null);
1090     }
1091     else
1092     {
1093       saveAlignment(fileName, currentFileFormat);
1094     }
1095   }
1096
1097   /**
1098    * DOCUMENT ME!
1099    *
1100    * @param e
1101    *          DOCUMENT ME!
1102    */
1103   @Override
1104   public void saveAs_actionPerformed(ActionEvent e)
1105   {
1106     JalviewFileChooser chooser = new JalviewFileChooser(
1107             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1108             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1109             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1110             currentFileFormat, false);
1111
1112     chooser.setFileView(new JalviewFileView());
1113     chooser.setDialogTitle(MessageManager
1114             .getString("label.save_alignment_to_file"));
1115     chooser.setToolTipText(MessageManager.getString("action.save"));
1116
1117     int value = chooser.showSaveDialog(this);
1118
1119     if (value == JalviewFileChooser.APPROVE_OPTION)
1120     {
1121       currentFileFormat = chooser.getSelectedFormat();
1122       while (currentFileFormat == null)
1123       {
1124         JOptionPane
1125                 .showInternalMessageDialog(
1126                         Desktop.desktop,
1127                         MessageManager
1128                                 .getString("label.select_file_format_before_saving"),
1129                         MessageManager
1130                                 .getString("label.file_format_not_specified"),
1131                         JOptionPane.WARNING_MESSAGE);
1132         currentFileFormat = chooser.getSelectedFormat();
1133         value = chooser.showSaveDialog(this);
1134         if (value != JalviewFileChooser.APPROVE_OPTION)
1135         {
1136           return;
1137         }
1138       }
1139
1140       fileName = chooser.getSelectedFile().getPath();
1141
1142       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1143               currentFileFormat);
1144
1145       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1146       if (currentFileFormat.indexOf(" ") > -1)
1147       {
1148         currentFileFormat = currentFileFormat.substring(0,
1149                 currentFileFormat.indexOf(" "));
1150       }
1151       saveAlignment(fileName, currentFileFormat);
1152     }
1153   }
1154
1155   public boolean saveAlignment(String file, String format)
1156   {
1157     boolean success = true;
1158
1159     if (format.equalsIgnoreCase("Jalview"))
1160     {
1161       String shortName = title;
1162
1163       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1164       {
1165         shortName = shortName.substring(shortName
1166                 .lastIndexOf(java.io.File.separatorChar) + 1);
1167       }
1168
1169       success = new Jalview2XML().saveAlignment(this, file, shortName);
1170
1171       statusBar.setText(MessageManager.formatMessage(
1172               "label.successfully_saved_to_file_in_format", new Object[] {
1173                   fileName, format }));
1174
1175     }
1176     else
1177     {
1178       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1179       {
1180         warningMessage("Cannot save file " + fileName + " using format "
1181                 + format, "Alignment output format not supported");
1182         if (!Jalview.isHeadlessMode())
1183         {
1184           saveAs_actionPerformed(null);
1185         }
1186         return false;
1187       }
1188
1189       AlignmentExportData exportData = getAlignmentForExport(format,
1190               viewport, null);
1191       if (exportData.getSettings().isCancelled())
1192       {
1193         return false;
1194       }
1195       FormatAdapter f = new FormatAdapter(alignPanel,
1196               exportData.getSettings());
1197       String output = f.formatSequences(
1198               format,
1199               exportData.getAlignment(), // class cast exceptions will
1200               // occur in the distant future
1201               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1202               f.getCacheSuffixDefault(format),
1203               viewport.getColumnSelection());
1204
1205       if (output == null)
1206       {
1207         success = false;
1208       }
1209       else
1210       {
1211         try
1212         {
1213           java.io.PrintWriter out = new java.io.PrintWriter(
1214                   new java.io.FileWriter(file));
1215
1216           out.print(output);
1217           out.close();
1218           this.setTitle(file);
1219           statusBar.setText(MessageManager.formatMessage(
1220                   "label.successfully_saved_to_file_in_format",
1221                   new Object[] { fileName, format }));
1222         } catch (Exception ex)
1223         {
1224           success = false;
1225           ex.printStackTrace();
1226         }
1227       }
1228     }
1229
1230     if (!success)
1231     {
1232       JOptionPane.showInternalMessageDialog(this, MessageManager
1233               .formatMessage("label.couldnt_save_file",
1234                       new Object[] { fileName }), MessageManager
1235               .getString("label.error_saving_file"),
1236               JOptionPane.WARNING_MESSAGE);
1237     }
1238
1239     return success;
1240   }
1241
1242   private void warningMessage(String warning, String title)
1243   {
1244     if (new jalview.util.Platform().isHeadless())
1245     {
1246       System.err.println("Warning: " + title + "\nWarning: " + warning);
1247
1248     }
1249     else
1250     {
1251       JOptionPane.showInternalMessageDialog(this, warning, title,
1252               JOptionPane.WARNING_MESSAGE);
1253     }
1254     return;
1255   }
1256
1257   /**
1258    * DOCUMENT ME!
1259    *
1260    * @param e
1261    *          DOCUMENT ME!
1262    */
1263   @Override
1264   protected void outputText_actionPerformed(ActionEvent e)
1265   {
1266
1267     AlignmentExportData exportData = getAlignmentForExport(
1268             e.getActionCommand(), viewport, null);
1269     if (exportData.getSettings().isCancelled())
1270     {
1271       return;
1272     }
1273     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1274     cap.setForInput(null);
1275     try
1276     {
1277       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1278               .formatSequences(e.getActionCommand(),
1279                       exportData.getAlignment(),
1280                       exportData.getOmitHidden(),
1281                       exportData.getStartEndPostions(),
1282                       viewport.getColumnSelection()));
1283       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1284               "label.alignment_output_command",
1285               new Object[] { e.getActionCommand() }), 600, 500);
1286     } catch (OutOfMemoryError oom)
1287     {
1288       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1289       cap.dispose();
1290     }
1291
1292   }
1293
1294   public static AlignmentExportData getAlignmentForExport(
1295           String exportFormat, AlignViewportI viewport,
1296           AlignExportSettingI exportSettings)
1297   {
1298     AlignmentI alignmentToExport = null;
1299     AlignExportSettingI settings = exportSettings;
1300     String[] omitHidden = null;
1301
1302     HiddenSequences hiddenSeqs = viewport.getAlignment()
1303             .getHiddenSequences();
1304
1305     alignmentToExport = viewport.getAlignment();
1306
1307     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1308     if (settings == null)
1309     {
1310       settings = new AlignExportSettings(hasHiddenSeqs,
1311               viewport.hasHiddenColumns(), exportFormat);
1312     }
1313     // settings.isExportAnnotations();
1314
1315     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1316     {
1317       omitHidden = viewport.getViewAsString(false);
1318     }
1319
1320     int[] alignmentStartEnd = new int[2];
1321     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1322     {
1323       alignmentToExport = hiddenSeqs.getFullAlignment();
1324     }
1325     else
1326     {
1327       alignmentToExport = viewport.getAlignment();
1328       alignmentStartEnd = viewport.getAlignment()
1329               .getVisibleStartAndEndIndex(
1330                       viewport
1331               .getColumnSelection().getHiddenColumns());
1332     }
1333     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1334             omitHidden, alignmentStartEnd, settings);
1335     return ed;
1336   }
1337
1338
1339   /**
1340    * DOCUMENT ME!
1341    *
1342    * @param e
1343    *          DOCUMENT ME!
1344    */
1345   @Override
1346   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1347   {
1348     new HtmlSvgOutput(null, alignPanel);
1349   }
1350
1351   @Override
1352   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1353   {
1354     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1355     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1356   }
1357
1358   public void createImageMap(File file, String image)
1359   {
1360     alignPanel.makePNGImageMap(file, image);
1361   }
1362
1363   /**
1364    * DOCUMENT ME!
1365    *
1366    * @param e
1367    *          DOCUMENT ME!
1368    */
1369   @Override
1370   public void createPNG(File f)
1371   {
1372     alignPanel.makePNG(f);
1373   }
1374
1375   /**
1376    * DOCUMENT ME!
1377    *
1378    * @param e
1379    *          DOCUMENT ME!
1380    */
1381   @Override
1382   public void createEPS(File f)
1383   {
1384     alignPanel.makeEPS(f);
1385   }
1386
1387   @Override
1388   public void createSVG(File f)
1389   {
1390     alignPanel.makeSVG(f);
1391   }
1392
1393   @Override
1394   public void pageSetup_actionPerformed(ActionEvent e)
1395   {
1396     PrinterJob printJob = PrinterJob.getPrinterJob();
1397     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1398   }
1399
1400   /**
1401    * DOCUMENT ME!
1402    *
1403    * @param e
1404    *          DOCUMENT ME!
1405    */
1406   @Override
1407   public void printMenuItem_actionPerformed(ActionEvent e)
1408   {
1409     // Putting in a thread avoids Swing painting problems
1410     PrintThread thread = new PrintThread(alignPanel);
1411     thread.start();
1412   }
1413
1414   @Override
1415   public void exportFeatures_actionPerformed(ActionEvent e)
1416   {
1417     new AnnotationExporter().exportFeatures(alignPanel);
1418   }
1419
1420   @Override
1421   public void exportAnnotations_actionPerformed(ActionEvent e)
1422   {
1423     new AnnotationExporter().exportAnnotations(alignPanel);
1424   }
1425
1426   @Override
1427   public void associatedData_actionPerformed(ActionEvent e)
1428   {
1429     // Pick the tree file
1430     JalviewFileChooser chooser = new JalviewFileChooser(
1431             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1432     chooser.setFileView(new JalviewFileView());
1433     chooser.setDialogTitle(MessageManager
1434             .getString("label.load_jalview_annotations"));
1435     chooser.setToolTipText(MessageManager
1436             .getString("label.load_jalview_annotations"));
1437
1438     int value = chooser.showOpenDialog(null);
1439
1440     if (value == JalviewFileChooser.APPROVE_OPTION)
1441     {
1442       String choice = chooser.getSelectedFile().getPath();
1443       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1444       loadJalviewDataFile(choice, null, null, null);
1445     }
1446
1447   }
1448
1449   /**
1450    * Close the current view or all views in the alignment frame. If the frame
1451    * only contains one view then the alignment will be removed from memory.
1452    *
1453    * @param closeAllTabs
1454    */
1455   @Override
1456   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1457   {
1458     if (alignPanels != null && alignPanels.size() < 2)
1459     {
1460       closeAllTabs = true;
1461     }
1462
1463     try
1464     {
1465       if (alignPanels != null)
1466       {
1467         if (closeAllTabs)
1468         {
1469           if (this.isClosed())
1470           {
1471             // really close all the windows - otherwise wait till
1472             // setClosed(true) is called
1473             for (int i = 0; i < alignPanels.size(); i++)
1474             {
1475               AlignmentPanel ap = alignPanels.get(i);
1476               ap.closePanel();
1477             }
1478           }
1479         }
1480         else
1481         {
1482           closeView(alignPanel);
1483         }
1484       }
1485
1486       if (closeAllTabs)
1487       {
1488         /*
1489          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1490          * be called recursively, with the frame now in 'closed' state
1491          */
1492         this.setClosed(true);
1493       }
1494     } catch (Exception ex)
1495     {
1496       ex.printStackTrace();
1497     }
1498   }
1499
1500   /**
1501    * Close the specified panel and close up tabs appropriately.
1502    *
1503    * @param panelToClose
1504    */
1505   public void closeView(AlignmentPanel panelToClose)
1506   {
1507     int index = tabbedPane.getSelectedIndex();
1508     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1509     alignPanels.remove(panelToClose);
1510     panelToClose.closePanel();
1511     panelToClose = null;
1512
1513     tabbedPane.removeTabAt(closedindex);
1514     tabbedPane.validate();
1515
1516     if (index > closedindex || index == tabbedPane.getTabCount())
1517     {
1518       // modify currently selected tab index if necessary.
1519       index--;
1520     }
1521
1522     this.tabSelectionChanged(index);
1523   }
1524
1525   /**
1526    * DOCUMENT ME!
1527    */
1528   void updateEditMenuBar()
1529   {
1530
1531     if (viewport.getHistoryList().size() > 0)
1532     {
1533       undoMenuItem.setEnabled(true);
1534       CommandI command = viewport.getHistoryList().peek();
1535       undoMenuItem.setText(MessageManager.formatMessage(
1536               "label.undo_command",
1537               new Object[] { command.getDescription() }));
1538     }
1539     else
1540     {
1541       undoMenuItem.setEnabled(false);
1542       undoMenuItem.setText(MessageManager.getString("action.undo"));
1543     }
1544
1545     if (viewport.getRedoList().size() > 0)
1546     {
1547       redoMenuItem.setEnabled(true);
1548
1549       CommandI command = viewport.getRedoList().peek();
1550       redoMenuItem.setText(MessageManager.formatMessage(
1551               "label.redo_command",
1552               new Object[] { command.getDescription() }));
1553     }
1554     else
1555     {
1556       redoMenuItem.setEnabled(false);
1557       redoMenuItem.setText(MessageManager.getString("action.redo"));
1558     }
1559   }
1560
1561   @Override
1562   public void addHistoryItem(CommandI command)
1563   {
1564     if (command.getSize() > 0)
1565     {
1566       viewport.addToHistoryList(command);
1567       viewport.clearRedoList();
1568       updateEditMenuBar();
1569       viewport.updateHiddenColumns();
1570       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1571       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1572       // viewport.getColumnSelection()
1573       // .getHiddenColumns().size() > 0);
1574     }
1575   }
1576
1577   /**
1578    *
1579    * @return alignment objects for all views
1580    */
1581   AlignmentI[] getViewAlignments()
1582   {
1583     if (alignPanels != null)
1584     {
1585       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1586       int i = 0;
1587       for (AlignmentPanel ap : alignPanels)
1588       {
1589         als[i++] = ap.av.getAlignment();
1590       }
1591       return als;
1592     }
1593     if (viewport != null)
1594     {
1595       return new AlignmentI[] { viewport.getAlignment() };
1596     }
1597     return null;
1598   }
1599
1600   /**
1601    * DOCUMENT ME!
1602    *
1603    * @param e
1604    *          DOCUMENT ME!
1605    */
1606   @Override
1607   protected void undoMenuItem_actionPerformed(ActionEvent e)
1608   {
1609     if (viewport.getHistoryList().isEmpty())
1610     {
1611       return;
1612     }
1613     CommandI command = viewport.getHistoryList().pop();
1614     viewport.addToRedoList(command);
1615     command.undoCommand(getViewAlignments());
1616
1617     AlignmentViewport originalSource = getOriginatingSource(command);
1618     updateEditMenuBar();
1619
1620     if (originalSource != null)
1621     {
1622       if (originalSource != viewport)
1623       {
1624         Cache.log
1625                 .warn("Implementation worry: mismatch of viewport origin for undo");
1626       }
1627       originalSource.updateHiddenColumns();
1628       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1629       // null
1630       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1631       // viewport.getColumnSelection()
1632       // .getHiddenColumns().size() > 0);
1633       originalSource.firePropertyChange("alignment", null, originalSource
1634               .getAlignment().getSequences());
1635     }
1636   }
1637
1638   /**
1639    * DOCUMENT ME!
1640    *
1641    * @param e
1642    *          DOCUMENT ME!
1643    */
1644   @Override
1645   protected void redoMenuItem_actionPerformed(ActionEvent e)
1646   {
1647     if (viewport.getRedoList().size() < 1)
1648     {
1649       return;
1650     }
1651
1652     CommandI command = viewport.getRedoList().pop();
1653     viewport.addToHistoryList(command);
1654     command.doCommand(getViewAlignments());
1655
1656     AlignmentViewport originalSource = getOriginatingSource(command);
1657     updateEditMenuBar();
1658
1659     if (originalSource != null)
1660     {
1661
1662       if (originalSource != viewport)
1663       {
1664         Cache.log
1665                 .warn("Implementation worry: mismatch of viewport origin for redo");
1666       }
1667       originalSource.updateHiddenColumns();
1668       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1669       // null
1670       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1671       // viewport.getColumnSelection()
1672       // .getHiddenColumns().size() > 0);
1673       originalSource.firePropertyChange("alignment", null, originalSource
1674               .getAlignment().getSequences());
1675     }
1676   }
1677
1678   AlignmentViewport getOriginatingSource(CommandI command)
1679   {
1680     AlignmentViewport originalSource = null;
1681     // For sequence removal and addition, we need to fire
1682     // the property change event FROM the viewport where the
1683     // original alignment was altered
1684     AlignmentI al = null;
1685     if (command instanceof EditCommand)
1686     {
1687       EditCommand editCommand = (EditCommand) command;
1688       al = editCommand.getAlignment();
1689       List<Component> comps = PaintRefresher.components.get(viewport
1690               .getSequenceSetId());
1691
1692       for (Component comp : comps)
1693       {
1694         if (comp instanceof AlignmentPanel)
1695         {
1696           if (al == ((AlignmentPanel) comp).av.getAlignment())
1697           {
1698             originalSource = ((AlignmentPanel) comp).av;
1699             break;
1700           }
1701         }
1702       }
1703     }
1704
1705     if (originalSource == null)
1706     {
1707       // The original view is closed, we must validate
1708       // the current view against the closed view first
1709       if (al != null)
1710       {
1711         PaintRefresher.validateSequences(al, viewport.getAlignment());
1712       }
1713
1714       originalSource = viewport;
1715     }
1716
1717     return originalSource;
1718   }
1719
1720   /**
1721    * DOCUMENT ME!
1722    *
1723    * @param up
1724    *          DOCUMENT ME!
1725    */
1726   public void moveSelectedSequences(boolean up)
1727   {
1728     SequenceGroup sg = viewport.getSelectionGroup();
1729
1730     if (sg == null)
1731     {
1732       return;
1733     }
1734     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1735             viewport.getHiddenRepSequences(), up);
1736     alignPanel.paintAlignment(true);
1737   }
1738
1739   synchronized void slideSequences(boolean right, int size)
1740   {
1741     List<SequenceI> sg = new ArrayList<SequenceI>();
1742     if (viewport.cursorMode)
1743     {
1744       sg.add(viewport.getAlignment().getSequenceAt(
1745               alignPanel.getSeqPanel().seqCanvas.cursorY));
1746     }
1747     else if (viewport.getSelectionGroup() != null
1748             && viewport.getSelectionGroup().getSize() != viewport
1749                     .getAlignment().getHeight())
1750     {
1751       sg = viewport.getSelectionGroup().getSequences(
1752               viewport.getHiddenRepSequences());
1753     }
1754
1755     if (sg.size() < 1)
1756     {
1757       return;
1758     }
1759
1760     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1761
1762     for (SequenceI seq : viewport.getAlignment().getSequences())
1763     {
1764       if (!sg.contains(seq))
1765       {
1766         invertGroup.add(seq);
1767       }
1768     }
1769
1770     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1771
1772     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1773     for (int i = 0; i < invertGroup.size(); i++)
1774     {
1775       seqs2[i] = invertGroup.get(i);
1776     }
1777
1778     SlideSequencesCommand ssc;
1779     if (right)
1780     {
1781       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1782               size, viewport.getGapCharacter());
1783     }
1784     else
1785     {
1786       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1787               size, viewport.getGapCharacter());
1788     }
1789
1790     int groupAdjustment = 0;
1791     if (ssc.getGapsInsertedBegin() && right)
1792     {
1793       if (viewport.cursorMode)
1794       {
1795         alignPanel.getSeqPanel().moveCursor(size, 0);
1796       }
1797       else
1798       {
1799         groupAdjustment = size;
1800       }
1801     }
1802     else if (!ssc.getGapsInsertedBegin() && !right)
1803     {
1804       if (viewport.cursorMode)
1805       {
1806         alignPanel.getSeqPanel().moveCursor(-size, 0);
1807       }
1808       else
1809       {
1810         groupAdjustment = -size;
1811       }
1812     }
1813
1814     if (groupAdjustment != 0)
1815     {
1816       viewport.getSelectionGroup().setStartRes(
1817               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1818       viewport.getSelectionGroup().setEndRes(
1819               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1820     }
1821
1822     /*
1823      * just extend the last slide command if compatible; but not if in
1824      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1825      */
1826     boolean appendHistoryItem = false;
1827     Deque<CommandI> historyList = viewport.getHistoryList();
1828     boolean inSplitFrame = getSplitViewContainer() != null;
1829     if (!inSplitFrame && historyList != null && historyList.size() > 0
1830             && historyList.peek() instanceof SlideSequencesCommand)
1831     {
1832       appendHistoryItem = ssc
1833               .appendSlideCommand((SlideSequencesCommand) historyList
1834                       .peek());
1835     }
1836
1837     if (!appendHistoryItem)
1838     {
1839       addHistoryItem(ssc);
1840     }
1841
1842     repaint();
1843   }
1844
1845   /**
1846    * DOCUMENT ME!
1847    *
1848    * @param e
1849    *          DOCUMENT ME!
1850    */
1851   @Override
1852   protected void copy_actionPerformed(ActionEvent e)
1853   {
1854     System.gc();
1855     if (viewport.getSelectionGroup() == null)
1856     {
1857       return;
1858     }
1859     // TODO: preserve the ordering of displayed alignment annotation in any
1860     // internal paste (particularly sequence associated annotation)
1861     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1862     String[] omitHidden = null;
1863
1864     if (viewport.hasHiddenColumns())
1865     {
1866       omitHidden = viewport.getViewAsString(true);
1867     }
1868
1869     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1870             omitHidden, null);
1871
1872     StringSelection ss = new StringSelection(output);
1873
1874     try
1875     {
1876       jalview.gui.Desktop.internalCopy = true;
1877       // Its really worth setting the clipboard contents
1878       // to empty before setting the large StringSelection!!
1879       Toolkit.getDefaultToolkit().getSystemClipboard()
1880               .setContents(new StringSelection(""), null);
1881
1882       Toolkit.getDefaultToolkit().getSystemClipboard()
1883               .setContents(ss, Desktop.instance);
1884     } catch (OutOfMemoryError er)
1885     {
1886       new OOMWarning("copying region", er);
1887       return;
1888     }
1889
1890     ArrayList<int[]> hiddenColumns = null;
1891     if (viewport.hasHiddenColumns())
1892     {
1893       hiddenColumns = new ArrayList<int[]>();
1894       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1895               .getSelectionGroup().getEndRes();
1896       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1897       {
1898         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1899         {
1900           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1901               region[1] - hiddenOffset });
1902         }
1903       }
1904     }
1905
1906     Desktop.jalviewClipboard = new Object[] { seqs,
1907         viewport.getAlignment().getDataset(), hiddenColumns };
1908     statusBar.setText(MessageManager.formatMessage(
1909             "label.copied_sequences_to_clipboard", new Object[] { Integer
1910                     .valueOf(seqs.length).toString() }));
1911   }
1912
1913   /**
1914    * DOCUMENT ME!
1915    *
1916    * @param e
1917    *          DOCUMENT ME!
1918    */
1919   @Override
1920   protected void pasteNew_actionPerformed(ActionEvent e)
1921   {
1922     paste(true);
1923   }
1924
1925   /**
1926    * DOCUMENT ME!
1927    *
1928    * @param e
1929    *          DOCUMENT ME!
1930    */
1931   @Override
1932   protected void pasteThis_actionPerformed(ActionEvent e)
1933   {
1934     paste(false);
1935   }
1936
1937   /**
1938    * Paste contents of Jalview clipboard
1939    *
1940    * @param newAlignment
1941    *          true to paste to a new alignment, otherwise add to this.
1942    */
1943   void paste(boolean newAlignment)
1944   {
1945     boolean externalPaste = true;
1946     try
1947     {
1948       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1949       Transferable contents = c.getContents(this);
1950
1951       if (contents == null)
1952       {
1953         return;
1954       }
1955
1956       String str, format;
1957       try
1958       {
1959         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1960         if (str.length() < 1)
1961         {
1962           return;
1963         }
1964
1965         format = new IdentifyFile().identify(str, "Paste");
1966
1967       } catch (OutOfMemoryError er)
1968       {
1969         new OOMWarning("Out of memory pasting sequences!!", er);
1970         return;
1971       }
1972
1973       SequenceI[] sequences;
1974       boolean annotationAdded = false;
1975       AlignmentI alignment = null;
1976
1977       if (Desktop.jalviewClipboard != null)
1978       {
1979         // The clipboard was filled from within Jalview, we must use the
1980         // sequences
1981         // And dataset from the copied alignment
1982         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1983         // be doubly sure that we create *new* sequence objects.
1984         sequences = new SequenceI[newseq.length];
1985         for (int i = 0; i < newseq.length; i++)
1986         {
1987           sequences[i] = new Sequence(newseq[i]);
1988         }
1989         alignment = new Alignment(sequences);
1990         externalPaste = false;
1991       }
1992       else
1993       {
1994         // parse the clipboard as an alignment.
1995         alignment = new FormatAdapter().readFile(str, "Paste", format);
1996         sequences = alignment.getSequencesArray();
1997       }
1998
1999       int alwidth = 0;
2000       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2001       int fgroup = -1;
2002
2003       if (newAlignment)
2004       {
2005
2006         if (Desktop.jalviewClipboard != null)
2007         {
2008           // dataset is inherited
2009           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2010         }
2011         else
2012         {
2013           // new dataset is constructed
2014           alignment.setDataset(null);
2015         }
2016         alwidth = alignment.getWidth() + 1;
2017       }
2018       else
2019       {
2020         AlignmentI pastedal = alignment; // preserve pasted alignment object
2021         // Add pasted sequences and dataset into existing alignment.
2022         alignment = viewport.getAlignment();
2023         alwidth = alignment.getWidth() + 1;
2024         // decide if we need to import sequences from an existing dataset
2025         boolean importDs = Desktop.jalviewClipboard != null
2026                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2027         // importDs==true instructs us to copy over new dataset sequences from
2028         // an existing alignment
2029         Vector newDs = (importDs) ? new Vector() : null; // used to create
2030         // minimum dataset set
2031
2032         for (int i = 0; i < sequences.length; i++)
2033         {
2034           if (importDs)
2035           {
2036             newDs.addElement(null);
2037           }
2038           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2039           // paste
2040           if (importDs && ds != null)
2041           {
2042             if (!newDs.contains(ds))
2043             {
2044               newDs.setElementAt(ds, i);
2045               ds = new Sequence(ds);
2046               // update with new dataset sequence
2047               sequences[i].setDatasetSequence(ds);
2048             }
2049             else
2050             {
2051               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2052             }
2053           }
2054           else
2055           {
2056             // copy and derive new dataset sequence
2057             sequences[i] = sequences[i].deriveSequence();
2058             alignment.getDataset().addSequence(
2059                     sequences[i].getDatasetSequence());
2060             // TODO: avoid creation of duplicate dataset sequences with a
2061             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2062           }
2063           alignment.addSequence(sequences[i]); // merges dataset
2064         }
2065         if (newDs != null)
2066         {
2067           newDs.clear(); // tidy up
2068         }
2069         if (alignment.getAlignmentAnnotation() != null)
2070         {
2071           for (AlignmentAnnotation alan : alignment
2072                   .getAlignmentAnnotation())
2073           {
2074             if (alan.graphGroup > fgroup)
2075             {
2076               fgroup = alan.graphGroup;
2077             }
2078           }
2079         }
2080         if (pastedal.getAlignmentAnnotation() != null)
2081         {
2082           // Add any annotation attached to alignment.
2083           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2084           for (int i = 0; i < alann.length; i++)
2085           {
2086             annotationAdded = true;
2087             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2088             {
2089               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2090               if (newann.graphGroup > -1)
2091               {
2092                 if (newGraphGroups.size() <= newann.graphGroup
2093                         || newGraphGroups.get(newann.graphGroup) == null)
2094                 {
2095                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2096                   {
2097                     newGraphGroups.add(q, null);
2098                   }
2099                   newGraphGroups.set(newann.graphGroup, new Integer(
2100                           ++fgroup));
2101                 }
2102                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2103                         .intValue();
2104               }
2105
2106               newann.padAnnotation(alwidth);
2107               alignment.addAnnotation(newann);
2108             }
2109           }
2110         }
2111       }
2112       if (!newAlignment)
2113       {
2114         // /////
2115         // ADD HISTORY ITEM
2116         //
2117         addHistoryItem(new EditCommand(
2118                 MessageManager.getString("label.add_sequences"),
2119                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2120       }
2121       // Add any annotations attached to sequences
2122       for (int i = 0; i < sequences.length; i++)
2123       {
2124         if (sequences[i].getAnnotation() != null)
2125         {
2126           AlignmentAnnotation newann;
2127           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2128           {
2129             annotationAdded = true;
2130             newann = sequences[i].getAnnotation()[a];
2131             newann.adjustForAlignment();
2132             newann.padAnnotation(alwidth);
2133             if (newann.graphGroup > -1)
2134             {
2135               if (newann.graphGroup > -1)
2136               {
2137                 if (newGraphGroups.size() <= newann.graphGroup
2138                         || newGraphGroups.get(newann.graphGroup) == null)
2139                 {
2140                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2141                   {
2142                     newGraphGroups.add(q, null);
2143                   }
2144                   newGraphGroups.set(newann.graphGroup, new Integer(
2145                           ++fgroup));
2146                 }
2147                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2148                         .intValue();
2149               }
2150             }
2151             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2152             // was
2153             // duplicated
2154             // earlier
2155             alignment
2156                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2157           }
2158         }
2159       }
2160       if (!newAlignment)
2161       {
2162
2163         // propagate alignment changed.
2164         viewport.setEndSeq(alignment.getHeight());
2165         if (annotationAdded)
2166         {
2167           // Duplicate sequence annotation in all views.
2168           AlignmentI[] alview = this.getViewAlignments();
2169           for (int i = 0; i < sequences.length; i++)
2170           {
2171             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2172             if (sann == null)
2173             {
2174               continue;
2175             }
2176             for (int avnum = 0; avnum < alview.length; avnum++)
2177             {
2178               if (alview[avnum] != alignment)
2179               {
2180                 // duplicate in a view other than the one with input focus
2181                 int avwidth = alview[avnum].getWidth() + 1;
2182                 // this relies on sann being preserved after we
2183                 // modify the sequence's annotation array for each duplication
2184                 for (int a = 0; a < sann.length; a++)
2185                 {
2186                   AlignmentAnnotation newann = new AlignmentAnnotation(
2187                           sann[a]);
2188                   sequences[i].addAlignmentAnnotation(newann);
2189                   newann.padAnnotation(avwidth);
2190                   alview[avnum].addAnnotation(newann); // annotation was
2191                   // duplicated earlier
2192                   // TODO JAL-1145 graphGroups are not updated for sequence
2193                   // annotation added to several views. This may cause
2194                   // strangeness
2195                   alview[avnum].setAnnotationIndex(newann, a);
2196                 }
2197               }
2198             }
2199           }
2200           buildSortByAnnotationScoresMenu();
2201         }
2202         viewport.firePropertyChange("alignment", null,
2203                 alignment.getSequences());
2204         if (alignPanels != null)
2205         {
2206           for (AlignmentPanel ap : alignPanels)
2207           {
2208             ap.validateAnnotationDimensions(false);
2209           }
2210         }
2211         else
2212         {
2213           alignPanel.validateAnnotationDimensions(false);
2214         }
2215
2216       }
2217       else
2218       {
2219         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2220                 DEFAULT_HEIGHT);
2221         String newtitle = new String("Copied sequences");
2222
2223         if (Desktop.jalviewClipboard != null
2224                 && Desktop.jalviewClipboard[2] != null)
2225         {
2226           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2227           for (int[] region : hc)
2228           {
2229             af.viewport.hideColumns(region[0], region[1]);
2230           }
2231         }
2232
2233         // >>>This is a fix for the moment, until a better solution is
2234         // found!!<<<
2235         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2236                 .transferSettings(
2237                         alignPanel.getSeqPanel().seqCanvas
2238                                 .getFeatureRenderer());
2239
2240         // TODO: maintain provenance of an alignment, rather than just make the
2241         // title a concatenation of operations.
2242         if (!externalPaste)
2243         {
2244           if (title.startsWith("Copied sequences"))
2245           {
2246             newtitle = title;
2247           }
2248           else
2249           {
2250             newtitle = newtitle.concat("- from " + title);
2251           }
2252         }
2253         else
2254         {
2255           newtitle = new String("Pasted sequences");
2256         }
2257
2258         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2259                 DEFAULT_HEIGHT);
2260
2261       }
2262
2263     } catch (Exception ex)
2264     {
2265       ex.printStackTrace();
2266       System.out.println("Exception whilst pasting: " + ex);
2267       // could be anything being pasted in here
2268     }
2269
2270   }
2271
2272   @Override
2273   protected void expand_newalign(ActionEvent e)
2274   {
2275     try
2276     {
2277       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2278               .getAlignment(), -1);
2279       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2280               DEFAULT_HEIGHT);
2281       String newtitle = new String("Flanking alignment");
2282
2283       if (Desktop.jalviewClipboard != null
2284               && Desktop.jalviewClipboard[2] != null)
2285       {
2286         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2287         for (int region[] : hc)
2288         {
2289           af.viewport.hideColumns(region[0], region[1]);
2290         }
2291       }
2292
2293       // >>>This is a fix for the moment, until a better solution is
2294       // found!!<<<
2295       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2296               .transferSettings(
2297                       alignPanel.getSeqPanel().seqCanvas
2298                               .getFeatureRenderer());
2299
2300       // TODO: maintain provenance of an alignment, rather than just make the
2301       // title a concatenation of operations.
2302       {
2303         if (title.startsWith("Copied sequences"))
2304         {
2305           newtitle = title;
2306         }
2307         else
2308         {
2309           newtitle = newtitle.concat("- from " + title);
2310         }
2311       }
2312
2313       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2314
2315     } catch (Exception ex)
2316     {
2317       ex.printStackTrace();
2318       System.out.println("Exception whilst pasting: " + ex);
2319       // could be anything being pasted in here
2320     } catch (OutOfMemoryError oom)
2321     {
2322       new OOMWarning("Viewing flanking region of alignment", oom);
2323     }
2324   }
2325
2326   /**
2327    * DOCUMENT ME!
2328    *
2329    * @param e
2330    *          DOCUMENT ME!
2331    */
2332   @Override
2333   protected void cut_actionPerformed(ActionEvent e)
2334   {
2335     copy_actionPerformed(null);
2336     delete_actionPerformed(null);
2337   }
2338
2339   /**
2340    * DOCUMENT ME!
2341    *
2342    * @param e
2343    *          DOCUMENT ME!
2344    */
2345   @Override
2346   protected void delete_actionPerformed(ActionEvent evt)
2347   {
2348
2349     SequenceGroup sg = viewport.getSelectionGroup();
2350     if (sg == null)
2351     {
2352       return;
2353     }
2354
2355     /*
2356      * If the cut affects all sequences, warn, remove highlighted columns
2357      */
2358     if (sg.getSize() == viewport.getAlignment().getHeight())
2359     {
2360       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2361               .getAlignment().getWidth()) ? true : false;
2362       if (isEntireAlignWidth)
2363       {
2364         int confirm = JOptionPane.showConfirmDialog(this,
2365                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2366                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2367                 JOptionPane.OK_CANCEL_OPTION);
2368
2369         if (confirm == JOptionPane.CANCEL_OPTION
2370                 || confirm == JOptionPane.CLOSED_OPTION)
2371         {
2372           return;
2373         }
2374       }
2375       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2376               sg.getEndRes() + 1);
2377     }
2378     SequenceI[] cut = sg.getSequences()
2379             .toArray(new SequenceI[sg.getSize()]);
2380
2381     addHistoryItem(new EditCommand(
2382             MessageManager.getString("label.cut_sequences"), Action.CUT,
2383             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2384             viewport.getAlignment()));
2385
2386     viewport.setSelectionGroup(null);
2387     viewport.sendSelection();
2388     viewport.getAlignment().deleteGroup(sg);
2389
2390     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2391             .getSequences());
2392     if (viewport.getAlignment().getHeight() < 1)
2393     {
2394       try
2395       {
2396         this.setClosed(true);
2397       } catch (Exception ex)
2398       {
2399       }
2400     }
2401   }
2402
2403   /**
2404    * DOCUMENT ME!
2405    *
2406    * @param e
2407    *          DOCUMENT ME!
2408    */
2409   @Override
2410   protected void deleteGroups_actionPerformed(ActionEvent e)
2411   {
2412     if (avc.deleteGroups())
2413     {
2414       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2415       alignPanel.updateAnnotation();
2416       alignPanel.paintAlignment(true);
2417     }
2418   }
2419
2420   /**
2421    * DOCUMENT ME!
2422    *
2423    * @param e
2424    *          DOCUMENT ME!
2425    */
2426   @Override
2427   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2428   {
2429     SequenceGroup sg = new SequenceGroup();
2430
2431     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2432     {
2433       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2434     }
2435
2436     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2437     viewport.setSelectionGroup(sg);
2438     viewport.sendSelection();
2439     alignPanel.paintAlignment(true);
2440     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2441   }
2442
2443   /**
2444    * DOCUMENT ME!
2445    *
2446    * @param e
2447    *          DOCUMENT ME!
2448    */
2449   @Override
2450   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2451   {
2452     if (viewport.cursorMode)
2453     {
2454       alignPanel.getSeqPanel().keyboardNo1 = null;
2455       alignPanel.getSeqPanel().keyboardNo2 = null;
2456     }
2457     viewport.setSelectionGroup(null);
2458     viewport.getColumnSelection().clear();
2459     viewport.setSelectionGroup(null);
2460     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2461     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2462     alignPanel.paintAlignment(true);
2463     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2464     viewport.sendSelection();
2465   }
2466
2467   /**
2468    * DOCUMENT ME!
2469    *
2470    * @param e
2471    *          DOCUMENT ME!
2472    */
2473   @Override
2474   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2475   {
2476     SequenceGroup sg = viewport.getSelectionGroup();
2477
2478     if (sg == null)
2479     {
2480       selectAllSequenceMenuItem_actionPerformed(null);
2481
2482       return;
2483     }
2484
2485     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2486     {
2487       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2488     }
2489
2490     alignPanel.paintAlignment(true);
2491     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2492     viewport.sendSelection();
2493   }
2494
2495   @Override
2496   public void invertColSel_actionPerformed(ActionEvent e)
2497   {
2498     viewport.invertColumnSelection();
2499     alignPanel.paintAlignment(true);
2500     viewport.sendSelection();
2501   }
2502
2503   /**
2504    * DOCUMENT ME!
2505    *
2506    * @param e
2507    *          DOCUMENT ME!
2508    */
2509   @Override
2510   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2511   {
2512     trimAlignment(true);
2513   }
2514
2515   /**
2516    * DOCUMENT ME!
2517    *
2518    * @param e
2519    *          DOCUMENT ME!
2520    */
2521   @Override
2522   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2523   {
2524     trimAlignment(false);
2525   }
2526
2527   void trimAlignment(boolean trimLeft)
2528   {
2529     ColumnSelection colSel = viewport.getColumnSelection();
2530     int column;
2531
2532     if (!colSel.isEmpty())
2533     {
2534       if (trimLeft)
2535       {
2536         column = colSel.getMin();
2537       }
2538       else
2539       {
2540         column = colSel.getMax();
2541       }
2542
2543       SequenceI[] seqs;
2544       if (viewport.getSelectionGroup() != null)
2545       {
2546         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2547                 viewport.getHiddenRepSequences());
2548       }
2549       else
2550       {
2551         seqs = viewport.getAlignment().getSequencesArray();
2552       }
2553
2554       TrimRegionCommand trimRegion;
2555       if (trimLeft)
2556       {
2557         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2558                 column, viewport.getAlignment());
2559         viewport.setStartRes(0);
2560       }
2561       else
2562       {
2563         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2564                 column, viewport.getAlignment());
2565       }
2566
2567       statusBar.setText(MessageManager.formatMessage(
2568               "label.removed_columns",
2569               new String[] { Integer.valueOf(trimRegion.getSize())
2570                       .toString() }));
2571
2572       addHistoryItem(trimRegion);
2573
2574       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2575       {
2576         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2577                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2578         {
2579           viewport.getAlignment().deleteGroup(sg);
2580         }
2581       }
2582
2583       viewport.firePropertyChange("alignment", null, viewport
2584               .getAlignment().getSequences());
2585     }
2586   }
2587
2588   /**
2589    * DOCUMENT ME!
2590    *
2591    * @param e
2592    *          DOCUMENT ME!
2593    */
2594   @Override
2595   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2596   {
2597     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2598
2599     SequenceI[] seqs;
2600     if (viewport.getSelectionGroup() != null)
2601     {
2602       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2603               viewport.getHiddenRepSequences());
2604       start = viewport.getSelectionGroup().getStartRes();
2605       end = viewport.getSelectionGroup().getEndRes();
2606     }
2607     else
2608     {
2609       seqs = viewport.getAlignment().getSequencesArray();
2610     }
2611
2612     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2613             "Remove Gapped Columns", seqs, start, end,
2614             viewport.getAlignment());
2615
2616     addHistoryItem(removeGapCols);
2617
2618     statusBar.setText(MessageManager.formatMessage(
2619             "label.removed_empty_columns",
2620             new Object[] { Integer.valueOf(removeGapCols.getSize())
2621                     .toString() }));
2622
2623     // This is to maintain viewport position on first residue
2624     // of first sequence
2625     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2626     int startRes = seq.findPosition(viewport.startRes);
2627     // ShiftList shifts;
2628     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2629     // edit.alColumnChanges=shifts.getInverse();
2630     // if (viewport.hasHiddenColumns)
2631     // viewport.getColumnSelection().compensateForEdits(shifts);
2632     viewport.setStartRes(seq.findIndex(startRes) - 1);
2633     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2634             .getSequences());
2635
2636   }
2637
2638   /**
2639    * DOCUMENT ME!
2640    *
2641    * @param e
2642    *          DOCUMENT ME!
2643    */
2644   @Override
2645   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2646   {
2647     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2648
2649     SequenceI[] seqs;
2650     if (viewport.getSelectionGroup() != null)
2651     {
2652       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2653               viewport.getHiddenRepSequences());
2654       start = viewport.getSelectionGroup().getStartRes();
2655       end = viewport.getSelectionGroup().getEndRes();
2656     }
2657     else
2658     {
2659       seqs = viewport.getAlignment().getSequencesArray();
2660     }
2661
2662     // This is to maintain viewport position on first residue
2663     // of first sequence
2664     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2665     int startRes = seq.findPosition(viewport.startRes);
2666
2667     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2668             viewport.getAlignment()));
2669
2670     viewport.setStartRes(seq.findIndex(startRes) - 1);
2671
2672     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2673             .getSequences());
2674
2675   }
2676
2677   /**
2678    * DOCUMENT ME!
2679    *
2680    * @param e
2681    *          DOCUMENT ME!
2682    */
2683   @Override
2684   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2685   {
2686     viewport.setPadGaps(padGapsMenuitem.isSelected());
2687     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2688             .getSequences());
2689   }
2690
2691   /**
2692    * DOCUMENT ME!
2693    *
2694    * @param e
2695    *          DOCUMENT ME!
2696    */
2697   @Override
2698   public void findMenuItem_actionPerformed(ActionEvent e)
2699   {
2700     new Finder();
2701   }
2702
2703   /**
2704    * Create a new view of the current alignment.
2705    */
2706   @Override
2707   public void newView_actionPerformed(ActionEvent e)
2708   {
2709     newView(null, true);
2710   }
2711
2712   /**
2713    * Creates and shows a new view of the current alignment.
2714    *
2715    * @param viewTitle
2716    *          title of newly created view; if null, one will be generated
2717    * @param copyAnnotation
2718    *          if true then duplicate all annnotation, groups and settings
2719    * @return new alignment panel, already displayed.
2720    */
2721   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2722   {
2723     /*
2724      * Create a new AlignmentPanel (with its own, new Viewport)
2725      */
2726     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2727             true);
2728     if (!copyAnnotation)
2729     {
2730       /*
2731        * remove all groups and annotation except for the automatic stuff
2732        */
2733       newap.av.getAlignment().deleteAllGroups();
2734       newap.av.getAlignment().deleteAllAnnotations(false);
2735     }
2736
2737     newap.av.setGatherViewsHere(false);
2738
2739     if (viewport.viewName == null)
2740     {
2741       viewport.viewName = MessageManager
2742               .getString("label.view_name_original");
2743     }
2744
2745     /*
2746      * Views share the same edits undo and redo stacks
2747      */
2748     newap.av.setHistoryList(viewport.getHistoryList());
2749     newap.av.setRedoList(viewport.getRedoList());
2750
2751     /*
2752      * Views share the same mappings; need to deregister any new mappings
2753      * created by copyAlignPanel, and register the new reference to the shared
2754      * mappings
2755      */
2756     newap.av.replaceMappings(viewport.getAlignment());
2757
2758     newap.av.viewName = getNewViewName(viewTitle);
2759
2760     addAlignmentPanel(newap, true);
2761     newap.alignmentChanged();
2762
2763     if (alignPanels.size() == 2)
2764     {
2765       viewport.setGatherViewsHere(true);
2766     }
2767     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2768     return newap;
2769   }
2770
2771   /**
2772    * Make a new name for the view, ensuring it is unique within the current
2773    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2774    * these now use viewId. Unique view names are still desirable for usability.)
2775    *
2776    * @param viewTitle
2777    * @return
2778    */
2779   protected String getNewViewName(String viewTitle)
2780   {
2781     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2782     boolean addFirstIndex = false;
2783     if (viewTitle == null || viewTitle.trim().length() == 0)
2784     {
2785       viewTitle = MessageManager.getString("action.view");
2786       addFirstIndex = true;
2787     }
2788     else
2789     {
2790       index = 1;// we count from 1 if given a specific name
2791     }
2792     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2793
2794     List<Component> comps = PaintRefresher.components.get(viewport
2795             .getSequenceSetId());
2796
2797     List<String> existingNames = getExistingViewNames(comps);
2798
2799     while (existingNames.contains(newViewName))
2800     {
2801       newViewName = viewTitle + " " + (++index);
2802     }
2803     return newViewName;
2804   }
2805
2806   /**
2807    * Returns a list of distinct view names found in the given list of
2808    * components. View names are held on the viewport of an AlignmentPanel.
2809    *
2810    * @param comps
2811    * @return
2812    */
2813   protected List<String> getExistingViewNames(List<Component> comps)
2814   {
2815     List<String> existingNames = new ArrayList<String>();
2816     for (Component comp : comps)
2817     {
2818       if (comp instanceof AlignmentPanel)
2819       {
2820         AlignmentPanel ap = (AlignmentPanel) comp;
2821         if (!existingNames.contains(ap.av.viewName))
2822         {
2823           existingNames.add(ap.av.viewName);
2824         }
2825       }
2826     }
2827     return existingNames;
2828   }
2829
2830   /**
2831    * Explode tabbed views into separate windows.
2832    */
2833   @Override
2834   public void expandViews_actionPerformed(ActionEvent e)
2835   {
2836     Desktop.instance.explodeViews(this);
2837   }
2838
2839   /**
2840    * Gather views in separate windows back into a tabbed presentation.
2841    */
2842   @Override
2843   public void gatherViews_actionPerformed(ActionEvent e)
2844   {
2845     Desktop.instance.gatherViews(this);
2846   }
2847
2848   /**
2849    * DOCUMENT ME!
2850    *
2851    * @param e
2852    *          DOCUMENT ME!
2853    */
2854   @Override
2855   public void font_actionPerformed(ActionEvent e)
2856   {
2857     new FontChooser(alignPanel);
2858   }
2859
2860   /**
2861    * DOCUMENT ME!
2862    *
2863    * @param e
2864    *          DOCUMENT ME!
2865    */
2866   @Override
2867   protected void seqLimit_actionPerformed(ActionEvent e)
2868   {
2869     viewport.setShowJVSuffix(seqLimits.isSelected());
2870
2871     alignPanel.getIdPanel().getIdCanvas()
2872             .setPreferredSize(alignPanel.calculateIdWidth());
2873     alignPanel.paintAlignment(true);
2874   }
2875
2876   @Override
2877   public void idRightAlign_actionPerformed(ActionEvent e)
2878   {
2879     viewport.setRightAlignIds(idRightAlign.isSelected());
2880     alignPanel.paintAlignment(true);
2881   }
2882
2883   @Override
2884   public void centreColumnLabels_actionPerformed(ActionEvent e)
2885   {
2886     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2887     alignPanel.paintAlignment(true);
2888   }
2889
2890   /*
2891    * (non-Javadoc)
2892    *
2893    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2894    */
2895   @Override
2896   protected void followHighlight_actionPerformed()
2897   {
2898     /*
2899      * Set the 'follow' flag on the Viewport (and scroll to position if now
2900      * true).
2901      */
2902     final boolean state = this.followHighlightMenuItem.getState();
2903     viewport.setFollowHighlight(state);
2904     if (state)
2905     {
2906       alignPanel.scrollToPosition(
2907               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2908     }
2909   }
2910
2911   /**
2912    * DOCUMENT ME!
2913    *
2914    * @param e
2915    *          DOCUMENT ME!
2916    */
2917   @Override
2918   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2919   {
2920     viewport.setColourText(colourTextMenuItem.isSelected());
2921     alignPanel.paintAlignment(true);
2922   }
2923
2924   /**
2925    * DOCUMENT ME!
2926    *
2927    * @param e
2928    *          DOCUMENT ME!
2929    */
2930   @Override
2931   public void wrapMenuItem_actionPerformed(ActionEvent e)
2932   {
2933     scaleAbove.setVisible(wrapMenuItem.isSelected());
2934     scaleLeft.setVisible(wrapMenuItem.isSelected());
2935     scaleRight.setVisible(wrapMenuItem.isSelected());
2936     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2937     alignPanel.updateLayout();
2938   }
2939
2940   @Override
2941   public void showAllSeqs_actionPerformed(ActionEvent e)
2942   {
2943     viewport.showAllHiddenSeqs();
2944   }
2945
2946   @Override
2947   public void showAllColumns_actionPerformed(ActionEvent e)
2948   {
2949     viewport.showAllHiddenColumns();
2950     repaint();
2951     viewport.sendSelection();
2952   }
2953
2954   @Override
2955   public void hideSelSequences_actionPerformed(ActionEvent e)
2956   {
2957     viewport.hideAllSelectedSeqs();
2958     // alignPanel.paintAlignment(true);
2959   }
2960
2961   /**
2962    * called by key handler and the hide all/show all menu items
2963    *
2964    * @param toggleSeqs
2965    * @param toggleCols
2966    */
2967   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2968   {
2969
2970     boolean hide = false;
2971     SequenceGroup sg = viewport.getSelectionGroup();
2972     if (!toggleSeqs && !toggleCols)
2973     {
2974       // Hide everything by the current selection - this is a hack - we do the
2975       // invert and then hide
2976       // first check that there will be visible columns after the invert.
2977       if ((viewport.getColumnSelection() != null
2978               && viewport.getColumnSelection().getSelected() != null && viewport
2979               .getColumnSelection().getSelected().size() > 0)
2980               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2981                       .getEndRes()))
2982       {
2983         // now invert the sequence set, if required - empty selection implies
2984         // that no hiding is required.
2985         if (sg != null)
2986         {
2987           invertSequenceMenuItem_actionPerformed(null);
2988           sg = viewport.getSelectionGroup();
2989           toggleSeqs = true;
2990
2991         }
2992         viewport.expandColSelection(sg, true);
2993         // finally invert the column selection and get the new sequence
2994         // selection.
2995         invertColSel_actionPerformed(null);
2996         toggleCols = true;
2997       }
2998     }
2999
3000     if (toggleSeqs)
3001     {
3002       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3003       {
3004         hideSelSequences_actionPerformed(null);
3005         hide = true;
3006       }
3007       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3008               .size() > 0))
3009       {
3010         showAllSeqs_actionPerformed(null);
3011       }
3012     }
3013
3014     if (toggleCols)
3015     {
3016       if (viewport.getColumnSelection().getSelected().size() > 0)
3017       {
3018         hideSelColumns_actionPerformed(null);
3019         if (!toggleSeqs)
3020         {
3021           viewport.setSelectionGroup(sg);
3022         }
3023       }
3024       else if (!hide)
3025       {
3026         showAllColumns_actionPerformed(null);
3027       }
3028     }
3029   }
3030
3031   /*
3032    * (non-Javadoc)
3033    *
3034    * @see
3035    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3036    * event.ActionEvent)
3037    */
3038   @Override
3039   public void hideAllButSelection_actionPerformed(ActionEvent e)
3040   {
3041     toggleHiddenRegions(false, false);
3042     viewport.sendSelection();
3043   }
3044
3045   /*
3046    * (non-Javadoc)
3047    *
3048    * @see
3049    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3050    * .ActionEvent)
3051    */
3052   @Override
3053   public void hideAllSelection_actionPerformed(ActionEvent e)
3054   {
3055     SequenceGroup sg = viewport.getSelectionGroup();
3056     viewport.expandColSelection(sg, false);
3057     viewport.hideAllSelectedSeqs();
3058     viewport.hideSelectedColumns();
3059     alignPanel.paintAlignment(true);
3060     viewport.sendSelection();
3061   }
3062
3063   /*
3064    * (non-Javadoc)
3065    *
3066    * @see
3067    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3068    * ActionEvent)
3069    */
3070   @Override
3071   public void showAllhidden_actionPerformed(ActionEvent e)
3072   {
3073     viewport.showAllHiddenColumns();
3074     viewport.showAllHiddenSeqs();
3075     alignPanel.paintAlignment(true);
3076     viewport.sendSelection();
3077   }
3078
3079   @Override
3080   public void hideSelColumns_actionPerformed(ActionEvent e)
3081   {
3082     viewport.hideSelectedColumns();
3083     alignPanel.paintAlignment(true);
3084     viewport.sendSelection();
3085   }
3086
3087   @Override
3088   public void hiddenMarkers_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3091     repaint();
3092   }
3093
3094   /**
3095    * DOCUMENT ME!
3096    *
3097    * @param e
3098    *          DOCUMENT ME!
3099    */
3100   @Override
3101   protected void scaleAbove_actionPerformed(ActionEvent e)
3102   {
3103     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3104     alignPanel.paintAlignment(true);
3105   }
3106
3107   /**
3108    * DOCUMENT ME!
3109    *
3110    * @param e
3111    *          DOCUMENT ME!
3112    */
3113   @Override
3114   protected void scaleLeft_actionPerformed(ActionEvent e)
3115   {
3116     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3117     alignPanel.paintAlignment(true);
3118   }
3119
3120   /**
3121    * DOCUMENT ME!
3122    *
3123    * @param e
3124    *          DOCUMENT ME!
3125    */
3126   @Override
3127   protected void scaleRight_actionPerformed(ActionEvent e)
3128   {
3129     viewport.setScaleRightWrapped(scaleRight.isSelected());
3130     alignPanel.paintAlignment(true);
3131   }
3132
3133   /**
3134    * DOCUMENT ME!
3135    *
3136    * @param e
3137    *          DOCUMENT ME!
3138    */
3139   @Override
3140   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3141   {
3142     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3143     alignPanel.paintAlignment(true);
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setShowText(viewTextMenuItem.isSelected());
3156     alignPanel.paintAlignment(true);
3157   }
3158
3159   /**
3160    * DOCUMENT ME!
3161    *
3162    * @param e
3163    *          DOCUMENT ME!
3164    */
3165   @Override
3166   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3167   {
3168     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3169     alignPanel.paintAlignment(true);
3170   }
3171
3172   public FeatureSettings featureSettings;
3173
3174   @Override
3175   public FeatureSettingsControllerI getFeatureSettingsUI()
3176   {
3177     return featureSettings;
3178   }
3179
3180   @Override
3181   public void featureSettings_actionPerformed(ActionEvent e)
3182   {
3183     if (featureSettings != null)
3184     {
3185       featureSettings.close();
3186       featureSettings = null;
3187     }
3188     if (!showSeqFeatures.isSelected())
3189     {
3190       // make sure features are actually displayed
3191       showSeqFeatures.setSelected(true);
3192       showSeqFeatures_actionPerformed(null);
3193     }
3194     featureSettings = new FeatureSettings(this);
3195   }
3196
3197   /**
3198    * Set or clear 'Show Sequence Features'
3199    *
3200    * @param evt
3201    *          DOCUMENT ME!
3202    */
3203   @Override
3204   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3205   {
3206     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3207     alignPanel.paintAlignment(true);
3208     if (alignPanel.getOverviewPanel() != null)
3209     {
3210       alignPanel.getOverviewPanel().updateOverviewImage();
3211     }
3212   }
3213
3214   /**
3215    * Set or clear 'Show Sequence Features'
3216    *
3217    * @param evt
3218    *          DOCUMENT ME!
3219    */
3220   @Override
3221   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3222   {
3223     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3224             .isSelected());
3225     if (viewport.isShowSequenceFeaturesHeight())
3226     {
3227       // ensure we're actually displaying features
3228       viewport.setShowSequenceFeatures(true);
3229       showSeqFeatures.setSelected(true);
3230     }
3231     alignPanel.paintAlignment(true);
3232     if (alignPanel.getOverviewPanel() != null)
3233     {
3234       alignPanel.getOverviewPanel().updateOverviewImage();
3235     }
3236   }
3237
3238   /**
3239    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3240    * the annotations panel as a whole.
3241    *
3242    * The options to show/hide all annotations should be enabled when the panel
3243    * is shown, and disabled when the panel is hidden.
3244    *
3245    * @param e
3246    */
3247   @Override
3248   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3249   {
3250     final boolean setVisible = annotationPanelMenuItem.isSelected();
3251     viewport.setShowAnnotation(setVisible);
3252     this.showAllSeqAnnotations.setEnabled(setVisible);
3253     this.hideAllSeqAnnotations.setEnabled(setVisible);
3254     this.showAllAlAnnotations.setEnabled(setVisible);
3255     this.hideAllAlAnnotations.setEnabled(setVisible);
3256     alignPanel.updateLayout();
3257   }
3258
3259   @Override
3260   public void alignmentProperties()
3261   {
3262     JEditorPane editPane = new JEditorPane("text/html", "");
3263     editPane.setEditable(false);
3264     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3265             .formatAsHtml();
3266     editPane.setText(MessageManager.formatMessage("label.html_content",
3267             new Object[] { contents.toString() }));
3268     JInternalFrame frame = new JInternalFrame();
3269     frame.getContentPane().add(new JScrollPane(editPane));
3270
3271     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3272             "label.alignment_properties", new Object[] { getTitle() }),
3273             500, 400);
3274   }
3275
3276   /**
3277    * DOCUMENT ME!
3278    *
3279    * @param e
3280    *          DOCUMENT ME!
3281    */
3282   @Override
3283   public void overviewMenuItem_actionPerformed(ActionEvent e)
3284   {
3285     if (alignPanel.overviewPanel != null)
3286     {
3287       return;
3288     }
3289
3290     JInternalFrame frame = new JInternalFrame();
3291     OverviewPanel overview = new OverviewPanel(alignPanel);
3292     frame.setContentPane(overview);
3293     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3294             "label.overview_params", new Object[] { this.getTitle() }),
3295             frame.getWidth(), frame.getHeight());
3296     frame.pack();
3297     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3298     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3299     {
3300       @Override
3301       public void internalFrameClosed(
3302               javax.swing.event.InternalFrameEvent evt)
3303       {
3304         alignPanel.setOverviewPanel(null);
3305       };
3306     });
3307
3308     alignPanel.setOverviewPanel(overview);
3309   }
3310
3311   @Override
3312   public void textColour_actionPerformed(ActionEvent e)
3313   {
3314     new TextColourChooser().chooseColour(alignPanel, null);
3315   }
3316
3317   /**
3318    * DOCUMENT ME!
3319    *
3320    * @param e
3321    *          DOCUMENT ME!
3322    */
3323   @Override
3324   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3325   {
3326     changeColour(null);
3327   }
3328
3329   /**
3330    * DOCUMENT ME!
3331    *
3332    * @param e
3333    *          DOCUMENT ME!
3334    */
3335   @Override
3336   public void clustalColour_actionPerformed(ActionEvent e)
3337   {
3338     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3339             viewport.getHiddenRepSequences()));
3340   }
3341
3342   /**
3343    * DOCUMENT ME!
3344    *
3345    * @param e
3346    *          DOCUMENT ME!
3347    */
3348   @Override
3349   public void zappoColour_actionPerformed(ActionEvent e)
3350   {
3351     changeColour(new ZappoColourScheme());
3352   }
3353
3354   /**
3355    * DOCUMENT ME!
3356    *
3357    * @param e
3358    *          DOCUMENT ME!
3359    */
3360   @Override
3361   public void taylorColour_actionPerformed(ActionEvent e)
3362   {
3363     changeColour(new TaylorColourScheme());
3364   }
3365
3366   /**
3367    * DOCUMENT ME!
3368    *
3369    * @param e
3370    *          DOCUMENT ME!
3371    */
3372   @Override
3373   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3374   {
3375     changeColour(new HydrophobicColourScheme());
3376   }
3377
3378   /**
3379    * DOCUMENT ME!
3380    *
3381    * @param e
3382    *          DOCUMENT ME!
3383    */
3384   @Override
3385   public void helixColour_actionPerformed(ActionEvent e)
3386   {
3387     changeColour(new HelixColourScheme());
3388   }
3389
3390   /**
3391    * DOCUMENT ME!
3392    *
3393    * @param e
3394    *          DOCUMENT ME!
3395    */
3396   @Override
3397   public void strandColour_actionPerformed(ActionEvent e)
3398   {
3399     changeColour(new StrandColourScheme());
3400   }
3401
3402   /**
3403    * DOCUMENT ME!
3404    *
3405    * @param e
3406    *          DOCUMENT ME!
3407    */
3408   @Override
3409   public void turnColour_actionPerformed(ActionEvent e)
3410   {
3411     changeColour(new TurnColourScheme());
3412   }
3413
3414   /**
3415    * DOCUMENT ME!
3416    *
3417    * @param e
3418    *          DOCUMENT ME!
3419    */
3420   @Override
3421   public void buriedColour_actionPerformed(ActionEvent e)
3422   {
3423     changeColour(new BuriedColourScheme());
3424   }
3425
3426   /**
3427    * DOCUMENT ME!
3428    *
3429    * @param e
3430    *          DOCUMENT ME!
3431    */
3432   @Override
3433   public void nucleotideColour_actionPerformed(ActionEvent e)
3434   {
3435     changeColour(new NucleotideColourScheme());
3436   }
3437
3438   @Override
3439   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3440   {
3441     changeColour(new PurinePyrimidineColourScheme());
3442   }
3443
3444   /*
3445    * public void covariationColour_actionPerformed(ActionEvent e) {
3446    * changeColour(new
3447    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3448    * ()[0])); }
3449    */
3450   @Override
3451   public void annotationColour_actionPerformed(ActionEvent e)
3452   {
3453     new AnnotationColourChooser(viewport, alignPanel);
3454   }
3455
3456   @Override
3457   public void annotationColumn_actionPerformed(ActionEvent e)
3458   {
3459     new AnnotationColumnChooser(viewport, alignPanel);
3460   }
3461
3462   @Override
3463   public void rnahelicesColour_actionPerformed(ActionEvent e)
3464   {
3465     new RNAHelicesColourChooser(viewport, alignPanel);
3466   }
3467
3468   /**
3469    * DOCUMENT ME!
3470    *
3471    * @param e
3472    *          DOCUMENT ME!
3473    */
3474   @Override
3475   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3476   {
3477     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3478   }
3479
3480   /**
3481    * DOCUMENT ME!
3482    *
3483    * @param cs
3484    *          DOCUMENT ME!
3485    */
3486   @Override
3487   public void changeColour(ColourSchemeI cs)
3488   {
3489     // TODO: pull up to controller method
3490
3491     if (cs != null)
3492     {
3493       // Make sure viewport is up to date w.r.t. any sliders
3494       if (viewport.getAbovePIDThreshold())
3495       {
3496         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3497                 "Background");
3498         viewport.setThreshold(threshold);
3499       }
3500
3501       if (viewport.getConservationSelected())
3502       {
3503         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3504                 cs, "Background"));
3505       }
3506       if (cs instanceof TCoffeeColourScheme)
3507       {
3508         tcoffeeColour.setEnabled(true);
3509         tcoffeeColour.setSelected(true);
3510       }
3511     }
3512
3513     viewport.setGlobalColourScheme(cs);
3514
3515     alignPanel.paintAlignment(true);
3516   }
3517
3518   /**
3519    * DOCUMENT ME!
3520    *
3521    * @param e
3522    *          DOCUMENT ME!
3523    */
3524   @Override
3525   protected void modifyPID_actionPerformed(ActionEvent e)
3526   {
3527     if (viewport.getAbovePIDThreshold()
3528             && viewport.getGlobalColourScheme() != null)
3529     {
3530       SliderPanel.setPIDSliderSource(alignPanel,
3531               viewport.getGlobalColourScheme(), "Background");
3532       SliderPanel.showPIDSlider();
3533     }
3534   }
3535
3536   /**
3537    * DOCUMENT ME!
3538    *
3539    * @param e
3540    *          DOCUMENT ME!
3541    */
3542   @Override
3543   protected void modifyConservation_actionPerformed(ActionEvent e)
3544   {
3545     if (viewport.getConservationSelected()
3546             && viewport.getGlobalColourScheme() != null)
3547     {
3548       SliderPanel.setConservationSlider(alignPanel,
3549               viewport.getGlobalColourScheme(), "Background");
3550       SliderPanel.showConservationSlider();
3551     }
3552   }
3553
3554   /**
3555    * DOCUMENT ME!
3556    *
3557    * @param e
3558    *          DOCUMENT ME!
3559    */
3560   @Override
3561   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3562   {
3563     viewport.setConservationSelected(conservationMenuItem.isSelected());
3564
3565     viewport.setAbovePIDThreshold(false);
3566     abovePIDThreshold.setSelected(false);
3567
3568     changeColour(viewport.getGlobalColourScheme());
3569
3570     modifyConservation_actionPerformed(null);
3571   }
3572
3573   /**
3574    * DOCUMENT ME!
3575    *
3576    * @param e
3577    *          DOCUMENT ME!
3578    */
3579   @Override
3580   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3581   {
3582     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3583
3584     conservationMenuItem.setSelected(false);
3585     viewport.setConservationSelected(false);
3586
3587     changeColour(viewport.getGlobalColourScheme());
3588
3589     modifyPID_actionPerformed(null);
3590   }
3591
3592   /**
3593    * DOCUMENT ME!
3594    *
3595    * @param e
3596    *          DOCUMENT ME!
3597    */
3598   @Override
3599   public void userDefinedColour_actionPerformed(ActionEvent e)
3600   {
3601     if (e.getActionCommand().equals(
3602             MessageManager.getString("action.user_defined")))
3603     {
3604       new UserDefinedColours(alignPanel, null);
3605     }
3606     else
3607     {
3608       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3609               .getUserColourSchemes().get(e.getActionCommand());
3610
3611       changeColour(udc);
3612     }
3613   }
3614
3615   public void updateUserColourMenu()
3616   {
3617
3618     Component[] menuItems = colourMenu.getMenuComponents();
3619     int iSize = menuItems.length;
3620     for (int i = 0; i < iSize; i++)
3621     {
3622       if (menuItems[i].getName() != null
3623               && menuItems[i].getName().equals("USER_DEFINED"))
3624       {
3625         colourMenu.remove(menuItems[i]);
3626         iSize--;
3627       }
3628     }
3629     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3630     {
3631       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3632               .getUserColourSchemes().keys();
3633
3634       while (userColours.hasMoreElements())
3635       {
3636         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3637                 userColours.nextElement().toString());
3638         radioItem.setName("USER_DEFINED");
3639         radioItem.addMouseListener(new MouseAdapter()
3640         {
3641           @Override
3642           public void mousePressed(MouseEvent evt)
3643           {
3644             if (evt.isPopupTrigger())
3645             {
3646               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3647
3648               int option = JOptionPane.showInternalConfirmDialog(
3649                       jalview.gui.Desktop.desktop,
3650                       MessageManager
3651                               .getString("label.remove_from_default_list"),
3652                       MessageManager
3653                               .getString("label.remove_user_defined_colour"),
3654                       JOptionPane.YES_NO_OPTION);
3655               if (option == JOptionPane.YES_OPTION)
3656               {
3657                 jalview.gui.UserDefinedColours
3658                         .removeColourFromDefaults(radioItem.getText());
3659                 colourMenu.remove(radioItem);
3660               }
3661               else
3662               {
3663                 radioItem.addActionListener(new ActionListener()
3664                 {
3665                   @Override
3666                   public void actionPerformed(ActionEvent evt)
3667                   {
3668                     userDefinedColour_actionPerformed(evt);
3669                   }
3670                 });
3671               }
3672             }
3673           }
3674         });
3675         radioItem.addActionListener(new ActionListener()
3676         {
3677           @Override
3678           public void actionPerformed(ActionEvent evt)
3679           {
3680             userDefinedColour_actionPerformed(evt);
3681           }
3682         });
3683
3684         colourMenu.insert(radioItem, 15);
3685         colours.add(radioItem);
3686       }
3687     }
3688   }
3689
3690   /**
3691    * DOCUMENT ME!
3692    *
3693    * @param e
3694    *          DOCUMENT ME!
3695    */
3696   @Override
3697   public void PIDColour_actionPerformed(ActionEvent e)
3698   {
3699     changeColour(new PIDColourScheme());
3700   }
3701
3702   /**
3703    * DOCUMENT ME!
3704    *
3705    * @param e
3706    *          DOCUMENT ME!
3707    */
3708   @Override
3709   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3710   {
3711     changeColour(new Blosum62ColourScheme());
3712   }
3713
3714   /**
3715    * DOCUMENT ME!
3716    *
3717    * @param e
3718    *          DOCUMENT ME!
3719    */
3720   @Override
3721   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3722   {
3723     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3724     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3725             .getAlignment().getSequenceAt(0), null);
3726     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3727             viewport.getAlignment()));
3728     alignPanel.paintAlignment(true);
3729   }
3730
3731   /**
3732    * DOCUMENT ME!
3733    *
3734    * @param e
3735    *          DOCUMENT ME!
3736    */
3737   @Override
3738   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3739   {
3740     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3741     AlignmentSorter.sortByID(viewport.getAlignment());
3742     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3743             viewport.getAlignment()));
3744     alignPanel.paintAlignment(true);
3745   }
3746
3747   /**
3748    * DOCUMENT ME!
3749    *
3750    * @param e
3751    *          DOCUMENT ME!
3752    */
3753   @Override
3754   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3755   {
3756     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3757     AlignmentSorter.sortByLength(viewport.getAlignment());
3758     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3759             viewport.getAlignment()));
3760     alignPanel.paintAlignment(true);
3761   }
3762
3763   /**
3764    * DOCUMENT ME!
3765    *
3766    * @param e
3767    *          DOCUMENT ME!
3768    */
3769   @Override
3770   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3771   {
3772     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3773     AlignmentSorter.sortByGroup(viewport.getAlignment());
3774     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3775             viewport.getAlignment()));
3776
3777     alignPanel.paintAlignment(true);
3778   }
3779
3780   /**
3781    * DOCUMENT ME!
3782    *
3783    * @param e
3784    *          DOCUMENT ME!
3785    */
3786   @Override
3787   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3788   {
3789     new RedundancyPanel(alignPanel, this);
3790   }
3791
3792   /**
3793    * DOCUMENT ME!
3794    *
3795    * @param e
3796    *          DOCUMENT ME!
3797    */
3798   @Override
3799   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3800   {
3801     if ((viewport.getSelectionGroup() == null)
3802             || (viewport.getSelectionGroup().getSize() < 2))
3803     {
3804       JOptionPane.showInternalMessageDialog(this, MessageManager
3805               .getString("label.you_must_select_least_two_sequences"),
3806               MessageManager.getString("label.invalid_selection"),
3807               JOptionPane.WARNING_MESSAGE);
3808     }
3809     else
3810     {
3811       JInternalFrame frame = new JInternalFrame();
3812       frame.setContentPane(new PairwiseAlignPanel(viewport));
3813       Desktop.addInternalFrame(frame,
3814               MessageManager.getString("action.pairwise_alignment"), 600,
3815               500);
3816     }
3817   }
3818
3819   /**
3820    * DOCUMENT ME!
3821    *
3822    * @param e
3823    *          DOCUMENT ME!
3824    */
3825   @Override
3826   public void PCAMenuItem_actionPerformed(ActionEvent e)
3827   {
3828     if (((viewport.getSelectionGroup() != null)
3829             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3830             .getSelectionGroup().getSize() > 0))
3831             || (viewport.getAlignment().getHeight() < 4))
3832     {
3833       JOptionPane
3834               .showInternalMessageDialog(
3835                       this,
3836                       MessageManager
3837                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3838                       MessageManager
3839                               .getString("label.sequence_selection_insufficient"),
3840                       JOptionPane.WARNING_MESSAGE);
3841
3842       return;
3843     }
3844
3845     new PCAPanel(alignPanel);
3846   }
3847
3848   @Override
3849   public void autoCalculate_actionPerformed(ActionEvent e)
3850   {
3851     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3852     if (viewport.autoCalculateConsensus)
3853     {
3854       viewport.firePropertyChange("alignment", null, viewport
3855               .getAlignment().getSequences());
3856     }
3857   }
3858
3859   @Override
3860   public void sortByTreeOption_actionPerformed(ActionEvent e)
3861   {
3862     viewport.sortByTree = sortByTree.isSelected();
3863   }
3864
3865   @Override
3866   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3867   {
3868     viewport.followSelection = listenToViewSelections.isSelected();
3869   }
3870
3871   /**
3872    * DOCUMENT ME!
3873    *
3874    * @param e
3875    *          DOCUMENT ME!
3876    */
3877   @Override
3878   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3879   {
3880     newTreePanel("AV", "PID", "Average distance tree using PID");
3881   }
3882
3883   /**
3884    * DOCUMENT ME!
3885    *
3886    * @param e
3887    *          DOCUMENT ME!
3888    */
3889   @Override
3890   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3891   {
3892     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3893   }
3894
3895   /**
3896    * DOCUMENT ME!
3897    *
3898    * @param e
3899    *          DOCUMENT ME!
3900    */
3901   @Override
3902   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3903   {
3904     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3905   }
3906
3907   /**
3908    * DOCUMENT ME!
3909    *
3910    * @param e
3911    *          DOCUMENT ME!
3912    */
3913   @Override
3914   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3915   {
3916     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3917   }
3918
3919   /**
3920    * DOCUMENT ME!
3921    *
3922    * @param type
3923    *          DOCUMENT ME!
3924    * @param pwType
3925    *          DOCUMENT ME!
3926    * @param title
3927    *          DOCUMENT ME!
3928    */
3929   void newTreePanel(String type, String pwType, String title)
3930   {
3931     TreePanel tp;
3932
3933     if (viewport.getSelectionGroup() != null
3934             && viewport.getSelectionGroup().getSize() > 0)
3935     {
3936       if (viewport.getSelectionGroup().getSize() < 3)
3937       {
3938         JOptionPane
3939                 .showMessageDialog(
3940                         Desktop.desktop,
3941                         MessageManager
3942                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3943                         MessageManager
3944                                 .getString("label.not_enough_sequences"),
3945                         JOptionPane.WARNING_MESSAGE);
3946         return;
3947       }
3948
3949       SequenceGroup sg = viewport.getSelectionGroup();
3950
3951       /* Decide if the selection is a column region */
3952       for (SequenceI _s : sg.getSequences())
3953       {
3954         if (_s.getLength() < sg.getEndRes())
3955         {
3956           JOptionPane
3957                   .showMessageDialog(
3958                           Desktop.desktop,
3959                           MessageManager
3960                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3961                           MessageManager
3962                                   .getString("label.sequences_selection_not_aligned"),
3963                           JOptionPane.WARNING_MESSAGE);
3964
3965           return;
3966         }
3967       }
3968
3969       title = title + " on region";
3970       tp = new TreePanel(alignPanel, type, pwType);
3971     }
3972     else
3973     {
3974       // are the visible sequences aligned?
3975       if (!viewport.getAlignment().isAligned(false))
3976       {
3977         JOptionPane
3978                 .showMessageDialog(
3979                         Desktop.desktop,
3980                         MessageManager
3981                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3982                         MessageManager
3983                                 .getString("label.sequences_not_aligned"),
3984                         JOptionPane.WARNING_MESSAGE);
3985
3986         return;
3987       }
3988
3989       if (viewport.getAlignment().getHeight() < 2)
3990       {
3991         return;
3992       }
3993
3994       tp = new TreePanel(alignPanel, type, pwType);
3995     }
3996
3997     title += " from ";
3998
3999     if (viewport.viewName != null)
4000     {
4001       title += viewport.viewName + " of ";
4002     }
4003
4004     title += this.title;
4005
4006     Desktop.addInternalFrame(tp, title, 600, 500);
4007   }
4008
4009   /**
4010    * DOCUMENT ME!
4011    *
4012    * @param title
4013    *          DOCUMENT ME!
4014    * @param order
4015    *          DOCUMENT ME!
4016    */
4017   public void addSortByOrderMenuItem(String title,
4018           final AlignmentOrder order)
4019   {
4020     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4021             "action.by_title_param", new Object[] { title }));
4022     sort.add(item);
4023     item.addActionListener(new java.awt.event.ActionListener()
4024     {
4025       @Override
4026       public void actionPerformed(ActionEvent e)
4027       {
4028         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4029
4030         // TODO: JBPNote - have to map order entries to curent SequenceI
4031         // pointers
4032         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4033
4034         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4035                 .getAlignment()));
4036
4037         alignPanel.paintAlignment(true);
4038       }
4039     });
4040   }
4041
4042   /**
4043    * Add a new sort by annotation score menu item
4044    *
4045    * @param sort
4046    *          the menu to add the option to
4047    * @param scoreLabel
4048    *          the label used to retrieve scores for each sequence on the
4049    *          alignment
4050    */
4051   public void addSortByAnnotScoreMenuItem(JMenu sort,
4052           final String scoreLabel)
4053   {
4054     final JMenuItem item = new JMenuItem(scoreLabel);
4055     sort.add(item);
4056     item.addActionListener(new java.awt.event.ActionListener()
4057     {
4058       @Override
4059       public void actionPerformed(ActionEvent e)
4060       {
4061         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4062         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4063                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4064         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4065                 viewport.getAlignment()));
4066         alignPanel.paintAlignment(true);
4067       }
4068     });
4069   }
4070
4071   /**
4072    * last hash for alignment's annotation array - used to minimise cost of
4073    * rebuild.
4074    */
4075   protected int _annotationScoreVectorHash;
4076
4077   /**
4078    * search the alignment and rebuild the sort by annotation score submenu the
4079    * last alignment annotation vector hash is stored to minimize cost of
4080    * rebuilding in subsequence calls.
4081    *
4082    */
4083   @Override
4084   public void buildSortByAnnotationScoresMenu()
4085   {
4086     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4087     {
4088       return;
4089     }
4090
4091     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4092     {
4093       sortByAnnotScore.removeAll();
4094       // almost certainly a quicker way to do this - but we keep it simple
4095       Hashtable scoreSorts = new Hashtable();
4096       AlignmentAnnotation aann[];
4097       for (SequenceI sqa : viewport.getAlignment().getSequences())
4098       {
4099         aann = sqa.getAnnotation();
4100         for (int i = 0; aann != null && i < aann.length; i++)
4101         {
4102           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4103           {
4104             scoreSorts.put(aann[i].label, aann[i].label);
4105           }
4106         }
4107       }
4108       Enumeration labels = scoreSorts.keys();
4109       while (labels.hasMoreElements())
4110       {
4111         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4112                 (String) labels.nextElement());
4113       }
4114       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4115       scoreSorts.clear();
4116
4117       _annotationScoreVectorHash = viewport.getAlignment()
4118               .getAlignmentAnnotation().hashCode();
4119     }
4120   }
4121
4122   /**
4123    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4124    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4125    * call. Listeners are added to remove the menu item when the treePanel is
4126    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4127    * modified.
4128    *
4129    * @param treePanel
4130    *          Displayed tree window.
4131    * @param title
4132    *          SortBy menu item title.
4133    */
4134   @Override
4135   public void buildTreeMenu()
4136   {
4137     calculateTree.removeAll();
4138     // build the calculate menu
4139
4140     for (final String type : new String[] { "NJ", "AV" })
4141     {
4142       String treecalcnm = MessageManager.getString("label.tree_calc_"
4143               + type.toLowerCase());
4144       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4145       {
4146         JMenuItem tm = new JMenuItem();
4147         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4148         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4149                 || sm.isProtein() == !viewport.getAlignment()
4150                         .isNucleotide())
4151         {
4152           String smn = MessageManager.getStringOrReturn(
4153                   "label.score_model_", sm.getName());
4154           final String title = MessageManager.formatMessage(
4155                   "label.treecalc_title", treecalcnm, smn);
4156           tm.setText(title);//
4157           tm.addActionListener(new java.awt.event.ActionListener()
4158           {
4159             @Override
4160             public void actionPerformed(ActionEvent e)
4161             {
4162               newTreePanel(type, pwtype, title);
4163             }
4164           });
4165           calculateTree.add(tm);
4166         }
4167
4168       }
4169     }
4170     sortByTreeMenu.removeAll();
4171
4172     List<Component> comps = PaintRefresher.components.get(viewport
4173             .getSequenceSetId());
4174     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4175     for (Component comp : comps)
4176     {
4177       if (comp instanceof TreePanel)
4178       {
4179         treePanels.add((TreePanel) comp);
4180       }
4181     }
4182
4183     if (treePanels.size() < 1)
4184     {
4185       sortByTreeMenu.setVisible(false);
4186       return;
4187     }
4188
4189     sortByTreeMenu.setVisible(true);
4190
4191     for (final TreePanel tp : treePanels)
4192     {
4193       final JMenuItem item = new JMenuItem(tp.getTitle());
4194       item.addActionListener(new java.awt.event.ActionListener()
4195       {
4196         @Override
4197         public void actionPerformed(ActionEvent e)
4198         {
4199           tp.sortByTree_actionPerformed();
4200           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4201
4202         }
4203       });
4204
4205       sortByTreeMenu.add(item);
4206     }
4207   }
4208
4209   public boolean sortBy(AlignmentOrder alorder, String undoname)
4210   {
4211     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4212     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4213     if (undoname != null)
4214     {
4215       addHistoryItem(new OrderCommand(undoname, oldOrder,
4216               viewport.getAlignment()));
4217     }
4218     alignPanel.paintAlignment(true);
4219     return true;
4220   }
4221
4222   /**
4223    * Work out whether the whole set of sequences or just the selected set will
4224    * be submitted for multiple alignment.
4225    *
4226    */
4227   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4228   {
4229     // Now, check we have enough sequences
4230     AlignmentView msa = null;
4231
4232     if ((viewport.getSelectionGroup() != null)
4233             && (viewport.getSelectionGroup().getSize() > 1))
4234     {
4235       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4236       // some common interface!
4237       /*
4238        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4239        * SequenceI[sz = seqs.getSize(false)];
4240        *
4241        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4242        * seqs.getSequenceAt(i); }
4243        */
4244       msa = viewport.getAlignmentView(true);
4245     }
4246     else if (viewport.getSelectionGroup() != null
4247             && viewport.getSelectionGroup().getSize() == 1)
4248     {
4249       int option = JOptionPane.showConfirmDialog(this,
4250               MessageManager.getString("warn.oneseq_msainput_selection"),
4251               MessageManager.getString("label.invalid_selection"),
4252               JOptionPane.OK_CANCEL_OPTION);
4253       if (option == JOptionPane.OK_OPTION)
4254       {
4255         msa = viewport.getAlignmentView(false);
4256       }
4257     }
4258     else
4259     {
4260       msa = viewport.getAlignmentView(false);
4261     }
4262     return msa;
4263   }
4264
4265   /**
4266    * Decides what is submitted to a secondary structure prediction service: the
4267    * first sequence in the alignment, or in the current selection, or, if the
4268    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4269    * region or the whole alignment. (where the first sequence in the set is the
4270    * one that the prediction will be for).
4271    */
4272   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4273   {
4274     AlignmentView seqs = null;
4275
4276     if ((viewport.getSelectionGroup() != null)
4277             && (viewport.getSelectionGroup().getSize() > 0))
4278     {
4279       seqs = viewport.getAlignmentView(true);
4280     }
4281     else
4282     {
4283       seqs = viewport.getAlignmentView(false);
4284     }
4285     // limit sequences - JBPNote in future - could spawn multiple prediction
4286     // jobs
4287     // TODO: viewport.getAlignment().isAligned is a global state - the local
4288     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4289     if (!viewport.getAlignment().isAligned(false))
4290     {
4291       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4292       // TODO: if seqs.getSequences().length>1 then should really have warned
4293       // user!
4294
4295     }
4296     return seqs;
4297   }
4298
4299   /**
4300    * DOCUMENT ME!
4301    *
4302    * @param e
4303    *          DOCUMENT ME!
4304    */
4305   @Override
4306   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4307   {
4308     // Pick the tree file
4309     JalviewFileChooser chooser = new JalviewFileChooser(
4310             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4311     chooser.setFileView(new JalviewFileView());
4312     chooser.setDialogTitle(MessageManager
4313             .getString("label.select_newick_like_tree_file"));
4314     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4315
4316     int value = chooser.showOpenDialog(null);
4317
4318     if (value == JalviewFileChooser.APPROVE_OPTION)
4319     {
4320       String choice = chooser.getSelectedFile().getPath();
4321       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4322       jalview.io.NewickFile fin = null;
4323       try
4324       {
4325         fin = new jalview.io.NewickFile(choice, "File");
4326         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4327       } catch (Exception ex)
4328       {
4329         JOptionPane
4330                 .showMessageDialog(
4331                         Desktop.desktop,
4332                         ex.getMessage(),
4333                         MessageManager
4334                                 .getString("label.problem_reading_tree_file"),
4335                         JOptionPane.WARNING_MESSAGE);
4336         ex.printStackTrace();
4337       }
4338       if (fin != null && fin.hasWarningMessage())
4339       {
4340         JOptionPane.showMessageDialog(Desktop.desktop, fin
4341                 .getWarningMessage(), MessageManager
4342                 .getString("label.possible_problem_with_tree_file"),
4343                 JOptionPane.WARNING_MESSAGE);
4344       }
4345     }
4346   }
4347
4348   @Override
4349   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4350   {
4351     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4352   }
4353
4354   public TreePanel ShowNewickTree(NewickFile nf, String title)
4355   {
4356     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4357   }
4358
4359   public TreePanel ShowNewickTree(NewickFile nf, String title,
4360           AlignmentView input)
4361   {
4362     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4363   }
4364
4365   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4366           int h, int x, int y)
4367   {
4368     return ShowNewickTree(nf, title, null, w, h, x, y);
4369   }
4370
4371   /**
4372    * Add a treeviewer for the tree extracted from a newick file object to the
4373    * current alignment view
4374    *
4375    * @param nf
4376    *          the tree
4377    * @param title
4378    *          tree viewer title
4379    * @param input
4380    *          Associated alignment input data (or null)
4381    * @param w
4382    *          width
4383    * @param h
4384    *          height
4385    * @param x
4386    *          position
4387    * @param y
4388    *          position
4389    * @return TreePanel handle
4390    */
4391   public TreePanel ShowNewickTree(NewickFile nf, String title,
4392           AlignmentView input, int w, int h, int x, int y)
4393   {
4394     TreePanel tp = null;
4395
4396     try
4397     {
4398       nf.parse();
4399
4400       if (nf.getTree() != null)
4401       {
4402         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4403
4404         tp.setSize(w, h);
4405
4406         if (x > 0 && y > 0)
4407         {
4408           tp.setLocation(x, y);
4409         }
4410
4411         Desktop.addInternalFrame(tp, title, w, h);
4412       }
4413     } catch (Exception ex)
4414     {
4415       ex.printStackTrace();
4416     }
4417
4418     return tp;
4419   }
4420
4421   private boolean buildingMenu = false;
4422
4423   /**
4424    * Generates menu items and listener event actions for web service clients
4425    *
4426    */
4427   public void BuildWebServiceMenu()
4428   {
4429     while (buildingMenu)
4430     {
4431       try
4432       {
4433         System.err.println("Waiting for building menu to finish.");
4434         Thread.sleep(10);
4435       } catch (Exception e)
4436       {
4437       }
4438     }
4439     final AlignFrame me = this;
4440     buildingMenu = true;
4441     new Thread(new Runnable()
4442     {
4443       @Override
4444       public void run()
4445       {
4446         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4447         try
4448         {
4449           // System.err.println("Building ws menu again "
4450           // + Thread.currentThread());
4451           // TODO: add support for context dependent disabling of services based
4452           // on
4453           // alignment and current selection
4454           // TODO: add additional serviceHandle parameter to specify abstract
4455           // handler
4456           // class independently of AbstractName
4457           // TODO: add in rediscovery GUI function to restart discoverer
4458           // TODO: group services by location as well as function and/or
4459           // introduce
4460           // object broker mechanism.
4461           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4462           final IProgressIndicator af = me;
4463           final JMenu msawsmenu = new JMenu("Alignment");
4464           final JMenu secstrmenu = new JMenu(
4465                   "Secondary Structure Prediction");
4466           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4467           final JMenu analymenu = new JMenu("Analysis");
4468           final JMenu dismenu = new JMenu("Protein Disorder");
4469           // final JMenu msawsmenu = new
4470           // JMenu(MessageManager.getString("label.alignment"));
4471           // final JMenu secstrmenu = new
4472           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4473           // final JMenu seqsrchmenu = new
4474           // JMenu(MessageManager.getString("label.sequence_database_search"));
4475           // final JMenu analymenu = new
4476           // JMenu(MessageManager.getString("label.analysis"));
4477           // final JMenu dismenu = new
4478           // JMenu(MessageManager.getString("label.protein_disorder"));
4479           // JAL-940 - only show secondary structure prediction services from
4480           // the legacy server
4481           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4482               // &&
4483           Discoverer.services != null && (Discoverer.services.size() > 0))
4484           {
4485             // TODO: refactor to allow list of AbstractName/Handler bindings to
4486             // be
4487             // stored or retrieved from elsewhere
4488             // No MSAWS used any more:
4489             // Vector msaws = null; // (Vector)
4490             // Discoverer.services.get("MsaWS");
4491             Vector secstrpr = (Vector) Discoverer.services
4492                     .get("SecStrPred");
4493             if (secstrpr != null)
4494             {
4495               // Add any secondary structure prediction services
4496               for (int i = 0, j = secstrpr.size(); i < j; i++)
4497               {
4498                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4499                         .get(i);
4500                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4501                         .getServiceClient(sh);
4502                 int p = secstrmenu.getItemCount();
4503                 impl.attachWSMenuEntry(secstrmenu, me);
4504                 int q = secstrmenu.getItemCount();
4505                 for (int litm = p; litm < q; litm++)
4506                 {
4507                   legacyItems.add(secstrmenu.getItem(litm));
4508                 }
4509               }
4510             }
4511           }
4512
4513           // Add all submenus in the order they should appear on the web
4514           // services menu
4515           wsmenu.add(msawsmenu);
4516           wsmenu.add(secstrmenu);
4517           wsmenu.add(dismenu);
4518           wsmenu.add(analymenu);
4519           // No search services yet
4520           // wsmenu.add(seqsrchmenu);
4521
4522           javax.swing.SwingUtilities.invokeLater(new Runnable()
4523           {
4524             @Override
4525             public void run()
4526             {
4527               try
4528               {
4529                 webService.removeAll();
4530                 // first, add discovered services onto the webservices menu
4531                 if (wsmenu.size() > 0)
4532                 {
4533                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4534                   {
4535                     webService.add(wsmenu.get(i));
4536                   }
4537                 }
4538                 else
4539                 {
4540                   webService.add(me.webServiceNoServices);
4541                 }
4542                 // TODO: move into separate menu builder class.
4543                 boolean new_sspred = false;
4544                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4545                 {
4546                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4547                   if (jws2servs != null)
4548                   {
4549                     if (jws2servs.hasServices())
4550                     {
4551                       jws2servs.attachWSMenuEntry(webService, me);
4552                       for (Jws2Instance sv : jws2servs.getServices())
4553                       {
4554                         if (sv.description.toLowerCase().contains("jpred"))
4555                         {
4556                           for (JMenuItem jmi : legacyItems)
4557                           {
4558                             jmi.setVisible(false);
4559                           }
4560                         }
4561                       }
4562
4563                     }
4564                     if (jws2servs.isRunning())
4565                     {
4566                       JMenuItem tm = new JMenuItem(
4567                               "Still discovering JABA Services");
4568                       tm.setEnabled(false);
4569                       webService.add(tm);
4570                     }
4571                   }
4572                 }
4573                 build_urlServiceMenu(me.webService);
4574                 build_fetchdbmenu(webService);
4575                 for (JMenu item : wsmenu)
4576                 {
4577                   if (item.getItemCount() == 0)
4578                   {
4579                     item.setEnabled(false);
4580                   }
4581                   else
4582                   {
4583                     item.setEnabled(true);
4584                   }
4585                 }
4586               } catch (Exception e)
4587               {
4588                 Cache.log
4589                         .debug("Exception during web service menu building process.",
4590                                 e);
4591               }
4592             }
4593           });
4594         } catch (Exception e)
4595         {
4596         }
4597         buildingMenu = false;
4598       }
4599     }).start();
4600
4601   }
4602
4603   /**
4604    * construct any groupURL type service menu entries.
4605    *
4606    * @param webService
4607    */
4608   private void build_urlServiceMenu(JMenu webService)
4609   {
4610     // TODO: remove this code when 2.7 is released
4611     // DEBUG - alignmentView
4612     /*
4613      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4614      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4615      *
4616      * @Override public void actionPerformed(ActionEvent e) {
4617      * jalview.datamodel.AlignmentView
4618      * .testSelectionViews(af.viewport.getAlignment(),
4619      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4620      *
4621      * }); webService.add(testAlView);
4622      */
4623     // TODO: refactor to RestClient discoverer and merge menu entries for
4624     // rest-style services with other types of analysis/calculation service
4625     // SHmmr test client - still being implemented.
4626     // DEBUG - alignmentView
4627
4628     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4629             .getRestClients())
4630     {
4631       client.attachWSMenuEntry(
4632               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4633               this);
4634     }
4635   }
4636
4637   /**
4638    * Searches selected sequences for xRef products and builds the Show
4639    * Cross-References menu (formerly called Show Products)
4640    *
4641    * @return true if Show Cross-references menu should be enabled.
4642    */
4643   public boolean canShowProducts()
4644   {
4645     SequenceI[] selection = viewport.getSequenceSelection();
4646     AlignmentI dataset = viewport.getAlignment().getDataset();
4647     boolean showp = false;
4648     try
4649     {
4650       showProducts.removeAll();
4651       final boolean dna = viewport.getAlignment().isNucleotide();
4652       String[] ptypes = (selection == null || selection.length == 0) ? null
4653               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4654
4655       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4656       {
4657         showp = true;
4658         final AlignFrame af = this;
4659         final String source = ptypes[t];
4660         JMenuItem xtype = new JMenuItem(ptypes[t]);
4661         xtype.addActionListener(new ActionListener()
4662         {
4663
4664           @Override
4665           public void actionPerformed(ActionEvent e)
4666           {
4667             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4668           }
4669
4670         });
4671         showProducts.add(xtype);
4672       }
4673       showProducts.setVisible(showp);
4674       showProducts.setEnabled(showp);
4675     } catch (Exception e)
4676     {
4677       jalview.bin.Cache.log
4678               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4679                       e);
4680       return false;
4681     }
4682     return showp;
4683   }
4684
4685   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4686           final String source)
4687   {
4688     Runnable foo = new Runnable()
4689     {
4690
4691       @Override
4692       public void run()
4693       {
4694         final long sttime = System.currentTimeMillis();
4695         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4696                 "status.searching_for_sequences_from",
4697                 new Object[] { source }), sttime);
4698         try
4699         {
4700           AlignmentI alignment = AlignFrame.this.getViewport()
4701                   .getAlignment();
4702           AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4703                   alignment);
4704           if (xrefs != null)
4705           {
4706             /*
4707              * get display scheme (if any) to apply to features
4708              */
4709             FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4710                     .getFeatureColourScheme(source);
4711
4712             AlignmentI al = makeCrossReferencesAlignment(
4713                     alignment.getDataset(), xrefs);
4714
4715             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4716                     DEFAULT_HEIGHT);
4717             String newtitle = String.format("%s %s %s",
4718                     MessageManager.getString(dna ? "label.proteins"
4719                             : "label.nucleotides"), MessageManager
4720                             .getString("label.for"), getTitle());
4721             newFrame.setTitle(newtitle);
4722
4723             if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4724             {
4725               /*
4726                * split frame display is turned off in preferences file
4727                */
4728               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4729                       DEFAULT_HEIGHT);
4730               return; // via finally clause
4731             }
4732
4733             /*
4734              * Make a copy of this alignment (sharing the same dataset
4735              * sequences). If we are DNA, drop introns and update mappings
4736              */
4737             AlignmentI copyAlignment = null;
4738             final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4739                     .getSequenceSelection();
4740             List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4741             boolean copyAlignmentIsAligned = false;
4742             if (dna)
4743             {
4744               copyAlignment = AlignmentUtils.makeCdsAlignment(
4745                       sequenceSelection, cf, alignment);
4746               if (copyAlignment.getHeight() == 0)
4747               {
4748                 System.err.println("Failed to make CDS alignment");
4749               }
4750               al.getCodonFrames().clear();
4751               al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4752
4753               /*
4754                * pending getting Embl transcripts to 'align',
4755                * we are only doing this for Ensembl
4756                */
4757               // TODO proper criteria for 'can align as cdna'
4758               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4759                       || AlignmentUtils.looksLikeEnsembl(alignment))
4760               {
4761                 copyAlignment.alignAs(alignment);
4762                 copyAlignmentIsAligned = true;
4763               }
4764             }
4765             else
4766             {
4767               copyAlignment = AlignmentUtils.makeCopyAlignment(
4768                       sequenceSelection, xrefs.getSequencesArray());
4769               copyAlignment.getCodonFrames().addAll(cf);
4770             }
4771             copyAlignment.setGapCharacter(AlignFrame.this.viewport
4772                     .getGapCharacter());
4773
4774             StructureSelectionManager ssm = StructureSelectionManager
4775                     .getStructureSelectionManager(Desktop.instance);
4776             ssm.registerMappings(cf);
4777
4778             if (copyAlignment.getHeight() <= 0)
4779             {
4780               System.err.println("No Sequences generated for xRef type "
4781                       + source);
4782               return;
4783             }
4784             /*
4785              * align protein to dna
4786              */
4787             if (dna && copyAlignmentIsAligned)
4788             {
4789               al.alignAs(copyAlignment);
4790             }
4791             else
4792             {
4793               /*
4794                * align cdna to protein - currently only if
4795                * fetching and aligning Ensembl transcripts!
4796                */
4797               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4798               {
4799                 copyAlignment.alignAs(al);
4800               }
4801             }
4802
4803             AlignFrame copyThis = new AlignFrame(copyAlignment,
4804                     AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4805             copyThis.setTitle(AlignFrame.this.getTitle());
4806
4807             boolean showSequenceFeatures = viewport
4808                     .isShowSequenceFeatures();
4809             newFrame.setShowSeqFeatures(showSequenceFeatures);
4810             copyThis.setShowSeqFeatures(showSequenceFeatures);
4811             FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4812                     .getFeatureRenderer();
4813
4814             /*
4815              * copy feature rendering settings to split frame
4816              */
4817             newFrame.alignPanel.getSeqPanel().seqCanvas
4818                     .getFeatureRenderer()
4819                     .transferSettings(myFeatureStyling);
4820             copyThis.alignPanel.getSeqPanel().seqCanvas
4821                     .getFeatureRenderer()
4822                     .transferSettings(myFeatureStyling);
4823
4824             /*
4825              * apply 'database source' feature configuration
4826              * if any was found
4827              */
4828             // TODO is this the feature colouring for the original
4829             // alignment or the fetched xrefs? either could be Ensembl
4830             newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4831             copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4832
4833             SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4834                     dna ? newFrame : copyThis);
4835             newFrame.setVisible(true);
4836             copyThis.setVisible(true);
4837             String linkedTitle = MessageManager
4838                     .getString("label.linked_view_title");
4839             Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4840             sf.adjustDivider();
4841           }
4842         } catch (Exception e)
4843         {
4844           Cache.log.error(
4845                   "Exception when finding crossreferences", e);
4846         } catch (OutOfMemoryError e)
4847         {
4848           new OOMWarning("whilst fetching crossreferences", e);
4849         } catch (Throwable e)
4850         {
4851           Cache.log.error("Error when finding crossreferences",
4852                   e);
4853         } finally
4854         {
4855           AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4856                   "status.finished_searching_for_sequences_from",
4857                   new Object[] { source }), sttime);
4858         }
4859       }
4860
4861       /**
4862        * Makes an alignment containing the given sequences. If this is of the
4863        * same type as the given dataset (nucleotide/protein), then the new
4864        * alignment shares the same dataset, and its dataset sequences are added
4865        * to it. Otherwise a new dataset sequence is created for the
4866        * cross-references.
4867        *
4868        * @param dataset
4869        * @param seqs
4870        * @return
4871        */
4872       protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4873               AlignmentI seqs)
4874       {
4875         boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4876
4877         SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4878         for (int s = 0; s < sprods.length; s++)
4879         {
4880           sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4881           if (sameType)
4882           {
4883             if (dataset.getSequences() == null
4884                     || !dataset.getSequences().contains(
4885                             sprods[s].getDatasetSequence()))
4886             {
4887               dataset.addSequence(sprods[s].getDatasetSequence());
4888             }
4889           }
4890           sprods[s].updatePDBIds();
4891         }
4892         Alignment al = new Alignment(sprods);
4893         if (sameType)
4894         {
4895           al.setDataset((Alignment) dataset);
4896         }
4897         else
4898         {
4899           al.createDatasetAlignment();
4900         }
4901         return al;
4902       }
4903
4904     };
4905     Thread frunner = new Thread(foo);
4906     frunner.start();
4907   }
4908
4909   /**
4910    * Construct and display a new frame containing the translation of this
4911    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4912    */
4913   @Override
4914   public void showTranslation_actionPerformed(ActionEvent e)
4915   {
4916     AlignmentI al = null;
4917     try
4918     {
4919       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4920
4921       al = dna.translateCdna();
4922     } catch (Exception ex)
4923     {
4924       jalview.bin.Cache.log.error(
4925               "Exception during translation. Please report this !", ex);
4926       final String msg = MessageManager
4927               .getString("label.error_when_translating_sequences_submit_bug_report");
4928       final String errorTitle = MessageManager
4929               .getString("label.implementation_error")
4930               + MessageManager.getString("translation_failed");
4931       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4932               JOptionPane.ERROR_MESSAGE);
4933       return;
4934     }
4935     if (al == null || al.getHeight() == 0)
4936     {
4937       final String msg = MessageManager
4938               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4939       final String errorTitle = MessageManager
4940               .getString("label.translation_failed");
4941       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4942               JOptionPane.WARNING_MESSAGE);
4943     }
4944     else
4945     {
4946       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4947       af.setFileFormat(this.currentFileFormat);
4948       final String newTitle = MessageManager.formatMessage(
4949               "label.translation_of_params",
4950               new Object[] { this.getTitle() });
4951       af.setTitle(newTitle);
4952       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4953       {
4954         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4955         viewport.openSplitFrame(af, new Alignment(seqs));
4956       }
4957       else
4958       {
4959         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4960                 DEFAULT_HEIGHT);
4961       }
4962     }
4963   }
4964
4965   /**
4966    * Set the file format
4967    *
4968    * @param fileFormat
4969    */
4970   public void setFileFormat(String fileFormat)
4971   {
4972     this.currentFileFormat = fileFormat;
4973   }
4974
4975   /**
4976    * Try to load a features file onto the alignment.
4977    *
4978    * @param file
4979    *          contents or path to retrieve file
4980    * @param type
4981    *          access mode of file (see jalview.io.AlignFile)
4982    * @return true if features file was parsed correctly.
4983    */
4984   public boolean parseFeaturesFile(String file, String type)
4985   {
4986     return avc.parseFeaturesFile(file, type,
4987             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4988
4989   }
4990
4991   @Override
4992   public void refreshFeatureUI(boolean enableIfNecessary)
4993   {
4994     // note - currently this is only still here rather than in the controller
4995     // because of the featureSettings hard reference that is yet to be
4996     // abstracted
4997     if (enableIfNecessary)
4998     {
4999       viewport.setShowSequenceFeatures(true);
5000       showSeqFeatures.setSelected(true);
5001     }
5002
5003   }
5004
5005   @Override
5006   public void dragEnter(DropTargetDragEvent evt)
5007   {
5008   }
5009
5010   @Override
5011   public void dragExit(DropTargetEvent evt)
5012   {
5013   }
5014
5015   @Override
5016   public void dragOver(DropTargetDragEvent evt)
5017   {
5018   }
5019
5020   @Override
5021   public void dropActionChanged(DropTargetDragEvent evt)
5022   {
5023   }
5024
5025   @Override
5026   public void drop(DropTargetDropEvent evt)
5027   {
5028     Transferable t = evt.getTransferable();
5029     java.util.List files = null;
5030
5031     try
5032     {
5033       DataFlavor uriListFlavor = new DataFlavor(
5034               "text/uri-list;class=java.lang.String");
5035       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5036       {
5037         // Works on Windows and MacOSX
5038         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5039         files = (java.util.List) t
5040                 .getTransferData(DataFlavor.javaFileListFlavor);
5041       }
5042       else if (t.isDataFlavorSupported(uriListFlavor))
5043       {
5044         // This is used by Unix drag system
5045         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5046         String data = (String) t.getTransferData(uriListFlavor);
5047         files = new java.util.ArrayList(1);
5048         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5049                 data, "\r\n"); st.hasMoreTokens();)
5050         {
5051           String s = st.nextToken();
5052           if (s.startsWith("#"))
5053           {
5054             // the line is a comment (as per the RFC 2483)
5055             continue;
5056           }
5057
5058           java.net.URI uri = new java.net.URI(s);
5059           // check to see if we can handle this kind of URI
5060           if (uri.getScheme().toLowerCase().startsWith("http"))
5061           {
5062             files.add(uri.toString());
5063           }
5064           else
5065           {
5066             // otherwise preserve old behaviour: catch all for file objects
5067             java.io.File file = new java.io.File(uri);
5068             files.add(file.toString());
5069           }
5070         }
5071       }
5072     } catch (Exception e)
5073     {
5074       e.printStackTrace();
5075     }
5076     if (files != null)
5077     {
5078       try
5079       {
5080         // check to see if any of these files have names matching sequences in
5081         // the alignment
5082         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5083                 .getAlignment().getSequencesArray());
5084         /**
5085          * Object[] { String,SequenceI}
5086          */
5087         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5088         ArrayList<String> filesnotmatched = new ArrayList<String>();
5089         for (int i = 0; i < files.size(); i++)
5090         {
5091           String file = files.get(i).toString();
5092           String pdbfn = "";
5093           String protocol = FormatAdapter.checkProtocol(file);
5094           if (protocol == jalview.io.FormatAdapter.FILE)
5095           {
5096             File fl = new File(file);
5097             pdbfn = fl.getName();
5098           }
5099           else if (protocol == jalview.io.FormatAdapter.URL)
5100           {
5101             URL url = new URL(file);
5102             pdbfn = url.getFile();
5103           }
5104           if (pdbfn.length() > 0)
5105           {
5106             // attempt to find a match in the alignment
5107             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5108             int l = 0, c = pdbfn.indexOf(".");
5109             while (mtch == null && c != -1)
5110             {
5111               do
5112               {
5113                 l = c;
5114               } while ((c = pdbfn.indexOf(".", l)) > l);
5115               if (l > -1)
5116               {
5117                 pdbfn = pdbfn.substring(0, l);
5118               }
5119               mtch = idm.findAllIdMatches(pdbfn);
5120             }
5121             if (mtch != null)
5122             {
5123               String type = null;
5124               try
5125               {
5126                 type = new IdentifyFile().identify(file, protocol);
5127               } catch (Exception ex)
5128               {
5129                 type = null;
5130               }
5131               if (type != null)
5132               {
5133                 if (type.equalsIgnoreCase("PDB"))
5134                 {
5135                   filesmatched.add(new Object[] { file, protocol, mtch });
5136                   continue;
5137                 }
5138               }
5139             }
5140             // File wasn't named like one of the sequences or wasn't a PDB file.
5141             filesnotmatched.add(file);
5142           }
5143         }
5144         int assocfiles = 0;
5145         if (filesmatched.size() > 0)
5146         {
5147           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5148                   || JOptionPane
5149                           .showConfirmDialog(
5150                                   this,
5151                                   MessageManager
5152                                           .formatMessage(
5153                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5154                                                   new Object[] { Integer
5155                                                           .valueOf(
5156                                                                   filesmatched
5157                                                                           .size())
5158                                                           .toString() }),
5159                                   MessageManager
5160                                           .getString("label.automatically_associate_pdb_files_by_name"),
5161                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5162
5163           {
5164             for (Object[] fm : filesmatched)
5165             {
5166               // try and associate
5167               // TODO: may want to set a standard ID naming formalism for
5168               // associating PDB files which have no IDs.
5169               for (SequenceI toassoc : (SequenceI[]) fm[2])
5170               {
5171                 PDBEntry pe = new AssociatePdbFileWithSeq()
5172                         .associatePdbWithSeq((String) fm[0],
5173                                 (String) fm[1], toassoc, false,
5174                                 Desktop.instance);
5175                 if (pe != null)
5176                 {
5177                   System.err.println("Associated file : "
5178                           + ((String) fm[0]) + " with "
5179                           + toassoc.getDisplayId(true));
5180                   assocfiles++;
5181                 }
5182               }
5183               alignPanel.paintAlignment(true);
5184             }
5185           }
5186         }
5187         if (filesnotmatched.size() > 0)
5188         {
5189           if (assocfiles > 0
5190                   && (Cache.getDefault(
5191                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5192                           .showConfirmDialog(
5193                                   this,
5194                                   "<html>"
5195                                           + MessageManager
5196                                                   .formatMessage(
5197                                                           "label.ignore_unmatched_dropped_files_info",
5198                                                           new Object[] { Integer
5199                                                                   .valueOf(
5200                                                                           filesnotmatched
5201                                                                                   .size())
5202                                                                   .toString() })
5203                                           + "</html>",
5204                                   MessageManager
5205                                           .getString("label.ignore_unmatched_dropped_files"),
5206                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5207           {
5208             return;
5209           }
5210           for (String fn : filesnotmatched)
5211           {
5212             loadJalviewDataFile(fn, null, null, null);
5213           }
5214
5215         }
5216       } catch (Exception ex)
5217       {
5218         ex.printStackTrace();
5219       }
5220     }
5221   }
5222
5223   /**
5224    * Attempt to load a "dropped" file or URL string: First by testing whether
5225    * it's an Annotation file, then a JNet file, and finally a features file. If
5226    * all are false then the user may have dropped an alignment file onto this
5227    * AlignFrame.
5228    *
5229    * @param file
5230    *          either a filename or a URL string.
5231    */
5232   public void loadJalviewDataFile(String file, String protocol,
5233           String format, SequenceI assocSeq)
5234   {
5235     try
5236     {
5237       if (protocol == null)
5238       {
5239         protocol = FormatAdapter.checkProtocol(file);
5240       }
5241       // if the file isn't identified, or not positively identified as some
5242       // other filetype (PFAM is default unidentified alignment file type) then
5243       // try to parse as annotation.
5244       boolean isAnnotation = (format == null || format
5245               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5246               .annotateAlignmentView(viewport, file, protocol) : false;
5247
5248       if (!isAnnotation)
5249       {
5250         // first see if its a T-COFFEE score file
5251         TCoffeeScoreFile tcf = null;
5252         try
5253         {
5254           tcf = new TCoffeeScoreFile(file, protocol);
5255           if (tcf.isValid())
5256           {
5257             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5258             {
5259               tcoffeeColour.setEnabled(true);
5260               tcoffeeColour.setSelected(true);
5261               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5262               isAnnotation = true;
5263               statusBar
5264                       .setText(MessageManager
5265                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5266             }
5267             else
5268             {
5269               // some problem - if no warning its probable that the ID matching
5270               // process didn't work
5271               JOptionPane
5272                       .showMessageDialog(
5273                               Desktop.desktop,
5274                               tcf.getWarningMessage() == null ? MessageManager
5275                                       .getString("label.check_file_matches_sequence_ids_alignment")
5276                                       : tcf.getWarningMessage(),
5277                               MessageManager
5278                                       .getString("label.problem_reading_tcoffee_score_file"),
5279                               JOptionPane.WARNING_MESSAGE);
5280             }
5281           }
5282           else
5283           {
5284             tcf = null;
5285           }
5286         } catch (Exception x)
5287         {
5288           Cache.log
5289                   .debug("Exception when processing data source as T-COFFEE score file",
5290                           x);
5291           tcf = null;
5292         }
5293         if (tcf == null)
5294         {
5295           // try to see if its a JNet 'concise' style annotation file *before*
5296           // we
5297           // try to parse it as a features file
5298           if (format == null)
5299           {
5300             format = new IdentifyFile().identify(file, protocol);
5301           }
5302           if (format.equalsIgnoreCase("JnetFile"))
5303           {
5304             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5305                     file, protocol);
5306             new JnetAnnotationMaker();
5307             JnetAnnotationMaker.add_annotation(predictions,
5308                     viewport.getAlignment(), 0, false);
5309             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5310             viewport.getAlignment().setSeqrep(repseq);
5311             ColumnSelection cs = new ColumnSelection();
5312             cs.hideInsertionsFor(repseq);
5313             viewport.setColumnSelection(cs);
5314             isAnnotation = true;
5315           }
5316           else if (IdentifyFile.FeaturesFile.equals(format))
5317           {
5318             if (parseFeaturesFile(file, protocol))
5319             {
5320               alignPanel.paintAlignment(true);
5321             }
5322           }
5323           else
5324           {
5325             new FileLoader().LoadFile(viewport, file, protocol, format);
5326           }
5327         }
5328       }
5329       if (isAnnotation)
5330       {
5331
5332         alignPanel.adjustAnnotationHeight();
5333         viewport.updateSequenceIdColours();
5334         buildSortByAnnotationScoresMenu();
5335         alignPanel.paintAlignment(true);
5336       }
5337     } catch (Exception ex)
5338     {
5339       ex.printStackTrace();
5340     } catch (OutOfMemoryError oom)
5341     {
5342       try
5343       {
5344         System.gc();
5345       } catch (Exception x)
5346       {
5347       }
5348       new OOMWarning(
5349               "loading data "
5350                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5351                               : "using " + protocol + " from " + file)
5352                               : ".")
5353                       + (format != null ? "(parsing as '" + format
5354                               + "' file)" : ""), oom, Desktop.desktop);
5355     }
5356   }
5357
5358   /**
5359    * Method invoked by the ChangeListener on the tabbed pane, in other words
5360    * when a different tabbed pane is selected by the user or programmatically.
5361    */
5362   @Override
5363   public void tabSelectionChanged(int index)
5364   {
5365     if (index > -1)
5366     {
5367       alignPanel = alignPanels.get(index);
5368       viewport = alignPanel.av;
5369       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5370       setMenusFromViewport(viewport);
5371     }
5372
5373     /*
5374      * If there is a frame linked to this one in a SplitPane, switch it to the
5375      * same view tab index. No infinite recursion of calls should happen, since
5376      * tabSelectionChanged() should not get invoked on setting the selected
5377      * index to an unchanged value. Guard against setting an invalid index
5378      * before the new view peer tab has been created.
5379      */
5380     final AlignViewportI peer = viewport.getCodingComplement();
5381     if (peer != null)
5382     {
5383       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5384       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5385       {
5386         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5387       }
5388     }
5389   }
5390
5391   /**
5392    * On right mouse click on view tab, prompt for and set new view name.
5393    */
5394   @Override
5395   public void tabbedPane_mousePressed(MouseEvent e)
5396   {
5397     if (e.isPopupTrigger())
5398     {
5399       String msg = MessageManager.getString("label.enter_view_name");
5400       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5401               JOptionPane.QUESTION_MESSAGE);
5402
5403       if (reply != null)
5404       {
5405         viewport.viewName = reply;
5406         // TODO warn if reply is in getExistingViewNames()?
5407         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5408       }
5409     }
5410   }
5411
5412   public AlignViewport getCurrentView()
5413   {
5414     return viewport;
5415   }
5416
5417   /**
5418    * Open the dialog for regex description parsing.
5419    */
5420   @Override
5421   protected void extractScores_actionPerformed(ActionEvent e)
5422   {
5423     ParseProperties pp = new jalview.analysis.ParseProperties(
5424             viewport.getAlignment());
5425     // TODO: verify regex and introduce GUI dialog for version 2.5
5426     // if (pp.getScoresFromDescription("col", "score column ",
5427     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5428     // true)>0)
5429     if (pp.getScoresFromDescription("description column",
5430             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5431     {
5432       buildSortByAnnotationScoresMenu();
5433     }
5434   }
5435
5436   /*
5437    * (non-Javadoc)
5438    *
5439    * @see
5440    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5441    * )
5442    */
5443   @Override
5444   protected void showDbRefs_actionPerformed(ActionEvent e)
5445   {
5446     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5447   }
5448
5449   /*
5450    * (non-Javadoc)
5451    *
5452    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5453    * ActionEvent)
5454    */
5455   @Override
5456   protected void showNpFeats_actionPerformed(ActionEvent e)
5457   {
5458     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5459   }
5460
5461   /**
5462    * find the viewport amongst the tabs in this alignment frame and close that
5463    * tab
5464    *
5465    * @param av
5466    */
5467   public boolean closeView(AlignViewportI av)
5468   {
5469     if (viewport == av)
5470     {
5471       this.closeMenuItem_actionPerformed(false);
5472       return true;
5473     }
5474     Component[] comp = tabbedPane.getComponents();
5475     for (int i = 0; comp != null && i < comp.length; i++)
5476     {
5477       if (comp[i] instanceof AlignmentPanel)
5478       {
5479         if (((AlignmentPanel) comp[i]).av == av)
5480         {
5481           // close the view.
5482           closeView((AlignmentPanel) comp[i]);
5483           return true;
5484         }
5485       }
5486     }
5487     return false;
5488   }
5489
5490   protected void build_fetchdbmenu(JMenu webService)
5491   {
5492     // Temporary hack - DBRef Fetcher always top level ws entry.
5493     // TODO We probably want to store a sequence database checklist in
5494     // preferences and have checkboxes.. rather than individual sources selected
5495     // here
5496     final JMenu rfetch = new JMenu(
5497             MessageManager.getString("action.fetch_db_references"));
5498     rfetch.setToolTipText(MessageManager
5499             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5500     webService.add(rfetch);
5501
5502     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5503             MessageManager.getString("option.trim_retrieved_seqs"));
5504     trimrs.setToolTipText(MessageManager
5505             .getString("label.trim_retrieved_sequences"));
5506     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5507     trimrs.addActionListener(new ActionListener()
5508     {
5509       @Override
5510       public void actionPerformed(ActionEvent e)
5511       {
5512         trimrs.setSelected(trimrs.isSelected());
5513         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5514                 Boolean.valueOf(trimrs.isSelected()).toString());
5515       };
5516     });
5517     rfetch.add(trimrs);
5518     JMenuItem fetchr = new JMenuItem(
5519             MessageManager.getString("label.standard_databases"));
5520     fetchr.setToolTipText(MessageManager
5521             .getString("label.fetch_embl_uniprot"));
5522     fetchr.addActionListener(new ActionListener()
5523     {
5524
5525       @Override
5526       public void actionPerformed(ActionEvent e)
5527       {
5528         new Thread(new Runnable()
5529         {
5530           @Override
5531           public void run()
5532           {
5533             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5534                     .getAlignment().isNucleotide();
5535             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5536                     .getSequenceSelection(), alignPanel.alignFrame, null,
5537                     alignPanel.alignFrame.featureSettings, isNucleotide);
5538             dbRefFetcher.addListener(new FetchFinishedListenerI()
5539             {
5540               @Override
5541               public void finished()
5542               {
5543                 AlignFrame.this.setMenusForViewport();
5544               }
5545             });
5546             dbRefFetcher
5547                     .fetchDBRefs(false);
5548           }
5549         }).start();
5550
5551       }
5552
5553     });
5554     rfetch.add(fetchr);
5555     final AlignFrame me = this;
5556     new Thread(new Runnable()
5557     {
5558       @Override
5559       public void run()
5560       {
5561         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5562                 .getSequenceFetcherSingleton(me);
5563         javax.swing.SwingUtilities.invokeLater(new Runnable()
5564         {
5565           @Override
5566           public void run()
5567           {
5568             String[] dbclasses = sf.getOrderedSupportedSources();
5569             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5570             // jalview.util.QuickSort.sort(otherdb, otherdb);
5571             List<DbSourceProxy> otherdb;
5572             JMenu dfetch = new JMenu();
5573             JMenu ifetch = new JMenu();
5574             JMenuItem fetchr = null;
5575             int comp = 0, icomp = 0, mcomp = 15;
5576             String mname = null;
5577             int dbi = 0;
5578             for (String dbclass : dbclasses)
5579             {
5580               otherdb = sf.getSourceProxy(dbclass);
5581               // add a single entry for this class, or submenu allowing 'fetch
5582               // all' or pick one
5583               if (otherdb == null || otherdb.size() < 1)
5584               {
5585                 continue;
5586               }
5587               // List<DbSourceProxy> dbs=otherdb;
5588               // otherdb=new ArrayList<DbSourceProxy>();
5589               // for (DbSourceProxy db:dbs)
5590               // {
5591               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5592               // }
5593               if (mname == null)
5594               {
5595                 mname = "From " + dbclass;
5596               }
5597               if (otherdb.size() == 1)
5598               {
5599                 final DbSourceProxy[] dassource = otherdb
5600                         .toArray(new DbSourceProxy[0]);
5601                 DbSourceProxy src = otherdb.get(0);
5602                 fetchr = new JMenuItem(src.getDbSource());
5603                 fetchr.addActionListener(new ActionListener()
5604                 {
5605
5606                   @Override
5607                   public void actionPerformed(ActionEvent e)
5608                   {
5609                     new Thread(new Runnable()
5610                     {
5611
5612                       @Override
5613                       public void run()
5614                       {
5615                         boolean isNucleotide = alignPanel.alignFrame
5616                                 .getViewport().getAlignment()
5617                                 .isNucleotide();
5618                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5619                                 alignPanel.av.getSequenceSelection(),
5620                                 alignPanel.alignFrame, dassource,
5621                                 alignPanel.alignFrame.featureSettings,
5622                                 isNucleotide);
5623                         dbRefFetcher
5624                                 .addListener(new FetchFinishedListenerI()
5625                                 {
5626                                   @Override
5627                                   public void finished()
5628                                   {
5629                                     AlignFrame.this.setMenusForViewport();
5630                                   }
5631                                 });
5632                         dbRefFetcher.fetchDBRefs(false);
5633                       }
5634                     }).start();
5635                   }
5636
5637                 });
5638                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5639                         MessageManager.formatMessage(
5640                                 "label.fetch_retrieve_from",
5641                                 new Object[] { src.getDbName() })));
5642                 dfetch.add(fetchr);
5643                 comp++;
5644               }
5645               else
5646               {
5647                 final DbSourceProxy[] dassource = otherdb
5648                         .toArray(new DbSourceProxy[0]);
5649                 // fetch all entry
5650                 DbSourceProxy src = otherdb.get(0);
5651                 fetchr = new JMenuItem(MessageManager.formatMessage(
5652                         "label.fetch_all_param",
5653                         new Object[] { src.getDbSource() }));
5654                 fetchr.addActionListener(new ActionListener()
5655                 {
5656                   @Override
5657                   public void actionPerformed(ActionEvent e)
5658                   {
5659                     new Thread(new Runnable()
5660                     {
5661
5662                       @Override
5663                       public void run()
5664                       {
5665                         boolean isNucleotide = alignPanel.alignFrame
5666                                 .getViewport().getAlignment()
5667                                 .isNucleotide();
5668                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5669                                 alignPanel.av.getSequenceSelection(),
5670                                 alignPanel.alignFrame, dassource,
5671                                 alignPanel.alignFrame.featureSettings,
5672                                 isNucleotide);
5673                         dbRefFetcher
5674                                 .addListener(new FetchFinishedListenerI()
5675                                 {
5676                                   @Override
5677                                   public void finished()
5678                                   {
5679                                     AlignFrame.this.setMenusForViewport();
5680                                   }
5681                                 });
5682                         dbRefFetcher.fetchDBRefs(false);
5683                       }
5684                     }).start();
5685                   }
5686                 });
5687
5688                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5689                         MessageManager.formatMessage(
5690                                 "label.fetch_retrieve_from_all_sources",
5691                                 new Object[] {
5692                                     Integer.valueOf(otherdb.size())
5693                                             .toString(), src.getDbSource(),
5694                                     src.getDbName() })));
5695                 dfetch.add(fetchr);
5696                 comp++;
5697                 // and then build the rest of the individual menus
5698                 ifetch = new JMenu(MessageManager.formatMessage(
5699                         "label.source_from_db_source",
5700                         new Object[] { src.getDbSource() }));
5701                 icomp = 0;
5702                 String imname = null;
5703                 int i = 0;
5704                 for (DbSourceProxy sproxy : otherdb)
5705                 {
5706                   String dbname = sproxy.getDbName();
5707                   String sname = dbname.length() > 5 ? dbname.substring(0,
5708                           5) + "..." : dbname;
5709                   String msname = dbname.length() > 10 ? dbname.substring(
5710                           0, 10) + "..." : dbname;
5711                   if (imname == null)
5712                   {
5713                     imname = MessageManager.formatMessage(
5714                             "label.from_msname", new Object[] { sname });
5715                   }
5716                   fetchr = new JMenuItem(msname);
5717                   final DbSourceProxy[] dassrc = { sproxy };
5718                   fetchr.addActionListener(new ActionListener()
5719                   {
5720
5721                     @Override
5722                     public void actionPerformed(ActionEvent e)
5723                     {
5724                       new Thread(new Runnable()
5725                       {
5726
5727                         @Override
5728                         public void run()
5729                         {
5730                           boolean isNucleotide = alignPanel.alignFrame
5731                                   .getViewport().getAlignment()
5732                                   .isNucleotide();
5733                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5734                                   alignPanel.av.getSequenceSelection(),
5735                                   alignPanel.alignFrame, dassrc,
5736                                   alignPanel.alignFrame.featureSettings,
5737                                   isNucleotide);
5738                           dbRefFetcher
5739                                   .addListener(new FetchFinishedListenerI()
5740                                   {
5741                                     @Override
5742                                     public void finished()
5743                                     {
5744                                       AlignFrame.this.setMenusForViewport();
5745                                     }
5746                                   });
5747                           dbRefFetcher.fetchDBRefs(false);
5748                         }
5749                       }).start();
5750                     }
5751
5752                   });
5753                   fetchr.setToolTipText("<html>"
5754                           + MessageManager.formatMessage(
5755                                   "label.fetch_retrieve_from", new Object[]
5756                                   { dbname }));
5757                   ifetch.add(fetchr);
5758                   ++i;
5759                   if (++icomp >= mcomp || i == (otherdb.size()))
5760                   {
5761                     ifetch.setText(MessageManager.formatMessage(
5762                             "label.source_to_target", imname, sname));
5763                     dfetch.add(ifetch);
5764                     ifetch = new JMenu();
5765                     imname = null;
5766                     icomp = 0;
5767                     comp++;
5768                   }
5769                 }
5770               }
5771               ++dbi;
5772               if (comp >= mcomp || dbi >= (dbclasses.length))
5773               {
5774                 dfetch.setText(MessageManager.formatMessage(
5775                         "label.source_to_target", mname, dbclass));
5776                 rfetch.add(dfetch);
5777                 dfetch = new JMenu();
5778                 mname = null;
5779                 comp = 0;
5780               }
5781             }
5782           }
5783         });
5784       }
5785     }).start();
5786
5787   }
5788
5789   /**
5790    * Left justify the whole alignment.
5791    */
5792   @Override
5793   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5794   {
5795     AlignmentI al = viewport.getAlignment();
5796     al.justify(false);
5797     viewport.firePropertyChange("alignment", null, al);
5798   }
5799
5800   /**
5801    * Right justify the whole alignment.
5802    */
5803   @Override
5804   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5805   {
5806     AlignmentI al = viewport.getAlignment();
5807     al.justify(true);
5808     viewport.firePropertyChange("alignment", null, al);
5809   }
5810
5811   @Override
5812   public void setShowSeqFeatures(boolean b)
5813   {
5814     showSeqFeatures.setSelected(b);
5815     viewport.setShowSequenceFeatures(b);
5816   }
5817
5818   /*
5819    * (non-Javadoc)
5820    *
5821    * @see
5822    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5823    * awt.event.ActionEvent)
5824    */
5825   @Override
5826   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5827   {
5828     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5829     alignPanel.paintAlignment(true);
5830   }
5831
5832   /*
5833    * (non-Javadoc)
5834    *
5835    * @see
5836    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5837    * .ActionEvent)
5838    */
5839   @Override
5840   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5841   {
5842     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5843     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5844
5845   }
5846
5847   /*
5848    * (non-Javadoc)
5849    *
5850    * @see
5851    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5852    * .event.ActionEvent)
5853    */
5854   @Override
5855   protected void showGroupConservation_actionPerformed(ActionEvent e)
5856   {
5857     viewport.setShowGroupConservation(showGroupConservation.getState());
5858     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5859   }
5860
5861   /*
5862    * (non-Javadoc)
5863    *
5864    * @see
5865    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5866    * .event.ActionEvent)
5867    */
5868   @Override
5869   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5870   {
5871     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5872     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5873   }
5874
5875   /*
5876    * (non-Javadoc)
5877    *
5878    * @see
5879    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5880    * .event.ActionEvent)
5881    */
5882   @Override
5883   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5884   {
5885     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5886     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5887   }
5888
5889   @Override
5890   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5891   {
5892     showSequenceLogo.setState(true);
5893     viewport.setShowSequenceLogo(true);
5894     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5895     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5896   }
5897
5898   @Override
5899   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5900   {
5901     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5902   }
5903
5904   /*
5905    * (non-Javadoc)
5906    *
5907    * @see
5908    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5909    * .event.ActionEvent)
5910    */
5911   @Override
5912   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5913   {
5914     if (avc.makeGroupsFromSelection())
5915     {
5916       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5917       alignPanel.updateAnnotation();
5918       alignPanel.paintAlignment(true);
5919     }
5920   }
5921
5922   public void clearAlignmentSeqRep()
5923   {
5924     // TODO refactor alignmentseqrep to controller
5925     if (viewport.getAlignment().hasSeqrep())
5926     {
5927       viewport.getAlignment().setSeqrep(null);
5928       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5929       alignPanel.updateAnnotation();
5930       alignPanel.paintAlignment(true);
5931     }
5932   }
5933
5934   @Override
5935   protected void createGroup_actionPerformed(ActionEvent e)
5936   {
5937     if (avc.createGroup())
5938     {
5939       alignPanel.alignmentChanged();
5940     }
5941   }
5942
5943   @Override
5944   protected void unGroup_actionPerformed(ActionEvent e)
5945   {
5946     if (avc.unGroup())
5947     {
5948       alignPanel.alignmentChanged();
5949     }
5950   }
5951
5952   /**
5953    * make the given alignmentPanel the currently selected tab
5954    *
5955    * @param alignmentPanel
5956    */
5957   public void setDisplayedView(AlignmentPanel alignmentPanel)
5958   {
5959     if (!viewport.getSequenceSetId().equals(
5960             alignmentPanel.av.getSequenceSetId()))
5961     {
5962       throw new Error(
5963               MessageManager
5964                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5965     }
5966     if (tabbedPane != null
5967             && tabbedPane.getTabCount() > 0
5968             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5969                     .getSelectedIndex())
5970     {
5971       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5972     }
5973   }
5974
5975   /**
5976    * Action on selection of menu options to Show or Hide annotations.
5977    *
5978    * @param visible
5979    * @param forSequences
5980    *          update sequence-related annotations
5981    * @param forAlignment
5982    *          update non-sequence-related annotations
5983    */
5984   @Override
5985   protected void setAnnotationsVisibility(boolean visible,
5986           boolean forSequences, boolean forAlignment)
5987   {
5988     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5989             .getAlignmentAnnotation())
5990     {
5991       /*
5992        * don't display non-positional annotations on an alignment
5993        */
5994       if (aa.annotations == null)
5995       {
5996         continue;
5997       }
5998       boolean apply = (aa.sequenceRef == null && forAlignment)
5999               || (aa.sequenceRef != null && forSequences);
6000       if (apply)
6001       {
6002         aa.visible = visible;
6003       }
6004     }
6005     alignPanel.validateAnnotationDimensions(true);
6006     alignPanel.alignmentChanged();
6007   }
6008
6009   /**
6010    * Store selected annotation sort order for the view and repaint.
6011    */
6012   @Override
6013   protected void sortAnnotations_actionPerformed()
6014   {
6015     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6016     this.alignPanel.av
6017             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6018     alignPanel.paintAlignment(true);
6019   }
6020
6021   /**
6022    *
6023    * @return alignment panels in this alignment frame
6024    */
6025   public List<? extends AlignmentViewPanel> getAlignPanels()
6026   {
6027     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6028   }
6029
6030   /**
6031    * Open a new alignment window, with the cDNA associated with this (protein)
6032    * alignment, aligned as is the protein.
6033    */
6034   protected void viewAsCdna_actionPerformed()
6035   {
6036     // TODO no longer a menu action - refactor as required
6037     final AlignmentI alignment = getViewport().getAlignment();
6038     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6039     if (mappings == null)
6040     {
6041       return;
6042     }
6043     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6044     for (SequenceI aaSeq : alignment.getSequences())
6045     {
6046       for (AlignedCodonFrame acf : mappings)
6047       {
6048         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6049         if (dnaSeq != null)
6050         {
6051           /*
6052            * There is a cDNA mapping for this protein sequence - add to new
6053            * alignment. It will share the same dataset sequence as other mapped
6054            * cDNA (no new mappings need to be created).
6055            */
6056           final Sequence newSeq = new Sequence(dnaSeq);
6057           newSeq.setDatasetSequence(dnaSeq);
6058           cdnaSeqs.add(newSeq);
6059         }
6060       }
6061     }
6062     if (cdnaSeqs.size() == 0)
6063     {
6064       // show a warning dialog no mapped cDNA
6065       return;
6066     }
6067     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6068             .size()]));
6069     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6070             AlignFrame.DEFAULT_HEIGHT);
6071     cdna.alignAs(alignment);
6072     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6073             + this.title;
6074     Desktop.addInternalFrame(alignFrame, newtitle,
6075             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6076   }
6077
6078   /**
6079    * Set visibility of dna/protein complement view (available when shown in a
6080    * split frame).
6081    *
6082    * @param show
6083    */
6084   @Override
6085   protected void showComplement_actionPerformed(boolean show)
6086   {
6087     SplitContainerI sf = getSplitViewContainer();
6088     if (sf != null)
6089     {
6090       sf.setComplementVisible(this, show);
6091     }
6092   }
6093
6094   /**
6095    * Generate the reverse (optionally complemented) of the selected sequences,
6096    * and add them to the alignment
6097    */
6098   @Override
6099   protected void showReverse_actionPerformed(boolean complement)
6100   {
6101     AlignmentI al = null;
6102     try
6103     {
6104       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6105
6106       al = dna.reverseCdna(complement);
6107       viewport.addAlignment(al, "");
6108     } catch (Exception ex)
6109     {
6110       System.err.println(ex.getMessage());
6111       return;
6112     }
6113   }
6114
6115   /**
6116    * Try to run a script in the Groovy console, having first ensured that this
6117    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6118    * be targeted at this alignment.
6119    */
6120   @Override
6121   protected void runGroovy_actionPerformed()
6122   {
6123     Desktop.setCurrentAlignFrame(this);
6124     Object console = Desktop.instance.getGroovyConsole();
6125     if (console != null)
6126     {
6127       /*
6128        * use reflection here to avoid compile-time dependency
6129        * on Groovy libraries
6130        */
6131       try
6132       {
6133         Class<?> gcClass = getClass().getClassLoader().loadClass(
6134                 "groovy.ui.Console");
6135         Method runScript = gcClass.getMethod("runScript");
6136         runScript.invoke(console);
6137       } catch (Exception ex)
6138       {
6139         System.err.println((ex.toString()));
6140         JOptionPane
6141                 .showInternalMessageDialog(Desktop.desktop, MessageManager
6142                         .getString("label.couldnt_run_groovy_script"),
6143                         MessageManager
6144                                 .getString("label.groovy_support_failed"),
6145                         JOptionPane.ERROR_MESSAGE);
6146       }
6147     }
6148     else
6149     {
6150       System.err.println("Can't run Groovy script as console not found");
6151     }
6152   }
6153 }
6154
6155 class PrintThread extends Thread
6156 {
6157   AlignmentPanel ap;
6158
6159   public PrintThread(AlignmentPanel ap)
6160   {
6161     this.ap = ap;
6162   }
6163
6164   static PageFormat pf;
6165
6166   @Override
6167   public void run()
6168   {
6169     PrinterJob printJob = PrinterJob.getPrinterJob();
6170
6171     if (pf != null)
6172     {
6173       printJob.setPrintable(ap, pf);
6174     }
6175     else
6176     {
6177       printJob.setPrintable(ap);
6178     }
6179
6180     if (printJob.printDialog())
6181     {
6182       try
6183       {
6184         printJob.print();
6185       } catch (Exception PrintException)
6186       {
6187         PrintException.printStackTrace();
6188       }
6189     }
6190   }
6191 }