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