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