src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
   3  * Copyright (C) 2015 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  63 import jalview.io.AlignmentProperties;
  64 import jalview.io.AnnotationFile;
  65 import jalview.io.BioJsHTMLOutput;
  66 import jalview.io.FileLoader;
  67 import jalview.io.FormatAdapter;
  68 import jalview.io.HtmlSvgOutput;
  69 import jalview.io.IdentifyFile;
  70 import jalview.io.JalviewFileChooser;
  71 import jalview.io.JalviewFileView;
  72 import jalview.io.JnetAnnotationMaker;
  73 import jalview.io.NewickFile;
  74 import jalview.io.TCoffeeScoreFile;
  75 import jalview.jbgui.GAlignFrame;
  76 import jalview.schemes.Blosum62ColourScheme;
  77 import jalview.schemes.BuriedColourScheme;
  78 import jalview.schemes.ClustalxColourScheme;
  79 import jalview.schemes.ColourSchemeI;
  80 import jalview.schemes.ColourSchemeProperty;
  81 import jalview.schemes.HelixColourScheme;
  82 import jalview.schemes.HydrophobicColourScheme;
  83 import jalview.schemes.NucleotideColourScheme;
  84 import jalview.schemes.PIDColourScheme;
  85 import jalview.schemes.PurinePyrimidineColourScheme;
  86 import jalview.schemes.RNAHelicesColourChooser;
  87 import jalview.schemes.ResidueProperties;
  88 import jalview.schemes.StrandColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.schemes.TaylorColourScheme;
  91 import jalview.schemes.TurnColourScheme;
  92 import jalview.schemes.UserColourScheme;
  93 import jalview.schemes.ZappoColourScheme;
  94 import jalview.structure.StructureSelectionManager;
  95 import jalview.util.MessageManager;
  96 import jalview.viewmodel.AlignmentViewport;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Component;
 104 import java.awt.Rectangle;
 105 import java.awt.Toolkit;
 106 import java.awt.datatransfer.Clipboard;
 107 import java.awt.datatransfer.DataFlavor;
 108 import java.awt.datatransfer.StringSelection;
 109 import java.awt.datatransfer.Transferable;
 110 import java.awt.dnd.DnDConstants;
 111 import java.awt.dnd.DropTargetDragEvent;
 112 import java.awt.dnd.DropTargetDropEvent;
 113 import java.awt.dnd.DropTargetEvent;
 114 import java.awt.dnd.DropTargetListener;
 115 import java.awt.event.ActionEvent;
 116 import java.awt.event.ActionListener;
 117 import java.awt.event.ItemEvent;
 118 import java.awt.event.ItemListener;
 119 import java.awt.event.KeyAdapter;
 120 import java.awt.event.KeyEvent;
 121 import java.awt.event.MouseAdapter;
 122 import java.awt.event.MouseEvent;
 123 import java.awt.print.PageFormat;
 124 import java.awt.print.PrinterJob;
 125 import java.beans.PropertyChangeEvent;
 126 import java.io.File;
 127 import java.net.URL;
 128 import java.util.ArrayList;
 129 import java.util.Arrays;
 130 import java.util.Deque;
 131 import java.util.Enumeration;
 132 import java.util.Hashtable;
 133 import java.util.List;
 134 import java.util.Set;
 135 import java.util.Vector;
 136
 137 import javax.swing.JCheckBoxMenuItem;
 138 import javax.swing.JEditorPane;
 139 import javax.swing.JInternalFrame;
 140 import javax.swing.JLayeredPane;
 141 import javax.swing.JMenu;
 142 import javax.swing.JMenuItem;
 143 import javax.swing.JOptionPane;
 144 import javax.swing.JRadioButtonMenuItem;
 145 import javax.swing.JScrollPane;
 146 import javax.swing.SwingUtilities;
 147
 148 /**
 149  * DOCUMENT ME!
 150  *
 151  * @author $author$
 152  * @version $Revision$
 153  */
 154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 155         IProgressIndicator, AlignViewControllerGuiI
 156 {
 157
 158   public static final int DEFAULT_WIDTH = 700;
 159
 160   public static final int DEFAULT_HEIGHT = 500;
 161
 162   /*
 163    * The currently displayed panel (selected tabbed view if more than one)
 164    */
 165   public AlignmentPanel alignPanel;
 166
 167   AlignViewport viewport;
 168
 169   public AlignViewControllerI avc;
 170
 171   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 172
 173   /**
 174    * Last format used to load or save alignments in this window
 175    */
 176   String currentFileFormat = null;
 177
 178   /**
 179    * Current filename for this alignment
 180    */
 181   String fileName = null;
 182
 183   /**
 184    * Creates a new AlignFrame object with specific width and height.
 185    *
 186    * @param al
 187    * @param width
 188    * @param height
 189    */
 190   public AlignFrame(AlignmentI al, int width, int height)
 191   {
 192     this(al, null, width, height);
 193   }
 194
 195   /**
 196    * Creates a new AlignFrame object with specific width, height and
 197    * sequenceSetId
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    * @param sequenceSetId
 203    */
 204   public AlignFrame(AlignmentI al, int width, int height,
 205           String sequenceSetId)
 206   {
 207     this(al, null, width, height, sequenceSetId);
 208   }
 209
 210   /**
 211    * Creates a new AlignFrame object with specific width, height and
 212    * sequenceSetId
 213    *
 214    * @param al
 215    * @param width
 216    * @param height
 217    * @param sequenceSetId
 218    * @param viewId
 219    */
 220   public AlignFrame(AlignmentI al, int width, int height,
 221           String sequenceSetId, String viewId)
 222   {
 223     this(al, null, width, height, sequenceSetId, viewId);
 224   }
 225
 226   /**
 227    * new alignment window with hidden columns
 228    *
 229    * @param al
 230    *          AlignmentI
 231    * @param hiddenColumns
 232    *          ColumnSelection or null
 233    * @param width
 234    *          Width of alignment frame
 235    * @param height
 236    *          height of frame.
 237    */
 238   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 239           int width, int height)
 240   {
 241     this(al, hiddenColumns, width, height, null);
 242   }
 243
 244   /**
 245    * Create alignment frame for al with hiddenColumns, a specific width and
 246    * height, and specific sequenceId
 247    *
 248    * @param al
 249    * @param hiddenColumns
 250    * @param width
 251    * @param height
 252    * @param sequenceSetId
 253    *          (may be null)
 254    */
 255   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 256           int width, int height, String sequenceSetId)
 257   {
 258     this(al, hiddenColumns, width, height, sequenceSetId, null);
 259   }
 260
 261   /**
 262    * Create alignment frame for al with hiddenColumns, a specific width and
 263    * height, and specific sequenceId
 264    *
 265    * @param al
 266    * @param hiddenColumns
 267    * @param width
 268    * @param height
 269    * @param sequenceSetId
 270    *          (may be null)
 271    * @param viewId
 272    *          (may be null)
 273    */
 274   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 275           int width, int height, String sequenceSetId, String viewId)
 276   {
 277     setSize(width, height);
 278
 279     if (al.getDataset() == null)
 280     {
 281       al.setDataset(null);
 282     }
 283
 284     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 285
 286     alignPanel = new AlignmentPanel(this, viewport);
 287
 288     addAlignmentPanel(alignPanel, true);
 289     init();
 290   }
 291
 292   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 293           ColumnSelection hiddenColumns, int width, int height)
 294   {
 295     setSize(width, height);
 296
 297     if (al.getDataset() == null)
 298     {
 299       al.setDataset(null);
 300     }
 301
 302     viewport = new AlignViewport(al, hiddenColumns);
 303
 304     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 305     {
 306       viewport.hideSequence(hiddenSeqs);
 307     }
 308     alignPanel = new AlignmentPanel(this, viewport);
 309     addAlignmentPanel(alignPanel, true);
 310     init();
 311   }
 312
 313   /**
 314    * Make a new AlignFrame from existing alignmentPanels
 315    *
 316    * @param ap
 317    *          AlignmentPanel
 318    * @param av
 319    *          AlignViewport
 320    */
 321   public AlignFrame(AlignmentPanel ap)
 322   {
 323     viewport = ap.av;
 324     alignPanel = ap;
 325     addAlignmentPanel(ap, false);
 326     init();
 327   }
 328
 329   /**
 330    * initalise the alignframe from the underlying viewport data and the
 331    * configurations
 332    */
 333   void init()
 334   {
 335     if (!Jalview.isHeadlessMode())
 336     {
 337       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 338     }
 339
 340     avc = new jalview.controller.AlignViewController(this, viewport,
 341             alignPanel);
 342     if (viewport.getAlignmentConservationAnnotation() == null)
 343     {
 344       BLOSUM62Colour.setEnabled(false);
 345       conservationMenuItem.setEnabled(false);
 346       modifyConservation.setEnabled(false);
 347       // PIDColour.setEnabled(false);
 348       // abovePIDThreshold.setEnabled(false);
 349       // modifyPID.setEnabled(false);
 350     }
 351
 352     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 353             "No sort");
 354
 355     if (sortby.equals("Id"))
 356     {
 357       sortIDMenuItem_actionPerformed(null);
 358     }
 359     else if (sortby.equals("Pairwise Identity"))
 360     {
 361       sortPairwiseMenuItem_actionPerformed(null);
 362     }
 363
 364     if (Desktop.desktop != null)
 365     {
 366       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 367       addServiceListeners();
 368       setGUINucleotide(viewport.getAlignment().isNucleotide());
 369     }
 370
 371     this.alignPanel.av
 372             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 373
 374     setMenusFromViewport(viewport);
 375     buildSortByAnnotationScoresMenu();
 376     buildTreeMenu();
 377
 378     if (viewport.getWrapAlignment())
 379     {
 380       wrapMenuItem_actionPerformed(null);
 381     }
 382
 383     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 384     {
 385       this.overviewMenuItem_actionPerformed(null);
 386     }
 387
 388     addKeyListener();
 389
 390     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 391     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 392     final String menuLabel = MessageManager
 393             .getString("label.copy_format_from");
 394     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 395             new ViewSetProvider()
 396             {
 397
 398               @Override
 399               public AlignmentPanel[] getAllAlignmentPanels()
 400               {
 401                 origview.clear();
 402                 origview.add(alignPanel);
 403                 // make an array of all alignment panels except for this one
 404                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 405                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 406                 aps.remove(AlignFrame.this.alignPanel);
 407                 return aps.toArray(new AlignmentPanel[aps.size()]);
 408               }
 409             }, selviews, new ItemListener()
 410             {
 411
 412               @Override
 413               public void itemStateChanged(ItemEvent e)
 414               {
 415                 if (origview.size() > 0)
 416                 {
 417                   final AlignmentPanel ap = origview.get(0);
 418
 419                   /*
 420                    * Copy the ViewStyle of the selected panel to 'this one'.
 421                    * Don't change value of 'scaleProteinAsCdna' unless copying
 422                    * from a SplitFrame.
 423                    */
 424                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 425                           .getViewStyle();
 426                   boolean fromSplitFrame = selviews.get(0)
 427                           .getAlignViewport().getCodingComplement() != null;
 428                   if (!fromSplitFrame)
 429                   {
 430                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 431                             .getViewStyle().isScaleProteinAsCdna());
 432                   }
 433                   ap.getAlignViewport().setViewStyle(vs);
 434
 435                   /*
 436                    * Also rescale ViewStyle of SplitFrame complement if there is
 437                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 438                    * the whole ViewStyle (allow cDNA protein to have different
 439                    * fonts)
 440                    */
 441                   AlignViewportI complement = ap.getAlignViewport()
 442                           .getCodingComplement();
 443                   if (complement != null && vs.isScaleProteinAsCdna())
 444                   {
 445                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 446                     ((SplitFrame) af.getSplitViewContainer())
 447                             .adjustLayout();
 448                     af.setMenusForViewport();
 449                   }
 450
 451                   ap.updateLayout();
 452                   ap.setSelected(true);
 453                   ap.alignFrame.setMenusForViewport();
 454
 455                 }
 456               }
 457             });
 458     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 459             .indexOf("devel") > -1
 460             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 461                     .indexOf("test") > -1)
 462     {
 463       formatMenu.add(vsel);
 464     }
 465
 466   }
 467
 468   /**
 469    * Change the filename and format for the alignment, and enable the 'reload'
 470    * button functionality.
 471    *
 472    * @param file
 473    *          valid filename
 474    * @param format
 475    *          format of file
 476    */
 477   public void setFileName(String file, String format)
 478   {
 479     fileName = file;
 480     setFileFormat(format);
 481     reload.setEnabled(true);
 482   }
 483
 484   /**
 485    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 486    * events
 487    */
 488   void addKeyListener()
 489   {
 490     addKeyListener(new KeyAdapter()
 491     {
 492       @Override
 493       public void keyPressed(KeyEvent evt)
 494       {
 495         if (viewport.cursorMode
 496                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 497                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 498                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 499                 && Character.isDigit(evt.getKeyChar()))
 500         {
 501           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 502         }
 503
 504         switch (evt.getKeyCode())
 505         {
 506
 507         case 27: // escape key
 508           deselectAllSequenceMenuItem_actionPerformed(null);
 509
 510           break;
 511
 512         case KeyEvent.VK_DOWN:
 513           if (evt.isAltDown() || !viewport.cursorMode)
 514           {
 515             moveSelectedSequences(false);
 516           }
 517           if (viewport.cursorMode)
 518           {
 519             alignPanel.getSeqPanel().moveCursor(0, 1);
 520           }
 521           break;
 522
 523         case KeyEvent.VK_UP:
 524           if (evt.isAltDown() || !viewport.cursorMode)
 525           {
 526             moveSelectedSequences(true);
 527           }
 528           if (viewport.cursorMode)
 529           {
 530             alignPanel.getSeqPanel().moveCursor(0, -1);
 531           }
 532
 533           break;
 534
 535         case KeyEvent.VK_LEFT:
 536           if (evt.isAltDown() || !viewport.cursorMode)
 537           {
 538             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 539           }
 540           else
 541           {
 542             alignPanel.getSeqPanel().moveCursor(-1, 0);
 543           }
 544
 545           break;
 546
 547         case KeyEvent.VK_RIGHT:
 548           if (evt.isAltDown() || !viewport.cursorMode)
 549           {
 550             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 551           }
 552           else
 553           {
 554             alignPanel.getSeqPanel().moveCursor(1, 0);
 555           }
 556           break;
 557
 558         case KeyEvent.VK_SPACE:
 559           if (viewport.cursorMode)
 560           {
 561             alignPanel.getSeqPanel().insertGapAtCursor(
 562                     evt.isControlDown() || evt.isShiftDown()
 563                             || evt.isAltDown());
 564           }
 565           break;
 566
 567         // case KeyEvent.VK_A:
 568         // if (viewport.cursorMode)
 569         // {
 570         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 571         // //System.out.println("A");
 572         // }
 573         // break;
 574         /*
 575          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 576          * System.out.println("closing bracket"); } break;
 577          */
 578         case KeyEvent.VK_DELETE:
 579         case KeyEvent.VK_BACK_SPACE:
 580           if (!viewport.cursorMode)
 581           {
 582             cut_actionPerformed(null);
 583           }
 584           else
 585           {
 586             alignPanel.getSeqPanel().deleteGapAtCursor(
 587                     evt.isControlDown() || evt.isShiftDown()
 588                             || evt.isAltDown());
 589           }
 590
 591           break;
 592
 593         case KeyEvent.VK_S:
 594           if (viewport.cursorMode)
 595           {
 596             alignPanel.getSeqPanel().setCursorRow();
 597           }
 598           break;
 599         case KeyEvent.VK_C:
 600           if (viewport.cursorMode && !evt.isControlDown())
 601           {
 602             alignPanel.getSeqPanel().setCursorColumn();
 603           }
 604           break;
 605         case KeyEvent.VK_P:
 606           if (viewport.cursorMode)
 607           {
 608             alignPanel.getSeqPanel().setCursorPosition();
 609           }
 610           break;
 611
 612         case KeyEvent.VK_ENTER:
 613         case KeyEvent.VK_COMMA:
 614           if (viewport.cursorMode)
 615           {
 616             alignPanel.getSeqPanel().setCursorRowAndColumn();
 617           }
 618           break;
 619
 620         case KeyEvent.VK_Q:
 621           if (viewport.cursorMode)
 622           {
 623             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 624           }
 625           break;
 626         case KeyEvent.VK_M:
 627           if (viewport.cursorMode)
 628           {
 629             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 630           }
 631           break;
 632
 633         case KeyEvent.VK_F2:
 634           viewport.cursorMode = !viewport.cursorMode;
 635           statusBar.setText(MessageManager.formatMessage(
 636                   "label.keyboard_editing_mode",
 637                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 641             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 642           }
 643           alignPanel.getSeqPanel().seqCanvas.repaint();
 644           break;
 645
 646         case KeyEvent.VK_F1:
 647           try
 648           {
 649             Help.showHelpWindow();
 650           } catch (Exception ex)
 651           {
 652             ex.printStackTrace();
 653           }
 654           break;
 655         case KeyEvent.VK_H:
 656         {
 657           boolean toggleSeqs = !evt.isControlDown();
 658           boolean toggleCols = !evt.isShiftDown();
 659           toggleHiddenRegions(toggleSeqs, toggleCols);
 660           break;
 661         }
 662         case KeyEvent.VK_PAGE_UP:
 663           if (viewport.getWrapAlignment())
 664           {
 665             alignPanel.scrollUp(true);
 666           }
 667           else
 668           {
 669             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 670                     - viewport.endSeq + viewport.startSeq);
 671           }
 672           break;
 673         case KeyEvent.VK_PAGE_DOWN:
 674           if (viewport.getWrapAlignment())
 675           {
 676             alignPanel.scrollUp(false);
 677           }
 678           else
 679           {
 680             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 681                     + viewport.endSeq - viewport.startSeq);
 682           }
 683           break;
 684         }
 685       }
 686
 687       @Override
 688       public void keyReleased(KeyEvent evt)
 689       {
 690         switch (evt.getKeyCode())
 691         {
 692         case KeyEvent.VK_LEFT:
 693           if (evt.isAltDown() || !viewport.cursorMode)
 694           {
 695             viewport.firePropertyChange("alignment", null, viewport
 696                     .getAlignment().getSequences());
 697           }
 698           break;
 699
 700         case KeyEvent.VK_RIGHT:
 701           if (evt.isAltDown() || !viewport.cursorMode)
 702           {
 703             viewport.firePropertyChange("alignment", null, viewport
 704                     .getAlignment().getSequences());
 705           }
 706           break;
 707         }
 708       }
 709     });
 710   }
 711
 712   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 713   {
 714     ap.alignFrame = this;
 715     avc = new jalview.controller.AlignViewController(this, viewport,
 716             alignPanel);
 717
 718     alignPanels.add(ap);
 719
 720     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 721
 722     int aSize = alignPanels.size();
 723
 724     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 725
 726     if (aSize == 1 && ap.av.viewName == null)
 727     {
 728       this.getContentPane().add(ap, BorderLayout.CENTER);
 729     }
 730     else
 731     {
 732       if (aSize == 2)
 733       {
 734         setInitialTabVisible();
 735       }
 736
 737       expandViews.setEnabled(true);
 738       gatherViews.setEnabled(true);
 739       tabbedPane.addTab(ap.av.viewName, ap);
 740
 741       ap.setVisible(false);
 742     }
 743
 744     if (newPanel)
 745     {
 746       if (ap.av.isPadGaps())
 747       {
 748         ap.av.getAlignment().padGaps();
 749       }
 750       ap.av.updateConservation(ap);
 751       ap.av.updateConsensus(ap);
 752       ap.av.updateStrucConsensus(ap);
 753     }
 754   }
 755
 756   public void setInitialTabVisible()
 757   {
 758     expandViews.setEnabled(true);
 759     gatherViews.setEnabled(true);
 760     tabbedPane.setVisible(true);
 761     AlignmentPanel first = alignPanels.get(0);
 762     tabbedPane.addTab(first.av.viewName, first);
 763     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 764   }
 765
 766   public AlignViewport getViewport()
 767   {
 768     return viewport;
 769   }
 770
 771   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 772   private void addServiceListeners()
 773   {
 774     final java.beans.PropertyChangeListener thisListener;
 775     Desktop.instance.addJalviewPropertyChangeListener("services",
 776             thisListener = new java.beans.PropertyChangeListener()
 777             {
 778               @Override
 779               public void propertyChange(PropertyChangeEvent evt)
 780               {
 781                 // // System.out.println("Discoverer property change.");
 782                 // if (evt.getPropertyName().equals("services"))
 783                 {
 784                   SwingUtilities.invokeLater(new Runnable()
 785                   {
 786
 787                     @Override
 788                     public void run()
 789                     {
 790                       System.err
 791                               .println("Rebuild WS Menu for service change");
 792                       BuildWebServiceMenu();
 793                     }
 794
 795                   });
 796                 }
 797               }
 798             });
 799     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 800     {
 801       @Override
 802       public void internalFrameClosed(
 803               javax.swing.event.InternalFrameEvent evt)
 804       {
 805         // System.out.println("deregistering discoverer listener");
 806         Desktop.instance.removeJalviewPropertyChangeListener("services",
 807                 thisListener);
 808         closeMenuItem_actionPerformed(true);
 809       };
 810     });
 811     // Finally, build the menu once to get current service state
 812     new Thread(new Runnable()
 813     {
 814       @Override
 815       public void run()
 816       {
 817         BuildWebServiceMenu();
 818       }
 819     }).start();
 820   }
 821
 822   /**
 823    * Configure menu items that vary according to whether the alignment is
 824    * nucleotide or protein
 825    *
 826    * @param nucleotide
 827    */
 828   public void setGUINucleotide(boolean nucleotide)
 829   {
 830     showTranslation.setVisible(nucleotide);
 831     conservationMenuItem.setEnabled(!nucleotide);
 832     modifyConservation.setEnabled(!nucleotide);
 833     showGroupConservation.setEnabled(!nucleotide);
 834     rnahelicesColour.setEnabled(nucleotide);
 835     purinePyrimidineColour.setEnabled(nucleotide);
 836     showComplementMenuItem.setText(MessageManager
 837             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 838     setColourSelected(jalview.bin.Cache.getDefault(
 839             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 840                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 841   }
 842
 843   /**
 844    * set up menus for the current viewport. This may be called after any
 845    * operation that affects the data in the current view (selection changed,
 846    * etc) to update the menus to reflect the new state.
 847    */
 848   public void setMenusForViewport()
 849   {
 850     setMenusFromViewport(viewport);
 851   }
 852
 853   /**
 854    * Need to call this method when tabs are selected for multiple views, or when
 855    * loading from Jalview2XML.java
 856    *
 857    * @param av
 858    *          AlignViewport
 859    */
 860   void setMenusFromViewport(AlignViewport av)
 861   {
 862     padGapsMenuitem.setSelected(av.isPadGaps());
 863     colourTextMenuItem.setSelected(av.isShowColourText());
 864     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 865     conservationMenuItem.setSelected(av.getConservationSelected());
 866     seqLimits.setSelected(av.getShowJVSuffix());
 867     idRightAlign.setSelected(av.isRightAlignIds());
 868     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 869     renderGapsMenuItem.setSelected(av.isRenderGaps());
 870     wrapMenuItem.setSelected(av.getWrapAlignment());
 871     scaleAbove.setVisible(av.getWrapAlignment());
 872     scaleLeft.setVisible(av.getWrapAlignment());
 873     scaleRight.setVisible(av.getWrapAlignment());
 874     annotationPanelMenuItem.setState(av.isShowAnnotation());
 875     /*
 876      * Show/hide annotations only enabled if annotation panel is shown
 877      */
 878     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 879     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 880     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 881     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 882     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 883     viewTextMenuItem.setSelected(av.getShowText());
 884     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 885     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 886     showGroupConservation.setSelected(av.isShowGroupConservation());
 887     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 888     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 889     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 890
 891     setColourSelected(ColourSchemeProperty.getColourName(av
 892             .getGlobalColourScheme()));
 893
 894     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 895     hiddenMarkers.setState(av.getShowHiddenMarkers());
 896     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 897     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 898     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 899     autoCalculate.setSelected(av.autoCalculateConsensus);
 900     sortByTree.setSelected(av.sortByTree);
 901     listenToViewSelections.setSelected(av.followSelection);
 902     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 903     rnahelicesColour
 904             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 905     setShowProductsEnabled();
 906     updateEditMenuBar();
 907   }
 908
 909   private IProgressIndicator progressBar;
 910
 911   /*
 912    * (non-Javadoc)
 913    *
 914    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 915    */
 916   @Override
 917   public void setProgressBar(String message, long id)
 918   {
 919     progressBar.setProgressBar(message, id);
 920   }
 921
 922   @Override
 923   public void registerHandler(final long id,
 924           final IProgressIndicatorHandler handler)
 925   {
 926     progressBar.registerHandler(id, handler);
 927   }
 928
 929   /**
 930    *
 931    * @return true if any progress bars are still active
 932    */
 933   @Override
 934   public boolean operationInProgress()
 935   {
 936     return progressBar.operationInProgress();
 937   }
 938
 939   @Override
 940   public void setStatus(String text)
 941   {
 942     statusBar.setText(text);
 943   }
 944
 945   /*
 946    * Added so Castor Mapping file can obtain Jalview Version
 947    */
 948   public String getVersion()
 949   {
 950     return jalview.bin.Cache.getProperty("VERSION");
 951   }
 952
 953   public FeatureRenderer getFeatureRenderer()
 954   {
 955     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 956   }
 957
 958   @Override
 959   public void fetchSequence_actionPerformed(ActionEvent e)
 960   {
 961     new SequenceFetcher(this);
 962   }
 963
 964   @Override
 965   public void addFromFile_actionPerformed(ActionEvent e)
 966   {
 967     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 968   }
 969
 970   @Override
 971   public void reload_actionPerformed(ActionEvent e)
 972   {
 973     if (fileName != null)
 974     {
 975       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 976       // originating file's format
 977       // TODO: work out how to recover feature settings for correct view(s) when
 978       // file is reloaded.
 979       if (currentFileFormat.equals("Jalview"))
 980       {
 981         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 982         for (int i = 0; i < frames.length; i++)
 983         {
 984           if (frames[i] instanceof AlignFrame && frames[i] != this
 985                   && ((AlignFrame) frames[i]).fileName != null
 986                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 987           {
 988             try
 989             {
 990               frames[i].setSelected(true);
 991               Desktop.instance.closeAssociatedWindows();
 992             } catch (java.beans.PropertyVetoException ex)
 993             {
 994             }
 995           }
 996
 997         }
 998         Desktop.instance.closeAssociatedWindows();
 999
1000         FileLoader loader = new FileLoader();
1001         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1002         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1003       }
1004       else
1005       {
1006         Rectangle bounds = this.getBounds();
1007
1008         FileLoader loader = new FileLoader();
1009         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1010         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1011                 protocol, currentFileFormat);
1012
1013         newframe.setBounds(bounds);
1014         if (featureSettings != null && featureSettings.isShowing())
1015         {
1016           final Rectangle fspos = featureSettings.frame.getBounds();
1017           // TODO: need a 'show feature settings' function that takes bounds -
1018           // need to refactor Desktop.addFrame
1019           newframe.featureSettings_actionPerformed(null);
1020           final FeatureSettings nfs = newframe.featureSettings;
1021           SwingUtilities.invokeLater(new Runnable()
1022           {
1023             @Override
1024             public void run()
1025             {
1026               nfs.frame.setBounds(fspos);
1027             }
1028           });
1029           this.featureSettings.close();
1030           this.featureSettings = null;
1031         }
1032         this.closeMenuItem_actionPerformed(true);
1033       }
1034     }
1035   }
1036
1037   @Override
1038   public void addFromText_actionPerformed(ActionEvent e)
1039   {
1040     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1041             .getAlignPanel());
1042   }
1043
1044   @Override
1045   public void addFromURL_actionPerformed(ActionEvent e)
1046   {
1047     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1048   }
1049
1050   @Override
1051   public void save_actionPerformed(ActionEvent e)
1052   {
1053     if (fileName == null
1054             || (currentFileFormat == null || !jalview.io.FormatAdapter
1055                     .isValidIOFormat(currentFileFormat, true))
1056             || fileName.startsWith("http"))
1057     {
1058       saveAs_actionPerformed(null);
1059     }
1060     else
1061     {
1062       saveAlignment(fileName, currentFileFormat);
1063     }
1064   }
1065
1066   /**
1067    * DOCUMENT ME!
1068    *
1069    * @param e
1070    *          DOCUMENT ME!
1071    */
1072   @Override
1073   public void saveAs_actionPerformed(ActionEvent e)
1074   {
1075     JalviewFileChooser chooser = new JalviewFileChooser(
1076             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1077             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1078             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1079             currentFileFormat, false);
1080
1081     chooser.setFileView(new JalviewFileView());
1082     chooser.setDialogTitle(MessageManager
1083             .getString("label.save_alignment_to_file"));
1084     chooser.setToolTipText(MessageManager.getString("action.save"));
1085
1086     int value = chooser.showSaveDialog(this);
1087
1088     if (value == JalviewFileChooser.APPROVE_OPTION)
1089     {
1090       currentFileFormat = chooser.getSelectedFormat();
1091       while (currentFileFormat == null)
1092       {
1093         JOptionPane
1094                 .showInternalMessageDialog(
1095                         Desktop.desktop,
1096                         MessageManager
1097                                 .getString("label.select_file_format_before_saving"),
1098                         MessageManager
1099                                 .getString("label.file_format_not_specified"),
1100                         JOptionPane.WARNING_MESSAGE);
1101         currentFileFormat = chooser.getSelectedFormat();
1102         value = chooser.showSaveDialog(this);
1103         if (value != JalviewFileChooser.APPROVE_OPTION)
1104         {
1105           return;
1106         }
1107       }
1108
1109       fileName = chooser.getSelectedFile().getPath();
1110
1111       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1112               currentFileFormat);
1113
1114       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1115       if (currentFileFormat.indexOf(" ") > -1)
1116       {
1117         currentFileFormat = currentFileFormat.substring(0,
1118                 currentFileFormat.indexOf(" "));
1119       }
1120       saveAlignment(fileName, currentFileFormat);
1121     }
1122   }
1123
1124   public boolean saveAlignment(String file, String format)
1125   {
1126     boolean success = true;
1127
1128     if (format.equalsIgnoreCase("Jalview"))
1129     {
1130       String shortName = title;
1131
1132       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1133       {
1134         shortName = shortName.substring(shortName
1135                 .lastIndexOf(java.io.File.separatorChar) + 1);
1136       }
1137
1138       success = new Jalview2XML().saveAlignment(this, file, shortName);
1139
1140       statusBar.setText(MessageManager.formatMessage(
1141               "label.successfully_saved_to_file_in_format", new Object[] {
1142                   fileName, format }));
1143
1144     }
1145     else
1146     {
1147       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1148       {
1149         warningMessage("Cannot save file " + fileName + " using format "
1150                 + format, "Alignment output format not supported");
1151         if (!Jalview.isHeadlessMode())
1152         {
1153           saveAs_actionPerformed(null);
1154         }
1155         return false;
1156       }
1157
1158       AlignmentExportData exportData = getAlignmentForExport(format,
1159               viewport, null);
1160       if (exportData.getSettings().isCancelled())
1161       {
1162         return false;
1163       }
1164       FormatAdapter f = new FormatAdapter(alignPanel,
1165               exportData.getSettings());
1166       String output = f.formatSequences(
1167               format,
1168               exportData.getAlignment(), // class cast exceptions will
1169               // occur in the distant future
1170               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1171               f.getCacheSuffixDefault(format),
1172               viewport.getColumnSelection());
1173
1174       if (output == null)
1175       {
1176         success = false;
1177       }
1178       else
1179       {
1180         try
1181         {
1182           java.io.PrintWriter out = new java.io.PrintWriter(
1183                   new java.io.FileWriter(file));
1184
1185           out.print(output);
1186           out.close();
1187           this.setTitle(file);
1188           statusBar.setText(MessageManager.formatMessage(
1189                   "label.successfully_saved_to_file_in_format",
1190                   new Object[] { fileName, format }));
1191         } catch (Exception ex)
1192         {
1193           success = false;
1194           ex.printStackTrace();
1195         }
1196       }
1197     }
1198
1199     if (!success)
1200     {
1201       JOptionPane.showInternalMessageDialog(this, MessageManager
1202               .formatMessage("label.couldnt_save_file",
1203                       new Object[] { fileName }), MessageManager
1204               .getString("label.error_saving_file"),
1205               JOptionPane.WARNING_MESSAGE);
1206     }
1207
1208     return success;
1209   }
1210
1211   private void warningMessage(String warning, String title)
1212   {
1213     if (new jalview.util.Platform().isHeadless())
1214     {
1215       System.err.println("Warning: " + title + "\nWarning: " + warning);
1216
1217     }
1218     else
1219     {
1220       JOptionPane.showInternalMessageDialog(this, warning, title,
1221               JOptionPane.WARNING_MESSAGE);
1222     }
1223     return;
1224   }
1225
1226   /**
1227    * DOCUMENT ME!
1228    *
1229    * @param e
1230    *          DOCUMENT ME!
1231    */
1232   @Override
1233   protected void outputText_actionPerformed(ActionEvent e)
1234   {
1235
1236     AlignmentExportData exportData = getAlignmentForExport(
1237             e.getActionCommand(), viewport, null);
1238     if (exportData.getSettings().isCancelled())
1239     {
1240       return;
1241     }
1242     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1243     cap.setForInput(null);
1244     try
1245     {
1246       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1247               .formatSequences(e.getActionCommand(),
1248                       exportData.getAlignment(),
1249                       exportData.getOmitHidden(),
1250                       exportData.getStartEndPostions(),
1251                       viewport.getColumnSelection()));
1252       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1253               "label.alignment_output_command",
1254               new Object[] { e.getActionCommand() }), 600, 500);
1255     } catch (OutOfMemoryError oom)
1256     {
1257       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1258       cap.dispose();
1259     }
1260
1261   }
1262
1263   public static AlignmentExportData getAlignmentForExport(
1264           String exportFormat, AlignViewportI viewport,
1265           AlignExportSettingI exportSettings)
1266   {
1267     AlignmentI alignmentToExport = null;
1268     AlignExportSettingI settings = exportSettings;
1269     String[] omitHidden = null;
1270     int[] alignmentStartEnd = new int[2];
1271
1272     HiddenSequences hiddenSeqs = viewport.getAlignment()
1273             .getHiddenSequences();
1274
1275     alignmentToExport = viewport.getAlignment();
1276     alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1277
1278     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1279     if (settings == null)
1280     {
1281       settings = new AlignExportSettings(hasHiddenSeqs,
1282               viewport.hasHiddenColumns(), exportFormat);
1283     }
1284     // settings.isExportAnnotations();
1285
1286     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1287     {
1288       omitHidden = viewport.getViewAsString(false);
1289     }
1290
1291     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1292     {
1293       alignmentToExport = hiddenSeqs.getFullAlignment();
1294     }
1295     else
1296     {
1297       alignmentToExport = viewport.getAlignment();
1298       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1299               .getColumnSelection().getHiddenColumns());
1300     }
1301     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1302             omitHidden, alignmentStartEnd, settings);
1303     return ed;
1304   }
1305
1306   public static int[] getStartEnd(int[] aligmentStartEnd,
1307           List<int[]> hiddenCols)
1308   {
1309     int startPos = aligmentStartEnd[0];
1310     int endPos = aligmentStartEnd[1];
1311
1312     int[] lowestRange = new int[] { -1, -1 };
1313     int[] higestRange = new int[] { -1, -1 };
1314
1315     for (int[] hiddenCol : hiddenCols)
1316     {
1317       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1318       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1319     }
1320
1321     if (lowestRange[0] == -1 && lowestRange[1] == -1)
1322     {
1323       startPos = aligmentStartEnd[0];
1324     }
1325     else
1326     {
1327       startPos = lowestRange[1] + 1;
1328     }
1329
1330     if (higestRange[0] == -1 && higestRange[1] == -1)
1331     {
1332       endPos = aligmentStartEnd[1];
1333     }
1334     else
1335     {
1336       endPos = higestRange[0] - 1;
1337     }
1338
1339     // System.out.println("Export range : " + startPos + " - " + endPos);
1340     return new int[] { startPos, endPos };
1341   }
1342
1343   public static void main(String[] args)
1344   {
1345     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1346     hiddenCols.add(new int[] { 0, 0 });
1347     hiddenCols.add(new int[] { 6, 9 });
1348     hiddenCols.add(new int[] { 11, 12 });
1349     hiddenCols.add(new int[] { 33, 33 });
1350     hiddenCols.add(new int[] { 50, 50 });
1351
1352     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1353     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1354   }
1355
1356   /**
1357    * DOCUMENT ME!
1358    *
1359    * @param e
1360    *          DOCUMENT ME!
1361    */
1362   @Override
1363   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1364   {
1365     new HtmlSvgOutput(null, alignPanel);
1366   }
1367
1368   @Override
1369   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1370   {
1371     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1372     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1373   }
1374
1375   public void createImageMap(File file, String image)
1376   {
1377     alignPanel.makePNGImageMap(file, image);
1378   }
1379
1380   /**
1381    * DOCUMENT ME!
1382    *
1383    * @param e
1384    *          DOCUMENT ME!
1385    */
1386   @Override
1387   public void createPNG(File f)
1388   {
1389     alignPanel.makePNG(f);
1390   }
1391
1392   /**
1393    * DOCUMENT ME!
1394    *
1395    * @param e
1396    *          DOCUMENT ME!
1397    */
1398   @Override
1399   public void createEPS(File f)
1400   {
1401     alignPanel.makeEPS(f);
1402   }
1403
1404   public void createSVG(File f)
1405   {
1406     alignPanel.makeSVG(f);
1407   }
1408
1409   @Override
1410   public void pageSetup_actionPerformed(ActionEvent e)
1411   {
1412     PrinterJob printJob = PrinterJob.getPrinterJob();
1413     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1414   }
1415
1416   /**
1417    * DOCUMENT ME!
1418    *
1419    * @param e
1420    *          DOCUMENT ME!
1421    */
1422   @Override
1423   public void printMenuItem_actionPerformed(ActionEvent e)
1424   {
1425     // Putting in a thread avoids Swing painting problems
1426     PrintThread thread = new PrintThread(alignPanel);
1427     thread.start();
1428   }
1429
1430   @Override
1431   public void exportFeatures_actionPerformed(ActionEvent e)
1432   {
1433     new AnnotationExporter().exportFeatures(alignPanel);
1434   }
1435
1436   @Override
1437   public void exportAnnotations_actionPerformed(ActionEvent e)
1438   {
1439     new AnnotationExporter().exportAnnotations(alignPanel);
1440   }
1441
1442   @Override
1443   public void associatedData_actionPerformed(ActionEvent e)
1444   {
1445     // Pick the tree file
1446     JalviewFileChooser chooser = new JalviewFileChooser(
1447             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1448     chooser.setFileView(new JalviewFileView());
1449     chooser.setDialogTitle(MessageManager
1450             .getString("label.load_jalview_annotations"));
1451     chooser.setToolTipText(MessageManager
1452             .getString("label.load_jalview_annotations"));
1453
1454     int value = chooser.showOpenDialog(null);
1455
1456     if (value == JalviewFileChooser.APPROVE_OPTION)
1457     {
1458       String choice = chooser.getSelectedFile().getPath();
1459       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1460       loadJalviewDataFile(choice, null, null, null);
1461     }
1462
1463   }
1464
1465   /**
1466    * Close the current view or all views in the alignment frame. If the frame
1467    * only contains one view then the alignment will be removed from memory.
1468    *
1469    * @param closeAllTabs
1470    */
1471   @Override
1472   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1473   {
1474     if (alignPanels != null && alignPanels.size() < 2)
1475     {
1476       closeAllTabs = true;
1477     }
1478
1479     try
1480     {
1481       if (alignPanels != null)
1482       {
1483         if (closeAllTabs)
1484         {
1485           if (this.isClosed())
1486           {
1487             // really close all the windows - otherwise wait till
1488             // setClosed(true) is called
1489             for (int i = 0; i < alignPanels.size(); i++)
1490             {
1491               AlignmentPanel ap = alignPanels.get(i);
1492               ap.closePanel();
1493             }
1494           }
1495         }
1496         else
1497         {
1498           closeView(alignPanel);
1499         }
1500       }
1501
1502       if (closeAllTabs)
1503       {
1504         /*
1505          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1506          * be called recursively, with the frame now in 'closed' state
1507          */
1508         this.setClosed(true);
1509       }
1510     } catch (Exception ex)
1511     {
1512       ex.printStackTrace();
1513     }
1514   }
1515
1516   /**
1517    * Close the specified panel and close up tabs appropriately.
1518    *
1519    * @param panelToClose
1520    */
1521   public void closeView(AlignmentPanel panelToClose)
1522   {
1523     int index = tabbedPane.getSelectedIndex();
1524     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1525     alignPanels.remove(panelToClose);
1526     panelToClose.closePanel();
1527     panelToClose = null;
1528
1529     tabbedPane.removeTabAt(closedindex);
1530     tabbedPane.validate();
1531
1532     if (index > closedindex || index == tabbedPane.getTabCount())
1533     {
1534       // modify currently selected tab index if necessary.
1535       index--;
1536     }
1537
1538     this.tabSelectionChanged(index);
1539   }
1540
1541   /**
1542    * DOCUMENT ME!
1543    */
1544   void updateEditMenuBar()
1545   {
1546
1547     if (viewport.getHistoryList().size() > 0)
1548     {
1549       undoMenuItem.setEnabled(true);
1550       CommandI command = viewport.getHistoryList().peek();
1551       undoMenuItem.setText(MessageManager.formatMessage(
1552               "label.undo_command",
1553               new Object[] { command.getDescription() }));
1554     }
1555     else
1556     {
1557       undoMenuItem.setEnabled(false);
1558       undoMenuItem.setText(MessageManager.getString("action.undo"));
1559     }
1560
1561     if (viewport.getRedoList().size() > 0)
1562     {
1563       redoMenuItem.setEnabled(true);
1564
1565       CommandI command = viewport.getRedoList().peek();
1566       redoMenuItem.setText(MessageManager.formatMessage(
1567               "label.redo_command",
1568               new Object[] { command.getDescription() }));
1569     }
1570     else
1571     {
1572       redoMenuItem.setEnabled(false);
1573       redoMenuItem.setText(MessageManager.getString("action.redo"));
1574     }
1575   }
1576
1577   public void addHistoryItem(CommandI command)
1578   {
1579     if (command.getSize() > 0)
1580     {
1581       viewport.addToHistoryList(command);
1582       viewport.clearRedoList();
1583       updateEditMenuBar();
1584       viewport.updateHiddenColumns();
1585       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1586       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1587       // viewport.getColumnSelection()
1588       // .getHiddenColumns().size() > 0);
1589     }
1590   }
1591
1592   /**
1593    *
1594    * @return alignment objects for all views
1595    */
1596   AlignmentI[] getViewAlignments()
1597   {
1598     if (alignPanels != null)
1599     {
1600       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1601       int i = 0;
1602       for (AlignmentPanel ap : alignPanels)
1603       {
1604         als[i++] = ap.av.getAlignment();
1605       }
1606       return als;
1607     }
1608     if (viewport != null)
1609     {
1610       return new AlignmentI[] { viewport.getAlignment() };
1611     }
1612     return null;
1613   }
1614
1615   /**
1616    * DOCUMENT ME!
1617    *
1618    * @param e
1619    *          DOCUMENT ME!
1620    */
1621   @Override
1622   protected void undoMenuItem_actionPerformed(ActionEvent e)
1623   {
1624     if (viewport.getHistoryList().isEmpty())
1625     {
1626       return;
1627     }
1628     CommandI command = viewport.getHistoryList().pop();
1629     viewport.addToRedoList(command);
1630     command.undoCommand(getViewAlignments());
1631
1632     AlignmentViewport originalSource = getOriginatingSource(command);
1633     updateEditMenuBar();
1634
1635     if (originalSource != null)
1636     {
1637       if (originalSource != viewport)
1638       {
1639         Cache.log
1640                 .warn("Implementation worry: mismatch of viewport origin for undo");
1641       }
1642       originalSource.updateHiddenColumns();
1643       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1644       // null
1645       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1646       // viewport.getColumnSelection()
1647       // .getHiddenColumns().size() > 0);
1648       originalSource.firePropertyChange("alignment", null, originalSource
1649               .getAlignment().getSequences());
1650     }
1651   }
1652
1653   /**
1654    * DOCUMENT ME!
1655    *
1656    * @param e
1657    *          DOCUMENT ME!
1658    */
1659   @Override
1660   protected void redoMenuItem_actionPerformed(ActionEvent e)
1661   {
1662     if (viewport.getRedoList().size() < 1)
1663     {
1664       return;
1665     }
1666
1667     CommandI command = viewport.getRedoList().pop();
1668     viewport.addToHistoryList(command);
1669     command.doCommand(getViewAlignments());
1670
1671     AlignmentViewport originalSource = getOriginatingSource(command);
1672     updateEditMenuBar();
1673
1674     if (originalSource != null)
1675     {
1676
1677       if (originalSource != viewport)
1678       {
1679         Cache.log
1680                 .warn("Implementation worry: mismatch of viewport origin for redo");
1681       }
1682       originalSource.updateHiddenColumns();
1683       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1684       // null
1685       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1686       // viewport.getColumnSelection()
1687       // .getHiddenColumns().size() > 0);
1688       originalSource.firePropertyChange("alignment", null, originalSource
1689               .getAlignment().getSequences());
1690     }
1691   }
1692
1693   AlignmentViewport getOriginatingSource(CommandI command)
1694   {
1695     AlignmentViewport originalSource = null;
1696     // For sequence removal and addition, we need to fire
1697     // the property change event FROM the viewport where the
1698     // original alignment was altered
1699     AlignmentI al = null;
1700     if (command instanceof EditCommand)
1701     {
1702       EditCommand editCommand = (EditCommand) command;
1703       al = editCommand.getAlignment();
1704       List<Component> comps = PaintRefresher.components.get(viewport
1705               .getSequenceSetId());
1706
1707       for (Component comp : comps)
1708       {
1709         if (comp instanceof AlignmentPanel)
1710         {
1711           if (al == ((AlignmentPanel) comp).av.getAlignment())
1712           {
1713             originalSource = ((AlignmentPanel) comp).av;
1714             break;
1715           }
1716         }
1717       }
1718     }
1719
1720     if (originalSource == null)
1721     {
1722       // The original view is closed, we must validate
1723       // the current view against the closed view first
1724       if (al != null)
1725       {
1726         PaintRefresher.validateSequences(al, viewport.getAlignment());
1727       }
1728
1729       originalSource = viewport;
1730     }
1731
1732     return originalSource;
1733   }
1734
1735   /**
1736    * DOCUMENT ME!
1737    *
1738    * @param up
1739    *          DOCUMENT ME!
1740    */
1741   public void moveSelectedSequences(boolean up)
1742   {
1743     SequenceGroup sg = viewport.getSelectionGroup();
1744
1745     if (sg == null)
1746     {
1747       return;
1748     }
1749     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1750             viewport.getHiddenRepSequences(), up);
1751     alignPanel.paintAlignment(true);
1752   }
1753
1754   synchronized void slideSequences(boolean right, int size)
1755   {
1756     List<SequenceI> sg = new ArrayList<SequenceI>();
1757     if (viewport.cursorMode)
1758     {
1759       sg.add(viewport.getAlignment().getSequenceAt(
1760               alignPanel.getSeqPanel().seqCanvas.cursorY));
1761     }
1762     else if (viewport.getSelectionGroup() != null
1763             && viewport.getSelectionGroup().getSize() != viewport
1764                     .getAlignment().getHeight())
1765     {
1766       sg = viewport.getSelectionGroup().getSequences(
1767               viewport.getHiddenRepSequences());
1768     }
1769
1770     if (sg.size() < 1)
1771     {
1772       return;
1773     }
1774
1775     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1776
1777     for (SequenceI seq : viewport.getAlignment().getSequences())
1778     {
1779       if (!sg.contains(seq))
1780       {
1781         invertGroup.add(seq);
1782       }
1783     }
1784
1785     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1786
1787     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1788     for (int i = 0; i < invertGroup.size(); i++)
1789     {
1790       seqs2[i] = invertGroup.get(i);
1791     }
1792
1793     SlideSequencesCommand ssc;
1794     if (right)
1795     {
1796       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1797               size, viewport.getGapCharacter());
1798     }
1799     else
1800     {
1801       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1802               size, viewport.getGapCharacter());
1803     }
1804
1805     int groupAdjustment = 0;
1806     if (ssc.getGapsInsertedBegin() && right)
1807     {
1808       if (viewport.cursorMode)
1809       {
1810         alignPanel.getSeqPanel().moveCursor(size, 0);
1811       }
1812       else
1813       {
1814         groupAdjustment = size;
1815       }
1816     }
1817     else if (!ssc.getGapsInsertedBegin() && !right)
1818     {
1819       if (viewport.cursorMode)
1820       {
1821         alignPanel.getSeqPanel().moveCursor(-size, 0);
1822       }
1823       else
1824       {
1825         groupAdjustment = -size;
1826       }
1827     }
1828
1829     if (groupAdjustment != 0)
1830     {
1831       viewport.getSelectionGroup().setStartRes(
1832               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1833       viewport.getSelectionGroup().setEndRes(
1834               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1835     }
1836
1837     /*
1838      * just extend the last slide command if compatible; but not if in
1839      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1840      */
1841     boolean appendHistoryItem = false;
1842     Deque<CommandI> historyList = viewport.getHistoryList();
1843     boolean inSplitFrame = getSplitViewContainer() != null;
1844     if (!inSplitFrame && historyList != null && historyList.size() > 0
1845             && historyList.peek() instanceof SlideSequencesCommand)
1846     {
1847       appendHistoryItem = ssc
1848               .appendSlideCommand((SlideSequencesCommand) historyList
1849                       .peek());
1850     }
1851
1852     if (!appendHistoryItem)
1853     {
1854       addHistoryItem(ssc);
1855     }
1856
1857     repaint();
1858   }
1859
1860   /**
1861    * DOCUMENT ME!
1862    *
1863    * @param e
1864    *          DOCUMENT ME!
1865    */
1866   @Override
1867   protected void copy_actionPerformed(ActionEvent e)
1868   {
1869     System.gc();
1870     if (viewport.getSelectionGroup() == null)
1871     {
1872       return;
1873     }
1874     // TODO: preserve the ordering of displayed alignment annotation in any
1875     // internal paste (particularly sequence associated annotation)
1876     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1877     String[] omitHidden = null;
1878
1879     if (viewport.hasHiddenColumns())
1880     {
1881       omitHidden = viewport.getViewAsString(true);
1882     }
1883
1884     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1885             omitHidden, null);
1886
1887     StringSelection ss = new StringSelection(output);
1888
1889     try
1890     {
1891       jalview.gui.Desktop.internalCopy = true;
1892       // Its really worth setting the clipboard contents
1893       // to empty before setting the large StringSelection!!
1894       Toolkit.getDefaultToolkit().getSystemClipboard()
1895               .setContents(new StringSelection(""), null);
1896
1897       Toolkit.getDefaultToolkit().getSystemClipboard()
1898               .setContents(ss, Desktop.instance);
1899     } catch (OutOfMemoryError er)
1900     {
1901       new OOMWarning("copying region", er);
1902       return;
1903     }
1904
1905     ArrayList<int[]> hiddenColumns = null;
1906     if (viewport.hasHiddenColumns())
1907     {
1908       hiddenColumns = new ArrayList<int[]>();
1909       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1910               .getSelectionGroup().getEndRes();
1911       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1912       {
1913         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1914         {
1915           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1916               region[1] - hiddenOffset });
1917         }
1918       }
1919     }
1920
1921     Desktop.jalviewClipboard = new Object[] { seqs,
1922         viewport.getAlignment().getDataset(), hiddenColumns };
1923     statusBar.setText(MessageManager.formatMessage(
1924             "label.copied_sequences_to_clipboard", new Object[] { Integer
1925                     .valueOf(seqs.length).toString() }));
1926   }
1927
1928   /**
1929    * DOCUMENT ME!
1930    *
1931    * @param e
1932    *          DOCUMENT ME!
1933    */
1934   @Override
1935   protected void pasteNew_actionPerformed(ActionEvent e)
1936   {
1937     paste(true);
1938   }
1939
1940   /**
1941    * DOCUMENT ME!
1942    *
1943    * @param e
1944    *          DOCUMENT ME!
1945    */
1946   @Override
1947   protected void pasteThis_actionPerformed(ActionEvent e)
1948   {
1949     paste(false);
1950   }
1951
1952   /**
1953    * Paste contents of Jalview clipboard
1954    *
1955    * @param newAlignment
1956    *          true to paste to a new alignment, otherwise add to this.
1957    */
1958   void paste(boolean newAlignment)
1959   {
1960     boolean externalPaste = true;
1961     try
1962     {
1963       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1964       Transferable contents = c.getContents(this);
1965
1966       if (contents == null)
1967       {
1968         return;
1969       }
1970
1971       String str, format;
1972       try
1973       {
1974         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1975         if (str.length() < 1)
1976         {
1977           return;
1978         }
1979
1980         format = new IdentifyFile().Identify(str, "Paste");
1981
1982       } catch (OutOfMemoryError er)
1983       {
1984         new OOMWarning("Out of memory pasting sequences!!", er);
1985         return;
1986       }
1987
1988       SequenceI[] sequences;
1989       boolean annotationAdded = false;
1990       AlignmentI alignment = null;
1991
1992       if (Desktop.jalviewClipboard != null)
1993       {
1994         // The clipboard was filled from within Jalview, we must use the
1995         // sequences
1996         // And dataset from the copied alignment
1997         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1998         // be doubly sure that we create *new* sequence objects.
1999         sequences = new SequenceI[newseq.length];
2000         for (int i = 0; i < newseq.length; i++)
2001         {
2002           sequences[i] = new Sequence(newseq[i]);
2003         }
2004         alignment = new Alignment(sequences);
2005         externalPaste = false;
2006       }
2007       else
2008       {
2009         // parse the clipboard as an alignment.
2010         alignment = new FormatAdapter().readFile(str, "Paste", format);
2011         sequences = alignment.getSequencesArray();
2012       }
2013
2014       int alwidth = 0;
2015       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2016       int fgroup = -1;
2017
2018       if (newAlignment)
2019       {
2020
2021         if (Desktop.jalviewClipboard != null)
2022         {
2023           // dataset is inherited
2024           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2025         }
2026         else
2027         {
2028           // new dataset is constructed
2029           alignment.setDataset(null);
2030         }
2031         alwidth = alignment.getWidth() + 1;
2032       }
2033       else
2034       {
2035         AlignmentI pastedal = alignment; // preserve pasted alignment object
2036         // Add pasted sequences and dataset into existing alignment.
2037         alignment = viewport.getAlignment();
2038         alwidth = alignment.getWidth() + 1;
2039         // decide if we need to import sequences from an existing dataset
2040         boolean importDs = Desktop.jalviewClipboard != null
2041                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2042         // importDs==true instructs us to copy over new dataset sequences from
2043         // an existing alignment
2044         Vector newDs = (importDs) ? new Vector() : null; // used to create
2045         // minimum dataset set
2046
2047         for (int i = 0; i < sequences.length; i++)
2048         {
2049           if (importDs)
2050           {
2051             newDs.addElement(null);
2052           }
2053           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2054           // paste
2055           if (importDs && ds != null)
2056           {
2057             if (!newDs.contains(ds))
2058             {
2059               newDs.setElementAt(ds, i);
2060               ds = new Sequence(ds);
2061               // update with new dataset sequence
2062               sequences[i].setDatasetSequence(ds);
2063             }
2064             else
2065             {
2066               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2067             }
2068           }
2069           else
2070           {
2071             // copy and derive new dataset sequence
2072             sequences[i] = sequences[i].deriveSequence();
2073             alignment.getDataset().addSequence(
2074                     sequences[i].getDatasetSequence());
2075             // TODO: avoid creation of duplicate dataset sequences with a
2076             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2077           }
2078           alignment.addSequence(sequences[i]); // merges dataset
2079         }
2080         if (newDs != null)
2081         {
2082           newDs.clear(); // tidy up
2083         }
2084         if (alignment.getAlignmentAnnotation() != null)
2085         {
2086           for (AlignmentAnnotation alan : alignment
2087                   .getAlignmentAnnotation())
2088           {
2089             if (alan.graphGroup > fgroup)
2090             {
2091               fgroup = alan.graphGroup;
2092             }
2093           }
2094         }
2095         if (pastedal.getAlignmentAnnotation() != null)
2096         {
2097           // Add any annotation attached to alignment.
2098           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2099           for (int i = 0; i < alann.length; i++)
2100           {
2101             annotationAdded = true;
2102             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2103             {
2104               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2105               if (newann.graphGroup > -1)
2106               {
2107                 if (newGraphGroups.size() <= newann.graphGroup
2108                         || newGraphGroups.get(newann.graphGroup) == null)
2109                 {
2110                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2111                   {
2112                     newGraphGroups.add(q, null);
2113                   }
2114                   newGraphGroups.set(newann.graphGroup, new Integer(
2115                           ++fgroup));
2116                 }
2117                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2118                         .intValue();
2119               }
2120
2121               newann.padAnnotation(alwidth);
2122               alignment.addAnnotation(newann);
2123             }
2124           }
2125         }
2126       }
2127       if (!newAlignment)
2128       {
2129         // /////
2130         // ADD HISTORY ITEM
2131         //
2132         addHistoryItem(new EditCommand(
2133                 MessageManager.getString("label.add_sequences"),
2134                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2135       }
2136       // Add any annotations attached to sequences
2137       for (int i = 0; i < sequences.length; i++)
2138       {
2139         if (sequences[i].getAnnotation() != null)
2140         {
2141           AlignmentAnnotation newann;
2142           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2143           {
2144             annotationAdded = true;
2145             newann = sequences[i].getAnnotation()[a];
2146             newann.adjustForAlignment();
2147             newann.padAnnotation(alwidth);
2148             if (newann.graphGroup > -1)
2149             {
2150               if (newann.graphGroup > -1)
2151               {
2152                 if (newGraphGroups.size() <= newann.graphGroup
2153                         || newGraphGroups.get(newann.graphGroup) == null)
2154                 {
2155                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2156                   {
2157                     newGraphGroups.add(q, null);
2158                   }
2159                   newGraphGroups.set(newann.graphGroup, new Integer(
2160                           ++fgroup));
2161                 }
2162                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2163                         .intValue();
2164               }
2165             }
2166             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2167             // was
2168             // duplicated
2169             // earlier
2170             alignment
2171                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2172           }
2173         }
2174       }
2175       if (!newAlignment)
2176       {
2177
2178         // propagate alignment changed.
2179         viewport.setEndSeq(alignment.getHeight());
2180         if (annotationAdded)
2181         {
2182           // Duplicate sequence annotation in all views.
2183           AlignmentI[] alview = this.getViewAlignments();
2184           for (int i = 0; i < sequences.length; i++)
2185           {
2186             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2187             if (sann == null)
2188             {
2189               continue;
2190             }
2191             for (int avnum = 0; avnum < alview.length; avnum++)
2192             {
2193               if (alview[avnum] != alignment)
2194               {
2195                 // duplicate in a view other than the one with input focus
2196                 int avwidth = alview[avnum].getWidth() + 1;
2197                 // this relies on sann being preserved after we
2198                 // modify the sequence's annotation array for each duplication
2199                 for (int a = 0; a < sann.length; a++)
2200                 {
2201                   AlignmentAnnotation newann = new AlignmentAnnotation(
2202                           sann[a]);
2203                   sequences[i].addAlignmentAnnotation(newann);
2204                   newann.padAnnotation(avwidth);
2205                   alview[avnum].addAnnotation(newann); // annotation was
2206                   // duplicated earlier
2207                   // TODO JAL-1145 graphGroups are not updated for sequence
2208                   // annotation added to several views. This may cause
2209                   // strangeness
2210                   alview[avnum].setAnnotationIndex(newann, a);
2211                 }
2212               }
2213             }
2214           }
2215           buildSortByAnnotationScoresMenu();
2216         }
2217         viewport.firePropertyChange("alignment", null,
2218                 alignment.getSequences());
2219         if (alignPanels != null)
2220         {
2221           for (AlignmentPanel ap : alignPanels)
2222           {
2223             ap.validateAnnotationDimensions(false);
2224           }
2225         }
2226         else
2227         {
2228           alignPanel.validateAnnotationDimensions(false);
2229         }
2230
2231       }
2232       else
2233       {
2234         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2235                 DEFAULT_HEIGHT);
2236         String newtitle = new String("Copied sequences");
2237
2238         if (Desktop.jalviewClipboard != null
2239                 && Desktop.jalviewClipboard[2] != null)
2240         {
2241           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2242           for (int[] region : hc)
2243           {
2244             af.viewport.hideColumns(region[0], region[1]);
2245           }
2246         }
2247
2248         // >>>This is a fix for the moment, until a better solution is
2249         // found!!<<<
2250         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2251                 .transferSettings(
2252                         alignPanel.getSeqPanel().seqCanvas
2253                                 .getFeatureRenderer());
2254
2255         // TODO: maintain provenance of an alignment, rather than just make the
2256         // title a concatenation of operations.
2257         if (!externalPaste)
2258         {
2259           if (title.startsWith("Copied sequences"))
2260           {
2261             newtitle = title;
2262           }
2263           else
2264           {
2265             newtitle = newtitle.concat("- from " + title);
2266           }
2267         }
2268         else
2269         {
2270           newtitle = new String("Pasted sequences");
2271         }
2272
2273         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2274                 DEFAULT_HEIGHT);
2275
2276       }
2277
2278     } catch (Exception ex)
2279     {
2280       ex.printStackTrace();
2281       System.out.println("Exception whilst pasting: " + ex);
2282       // could be anything being pasted in here
2283     }
2284
2285   }
2286
2287   @Override
2288   protected void expand_newalign(ActionEvent e)
2289   {
2290     try
2291     {
2292       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2293               .getAlignment(), -1);
2294       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2295               DEFAULT_HEIGHT);
2296       String newtitle = new String("Flanking alignment");
2297
2298       if (Desktop.jalviewClipboard != null
2299               && Desktop.jalviewClipboard[2] != null)
2300       {
2301         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2302         for (int region[] : hc)
2303         {
2304           af.viewport.hideColumns(region[0], region[1]);
2305         }
2306       }
2307
2308       // >>>This is a fix for the moment, until a better solution is
2309       // found!!<<<
2310       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2311               .transferSettings(
2312                       alignPanel.getSeqPanel().seqCanvas
2313                               .getFeatureRenderer());
2314
2315       // TODO: maintain provenance of an alignment, rather than just make the
2316       // title a concatenation of operations.
2317       {
2318         if (title.startsWith("Copied sequences"))
2319         {
2320           newtitle = title;
2321         }
2322         else
2323         {
2324           newtitle = newtitle.concat("- from " + title);
2325         }
2326       }
2327
2328       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2329
2330     } catch (Exception ex)
2331     {
2332       ex.printStackTrace();
2333       System.out.println("Exception whilst pasting: " + ex);
2334       // could be anything being pasted in here
2335     } catch (OutOfMemoryError oom)
2336     {
2337       new OOMWarning("Viewing flanking region of alignment", oom);
2338     }
2339   }
2340
2341   /**
2342    * DOCUMENT ME!
2343    *
2344    * @param e
2345    *          DOCUMENT ME!
2346    */
2347   @Override
2348   protected void cut_actionPerformed(ActionEvent e)
2349   {
2350     copy_actionPerformed(null);
2351     delete_actionPerformed(null);
2352   }
2353
2354   /**
2355    * DOCUMENT ME!
2356    *
2357    * @param e
2358    *          DOCUMENT ME!
2359    */
2360   @Override
2361   protected void delete_actionPerformed(ActionEvent evt)
2362   {
2363
2364     SequenceGroup sg = viewport.getSelectionGroup();
2365     if (sg == null)
2366     {
2367       return;
2368     }
2369
2370     /*
2371      * If the cut affects all sequences, warn, remove highlighted columns
2372      */
2373     if (sg.getSize() == viewport.getAlignment().getHeight())
2374     {
2375       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2376               .getAlignment().getWidth()) ? true : false;
2377       if (isEntireAlignWidth)
2378       {
2379         int confirm = JOptionPane.showConfirmDialog(this,
2380                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2381                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2382                 JOptionPane.OK_CANCEL_OPTION);
2383
2384         if (confirm == JOptionPane.CANCEL_OPTION
2385                 || confirm == JOptionPane.CLOSED_OPTION)
2386         {
2387           return;
2388         }
2389       }
2390       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2391               sg.getEndRes() + 1);
2392     }
2393     SequenceI[] cut = sg.getSequences()
2394             .toArray(new SequenceI[sg.getSize()]);
2395
2396     addHistoryItem(new EditCommand(
2397             MessageManager.getString("label.cut_sequences"), Action.CUT,
2398             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2399             viewport.getAlignment()));
2400
2401     viewport.setSelectionGroup(null);
2402     viewport.sendSelection();
2403     viewport.getAlignment().deleteGroup(sg);
2404
2405     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2406             .getSequences());
2407     if (viewport.getAlignment().getHeight() < 1)
2408     {
2409       try
2410       {
2411         this.setClosed(true);
2412       } catch (Exception ex)
2413       {
2414       }
2415     }
2416   }
2417
2418   /**
2419    * DOCUMENT ME!
2420    *
2421    * @param e
2422    *          DOCUMENT ME!
2423    */
2424   @Override
2425   protected void deleteGroups_actionPerformed(ActionEvent e)
2426   {
2427     if (avc.deleteGroups())
2428     {
2429       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2430       alignPanel.updateAnnotation();
2431       alignPanel.paintAlignment(true);
2432     }
2433   }
2434
2435   /**
2436    * DOCUMENT ME!
2437    *
2438    * @param e
2439    *          DOCUMENT ME!
2440    */
2441   @Override
2442   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2443   {
2444     SequenceGroup sg = new SequenceGroup();
2445
2446     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2447     {
2448       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2449     }
2450
2451     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2452     viewport.setSelectionGroup(sg);
2453     viewport.sendSelection();
2454     alignPanel.paintAlignment(true);
2455     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2456   }
2457
2458   /**
2459    * DOCUMENT ME!
2460    *
2461    * @param e
2462    *          DOCUMENT ME!
2463    */
2464   @Override
2465   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2466   {
2467     if (viewport.cursorMode)
2468     {
2469       alignPanel.getSeqPanel().keyboardNo1 = null;
2470       alignPanel.getSeqPanel().keyboardNo2 = null;
2471     }
2472     viewport.setSelectionGroup(null);
2473     viewport.getColumnSelection().clear();
2474     viewport.setSelectionGroup(null);
2475     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2476     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2477     alignPanel.paintAlignment(true);
2478     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2479     viewport.sendSelection();
2480   }
2481
2482   /**
2483    * DOCUMENT ME!
2484    *
2485    * @param e
2486    *          DOCUMENT ME!
2487    */
2488   @Override
2489   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2490   {
2491     SequenceGroup sg = viewport.getSelectionGroup();
2492
2493     if (sg == null)
2494     {
2495       selectAllSequenceMenuItem_actionPerformed(null);
2496
2497       return;
2498     }
2499
2500     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2501     {
2502       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2503     }
2504
2505     alignPanel.paintAlignment(true);
2506     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2507     viewport.sendSelection();
2508   }
2509
2510   @Override
2511   public void invertColSel_actionPerformed(ActionEvent e)
2512   {
2513     viewport.invertColumnSelection();
2514     alignPanel.paintAlignment(true);
2515     viewport.sendSelection();
2516   }
2517
2518   /**
2519    * DOCUMENT ME!
2520    *
2521    * @param e
2522    *          DOCUMENT ME!
2523    */
2524   @Override
2525   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2526   {
2527     trimAlignment(true);
2528   }
2529
2530   /**
2531    * DOCUMENT ME!
2532    *
2533    * @param e
2534    *          DOCUMENT ME!
2535    */
2536   @Override
2537   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2538   {
2539     trimAlignment(false);
2540   }
2541
2542   void trimAlignment(boolean trimLeft)
2543   {
2544     ColumnSelection colSel = viewport.getColumnSelection();
2545     int column;
2546
2547     if (colSel.size() > 0)
2548     {
2549       if (trimLeft)
2550       {
2551         column = colSel.getMin();
2552       }
2553       else
2554       {
2555         column = colSel.getMax();
2556       }
2557
2558       SequenceI[] seqs;
2559       if (viewport.getSelectionGroup() != null)
2560       {
2561         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2562                 viewport.getHiddenRepSequences());
2563       }
2564       else
2565       {
2566         seqs = viewport.getAlignment().getSequencesArray();
2567       }
2568
2569       TrimRegionCommand trimRegion;
2570       if (trimLeft)
2571       {
2572         trimRegion = new TrimRegionCommand("Remove Left",
2573                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2574                 viewport.getAlignment(), viewport.getColumnSelection(),
2575                 viewport.getSelectionGroup());
2576         viewport.setStartRes(0);
2577       }
2578       else
2579       {
2580         trimRegion = new TrimRegionCommand("Remove Right",
2581                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2582                 viewport.getAlignment(), viewport.getColumnSelection(),
2583                 viewport.getSelectionGroup());
2584       }
2585
2586       statusBar.setText(MessageManager.formatMessage(
2587               "label.removed_columns",
2588               new String[] { Integer.valueOf(trimRegion.getSize())
2589                       .toString() }));
2590
2591       addHistoryItem(trimRegion);
2592
2593       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2594       {
2595         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2596                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2597         {
2598           viewport.getAlignment().deleteGroup(sg);
2599         }
2600       }
2601
2602       viewport.firePropertyChange("alignment", null, viewport
2603               .getAlignment().getSequences());
2604     }
2605   }
2606
2607   /**
2608    * DOCUMENT ME!
2609    *
2610    * @param e
2611    *          DOCUMENT ME!
2612    */
2613   @Override
2614   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2615   {
2616     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2617
2618     SequenceI[] seqs;
2619     if (viewport.getSelectionGroup() != null)
2620     {
2621       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2622               viewport.getHiddenRepSequences());
2623       start = viewport.getSelectionGroup().getStartRes();
2624       end = viewport.getSelectionGroup().getEndRes();
2625     }
2626     else
2627     {
2628       seqs = viewport.getAlignment().getSequencesArray();
2629     }
2630
2631     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2632             "Remove Gapped Columns", seqs, start, end,
2633             viewport.getAlignment());
2634
2635     addHistoryItem(removeGapCols);
2636
2637     statusBar.setText(MessageManager.formatMessage(
2638             "label.removed_empty_columns",
2639             new Object[] { Integer.valueOf(removeGapCols.getSize())
2640                     .toString() }));
2641
2642     // This is to maintain viewport position on first residue
2643     // of first sequence
2644     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2645     int startRes = seq.findPosition(viewport.startRes);
2646     // ShiftList shifts;
2647     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2648     // edit.alColumnChanges=shifts.getInverse();
2649     // if (viewport.hasHiddenColumns)
2650     // viewport.getColumnSelection().compensateForEdits(shifts);
2651     viewport.setStartRes(seq.findIndex(startRes) - 1);
2652     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2653             .getSequences());
2654
2655   }
2656
2657   /**
2658    * DOCUMENT ME!
2659    *
2660    * @param e
2661    *          DOCUMENT ME!
2662    */
2663   @Override
2664   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2665   {
2666     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2667
2668     SequenceI[] seqs;
2669     if (viewport.getSelectionGroup() != null)
2670     {
2671       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2672               viewport.getHiddenRepSequences());
2673       start = viewport.getSelectionGroup().getStartRes();
2674       end = viewport.getSelectionGroup().getEndRes();
2675     }
2676     else
2677     {
2678       seqs = viewport.getAlignment().getSequencesArray();
2679     }
2680
2681     // This is to maintain viewport position on first residue
2682     // of first sequence
2683     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2684     int startRes = seq.findPosition(viewport.startRes);
2685
2686     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2687             viewport.getAlignment()));
2688
2689     viewport.setStartRes(seq.findIndex(startRes) - 1);
2690
2691     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2692             .getSequences());
2693
2694   }
2695
2696   /**
2697    * DOCUMENT ME!
2698    *
2699    * @param e
2700    *          DOCUMENT ME!
2701    */
2702   @Override
2703   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2704   {
2705     viewport.setPadGaps(padGapsMenuitem.isSelected());
2706     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2707             .getSequences());
2708   }
2709
2710   /**
2711    * DOCUMENT ME!
2712    *
2713    * @param e
2714    *          DOCUMENT ME!
2715    */
2716   @Override
2717   public void findMenuItem_actionPerformed(ActionEvent e)
2718   {
2719     new Finder();
2720   }
2721
2722   /**
2723    * Create a new view of the current alignment.
2724    */
2725   @Override
2726   public void newView_actionPerformed(ActionEvent e)
2727   {
2728     newView(null, true);
2729   }
2730
2731   /**
2732    * Creates and shows a new view of the current alignment.
2733    *
2734    * @param viewTitle
2735    *          title of newly created view; if null, one will be generated
2736    * @param copyAnnotation
2737    *          if true then duplicate all annnotation, groups and settings
2738    * @return new alignment panel, already displayed.
2739    */
2740   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2741   {
2742     /*
2743      * Create a new AlignmentPanel (with its own, new Viewport)
2744      */
2745     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2746             true);
2747     if (!copyAnnotation)
2748     {
2749       /*
2750        * remove all groups and annotation except for the automatic stuff
2751        */
2752       newap.av.getAlignment().deleteAllGroups();
2753       newap.av.getAlignment().deleteAllAnnotations(false);
2754     }
2755
2756     newap.av.setGatherViewsHere(false);
2757
2758     if (viewport.viewName == null)
2759     {
2760       viewport.viewName = MessageManager
2761               .getString("label.view_name_original");
2762     }
2763
2764     /*
2765      * Views share the same edits undo and redo stacks
2766      */
2767     newap.av.setHistoryList(viewport.getHistoryList());
2768     newap.av.setRedoList(viewport.getRedoList());
2769
2770     /*
2771      * Views share the same mappings; need to deregister any new mappings
2772      * created by copyAlignPanel, and register the new reference to the shared
2773      * mappings
2774      */
2775     newap.av.replaceMappings(viewport.getAlignment());
2776
2777     newap.av.viewName = getNewViewName(viewTitle);
2778
2779     addAlignmentPanel(newap, true);
2780     newap.alignmentChanged();
2781
2782     if (alignPanels.size() == 2)
2783     {
2784       viewport.setGatherViewsHere(true);
2785     }
2786     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2787     return newap;
2788   }
2789
2790   /**
2791    * Make a new name for the view, ensuring it is unique within the current
2792    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2793    * these now use viewId. Unique view names are still desirable for usability.)
2794    *
2795    * @param viewTitle
2796    * @return
2797    */
2798   protected String getNewViewName(String viewTitle)
2799   {
2800     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2801     boolean addFirstIndex = false;
2802     if (viewTitle == null || viewTitle.trim().length() == 0)
2803     {
2804       viewTitle = MessageManager.getString("action.view");
2805       addFirstIndex = true;
2806     }
2807     else
2808     {
2809       index = 1;// we count from 1 if given a specific name
2810     }
2811     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2812
2813     List<Component> comps = PaintRefresher.components.get(viewport
2814             .getSequenceSetId());
2815
2816     List<String> existingNames = getExistingViewNames(comps);
2817
2818     while (existingNames.contains(newViewName))
2819     {
2820       newViewName = viewTitle + " " + (++index);
2821     }
2822     return newViewName;
2823   }
2824
2825   /**
2826    * Returns a list of distinct view names found in the given list of
2827    * components. View names are held on the viewport of an AlignmentPanel.
2828    *
2829    * @param comps
2830    * @return
2831    */
2832   protected List<String> getExistingViewNames(List<Component> comps)
2833   {
2834     List<String> existingNames = new ArrayList<String>();
2835     for (Component comp : comps)
2836     {
2837       if (comp instanceof AlignmentPanel)
2838       {
2839         AlignmentPanel ap = (AlignmentPanel) comp;
2840         if (!existingNames.contains(ap.av.viewName))
2841         {
2842           existingNames.add(ap.av.viewName);
2843         }
2844       }
2845     }
2846     return existingNames;
2847   }
2848
2849   /**
2850    * Explode tabbed views into separate windows.
2851    */
2852   @Override
2853   public void expandViews_actionPerformed(ActionEvent e)
2854   {
2855     Desktop.instance.explodeViews(this);
2856   }
2857
2858   /**
2859    * Gather views in separate windows back into a tabbed presentation.
2860    */
2861   @Override
2862   public void gatherViews_actionPerformed(ActionEvent e)
2863   {
2864     Desktop.instance.gatherViews(this);
2865   }
2866
2867   /**
2868    * DOCUMENT ME!
2869    *
2870    * @param e
2871    *          DOCUMENT ME!
2872    */
2873   @Override
2874   public void font_actionPerformed(ActionEvent e)
2875   {
2876     new FontChooser(alignPanel);
2877   }
2878
2879   /**
2880    * DOCUMENT ME!
2881    *
2882    * @param e
2883    *          DOCUMENT ME!
2884    */
2885   @Override
2886   protected void seqLimit_actionPerformed(ActionEvent e)
2887   {
2888     viewport.setShowJVSuffix(seqLimits.isSelected());
2889
2890     alignPanel.getIdPanel().getIdCanvas()
2891             .setPreferredSize(alignPanel.calculateIdWidth());
2892     alignPanel.paintAlignment(true);
2893   }
2894
2895   @Override
2896   public void idRightAlign_actionPerformed(ActionEvent e)
2897   {
2898     viewport.setRightAlignIds(idRightAlign.isSelected());
2899     alignPanel.paintAlignment(true);
2900   }
2901
2902   @Override
2903   public void centreColumnLabels_actionPerformed(ActionEvent e)
2904   {
2905     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2906     alignPanel.paintAlignment(true);
2907   }
2908
2909   /*
2910    * (non-Javadoc)
2911    *
2912    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2913    */
2914   @Override
2915   protected void followHighlight_actionPerformed()
2916   {
2917     /*
2918      * Set the 'follow' flag on the Viewport (and scroll to position if now
2919      * true).
2920      */
2921     final boolean state = this.followHighlightMenuItem.getState();
2922     viewport.setFollowHighlight(state);
2923     if (state)
2924     {
2925       alignPanel.scrollToPosition(
2926               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2927     }
2928   }
2929
2930   /**
2931    * DOCUMENT ME!
2932    *
2933    * @param e
2934    *          DOCUMENT ME!
2935    */
2936   @Override
2937   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2938   {
2939     viewport.setColourText(colourTextMenuItem.isSelected());
2940     alignPanel.paintAlignment(true);
2941   }
2942
2943   /**
2944    * DOCUMENT ME!
2945    *
2946    * @param e
2947    *          DOCUMENT ME!
2948    */
2949   @Override
2950   public void wrapMenuItem_actionPerformed(ActionEvent e)
2951   {
2952     scaleAbove.setVisible(wrapMenuItem.isSelected());
2953     scaleLeft.setVisible(wrapMenuItem.isSelected());
2954     scaleRight.setVisible(wrapMenuItem.isSelected());
2955     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2956     alignPanel.updateLayout();
2957   }
2958
2959   @Override
2960   public void showAllSeqs_actionPerformed(ActionEvent e)
2961   {
2962     viewport.showAllHiddenSeqs();
2963   }
2964
2965   @Override
2966   public void showAllColumns_actionPerformed(ActionEvent e)
2967   {
2968     viewport.showAllHiddenColumns();
2969     repaint();
2970   }
2971
2972   @Override
2973   public void hideSelSequences_actionPerformed(ActionEvent e)
2974   {
2975     viewport.hideAllSelectedSeqs();
2976     // alignPanel.paintAlignment(true);
2977   }
2978
2979   /**
2980    * called by key handler and the hide all/show all menu items
2981    *
2982    * @param toggleSeqs
2983    * @param toggleCols
2984    */
2985   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2986   {
2987
2988     boolean hide = false;
2989     SequenceGroup sg = viewport.getSelectionGroup();
2990     if (!toggleSeqs && !toggleCols)
2991     {
2992       // Hide everything by the current selection - this is a hack - we do the
2993       // invert and then hide
2994       // first check that there will be visible columns after the invert.
2995       if ((viewport.getColumnSelection() != null
2996               && viewport.getColumnSelection().getSelected() != null && viewport
2997               .getColumnSelection().getSelected().size() > 0)
2998               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2999                       .getEndRes()))
3000       {
3001         // now invert the sequence set, if required - empty selection implies
3002         // that no hiding is required.
3003         if (sg != null)
3004         {
3005           invertSequenceMenuItem_actionPerformed(null);
3006           sg = viewport.getSelectionGroup();
3007           toggleSeqs = true;
3008
3009         }
3010         viewport.expandColSelection(sg, true);
3011         // finally invert the column selection and get the new sequence
3012         // selection.
3013         invertColSel_actionPerformed(null);
3014         toggleCols = true;
3015       }
3016     }
3017
3018     if (toggleSeqs)
3019     {
3020       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3021       {
3022         hideSelSequences_actionPerformed(null);
3023         hide = true;
3024       }
3025       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3026               .size() > 0))
3027       {
3028         showAllSeqs_actionPerformed(null);
3029       }
3030     }
3031
3032     if (toggleCols)
3033     {
3034       if (viewport.getColumnSelection().getSelected().size() > 0)
3035       {
3036         hideSelColumns_actionPerformed(null);
3037         if (!toggleSeqs)
3038         {
3039           viewport.setSelectionGroup(sg);
3040         }
3041       }
3042       else if (!hide)
3043       {
3044         showAllColumns_actionPerformed(null);
3045       }
3046     }
3047   }
3048
3049   /*
3050    * (non-Javadoc)
3051    *
3052    * @see
3053    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3054    * event.ActionEvent)
3055    */
3056   @Override
3057   public void hideAllButSelection_actionPerformed(ActionEvent e)
3058   {
3059     toggleHiddenRegions(false, false);
3060   }
3061
3062   /*
3063    * (non-Javadoc)
3064    *
3065    * @see
3066    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3067    * .ActionEvent)
3068    */
3069   @Override
3070   public void hideAllSelection_actionPerformed(ActionEvent e)
3071   {
3072     SequenceGroup sg = viewport.getSelectionGroup();
3073     viewport.expandColSelection(sg, false);
3074     viewport.hideAllSelectedSeqs();
3075     viewport.hideSelectedColumns();
3076     alignPanel.paintAlignment(true);
3077   }
3078
3079   /*
3080    * (non-Javadoc)
3081    *
3082    * @see
3083    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3084    * ActionEvent)
3085    */
3086   @Override
3087   public void showAllhidden_actionPerformed(ActionEvent e)
3088   {
3089     viewport.showAllHiddenColumns();
3090     viewport.showAllHiddenSeqs();
3091     alignPanel.paintAlignment(true);
3092   }
3093
3094   @Override
3095   public void hideSelColumns_actionPerformed(ActionEvent e)
3096   {
3097     viewport.hideSelectedColumns();
3098     alignPanel.paintAlignment(true);
3099   }
3100
3101   @Override
3102   public void hiddenMarkers_actionPerformed(ActionEvent e)
3103   {
3104     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3105     repaint();
3106   }
3107
3108   /**
3109    * DOCUMENT ME!
3110    *
3111    * @param e
3112    *          DOCUMENT ME!
3113    */
3114   @Override
3115   protected void scaleAbove_actionPerformed(ActionEvent e)
3116   {
3117     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3118     alignPanel.paintAlignment(true);
3119   }
3120
3121   /**
3122    * DOCUMENT ME!
3123    *
3124    * @param e
3125    *          DOCUMENT ME!
3126    */
3127   @Override
3128   protected void scaleLeft_actionPerformed(ActionEvent e)
3129   {
3130     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3131     alignPanel.paintAlignment(true);
3132   }
3133
3134   /**
3135    * DOCUMENT ME!
3136    *
3137    * @param e
3138    *          DOCUMENT ME!
3139    */
3140   @Override
3141   protected void scaleRight_actionPerformed(ActionEvent e)
3142   {
3143     viewport.setScaleRightWrapped(scaleRight.isSelected());
3144     alignPanel.paintAlignment(true);
3145   }
3146
3147   /**
3148    * DOCUMENT ME!
3149    *
3150    * @param e
3151    *          DOCUMENT ME!
3152    */
3153   @Override
3154   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3155   {
3156     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3157     alignPanel.paintAlignment(true);
3158   }
3159
3160   /**
3161    * DOCUMENT ME!
3162    *
3163    * @param e
3164    *          DOCUMENT ME!
3165    */
3166   @Override
3167   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3168   {
3169     viewport.setShowText(viewTextMenuItem.isSelected());
3170     alignPanel.paintAlignment(true);
3171   }
3172
3173   /**
3174    * DOCUMENT ME!
3175    *
3176    * @param e
3177    *          DOCUMENT ME!
3178    */
3179   @Override
3180   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3181   {
3182     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3183     alignPanel.paintAlignment(true);
3184   }
3185
3186   public FeatureSettings featureSettings;
3187
3188   @Override
3189   public FeatureSettingsControllerI getFeatureSettingsUI()
3190   {
3191     return featureSettings;
3192   }
3193
3194   @Override
3195   public void featureSettings_actionPerformed(ActionEvent e)
3196   {
3197     if (featureSettings != null)
3198     {
3199       featureSettings.close();
3200       featureSettings = null;
3201     }
3202     if (!showSeqFeatures.isSelected())
3203     {
3204       // make sure features are actually displayed
3205       showSeqFeatures.setSelected(true);
3206       showSeqFeatures_actionPerformed(null);
3207     }
3208     featureSettings = new FeatureSettings(this);
3209   }
3210
3211   /**
3212    * Set or clear 'Show Sequence Features'
3213    *
3214    * @param evt
3215    *          DOCUMENT ME!
3216    */
3217   @Override
3218   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3219   {
3220     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3221     alignPanel.paintAlignment(true);
3222     if (alignPanel.getOverviewPanel() != null)
3223     {
3224       alignPanel.getOverviewPanel().updateOverviewImage();
3225     }
3226   }
3227
3228   /**
3229    * Set or clear 'Show Sequence Features'
3230    *
3231    * @param evt
3232    *          DOCUMENT ME!
3233    */
3234   @Override
3235   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3236   {
3237     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3238             .isSelected());
3239     if (viewport.isShowSequenceFeaturesHeight())
3240     {
3241       // ensure we're actually displaying features
3242       viewport.setShowSequenceFeatures(true);
3243       showSeqFeatures.setSelected(true);
3244     }
3245     alignPanel.paintAlignment(true);
3246     if (alignPanel.getOverviewPanel() != null)
3247     {
3248       alignPanel.getOverviewPanel().updateOverviewImage();
3249     }
3250   }
3251
3252   /**
3253    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3254    * the annotations panel as a whole.
3255    *
3256    * The options to show/hide all annotations should be enabled when the panel
3257    * is shown, and disabled when the panel is hidden.
3258    *
3259    * @param e
3260    */
3261   @Override
3262   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3263   {
3264     final boolean setVisible = annotationPanelMenuItem.isSelected();
3265     viewport.setShowAnnotation(setVisible);
3266     this.showAllSeqAnnotations.setEnabled(setVisible);
3267     this.hideAllSeqAnnotations.setEnabled(setVisible);
3268     this.showAllAlAnnotations.setEnabled(setVisible);
3269     this.hideAllAlAnnotations.setEnabled(setVisible);
3270     alignPanel.updateLayout();
3271   }
3272
3273   @Override
3274   public void alignmentProperties()
3275   {
3276     JEditorPane editPane = new JEditorPane("text/html", "");
3277     editPane.setEditable(false);
3278     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3279             .formatAsHtml();
3280     editPane.setText(MessageManager.formatMessage("label.html_content",
3281             new Object[] { contents.toString() }));
3282     JInternalFrame frame = new JInternalFrame();
3283     frame.getContentPane().add(new JScrollPane(editPane));
3284
3285     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3286             "label.alignment_properties", new Object[] { getTitle() }),
3287             500, 400);
3288   }
3289
3290   /**
3291    * DOCUMENT ME!
3292    *
3293    * @param e
3294    *          DOCUMENT ME!
3295    */
3296   @Override
3297   public void overviewMenuItem_actionPerformed(ActionEvent e)
3298   {
3299     if (alignPanel.overviewPanel != null)
3300     {
3301       return;
3302     }
3303
3304     JInternalFrame frame = new JInternalFrame();
3305     OverviewPanel overview = new OverviewPanel(alignPanel);
3306     frame.setContentPane(overview);
3307     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3308             "label.overview_params", new Object[] { this.getTitle() }),
3309             frame.getWidth(), frame.getHeight());
3310     frame.pack();
3311     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3312     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3313     {
3314       @Override
3315       public void internalFrameClosed(
3316               javax.swing.event.InternalFrameEvent evt)
3317       {
3318         alignPanel.setOverviewPanel(null);
3319       };
3320     });
3321
3322     alignPanel.setOverviewPanel(overview);
3323   }
3324
3325   @Override
3326   public void textColour_actionPerformed(ActionEvent e)
3327   {
3328     new TextColourChooser().chooseColour(alignPanel, null);
3329   }
3330
3331   /**
3332    * DOCUMENT ME!
3333    *
3334    * @param e
3335    *          DOCUMENT ME!
3336    */
3337   @Override
3338   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3339   {
3340     changeColour(null);
3341   }
3342
3343   /**
3344    * DOCUMENT ME!
3345    *
3346    * @param e
3347    *          DOCUMENT ME!
3348    */
3349   @Override
3350   public void clustalColour_actionPerformed(ActionEvent e)
3351   {
3352     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3353             viewport.getHiddenRepSequences()));
3354   }
3355
3356   /**
3357    * DOCUMENT ME!
3358    *
3359    * @param e
3360    *          DOCUMENT ME!
3361    */
3362   @Override
3363   public void zappoColour_actionPerformed(ActionEvent e)
3364   {
3365     changeColour(new ZappoColourScheme());
3366   }
3367
3368   /**
3369    * DOCUMENT ME!
3370    *
3371    * @param e
3372    *          DOCUMENT ME!
3373    */
3374   @Override
3375   public void taylorColour_actionPerformed(ActionEvent e)
3376   {
3377     changeColour(new TaylorColourScheme());
3378   }
3379
3380   /**
3381    * DOCUMENT ME!
3382    *
3383    * @param e
3384    *          DOCUMENT ME!
3385    */
3386   @Override
3387   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3388   {
3389     changeColour(new HydrophobicColourScheme());
3390   }
3391
3392   /**
3393    * DOCUMENT ME!
3394    *
3395    * @param e
3396    *          DOCUMENT ME!
3397    */
3398   @Override
3399   public void helixColour_actionPerformed(ActionEvent e)
3400   {
3401     changeColour(new HelixColourScheme());
3402   }
3403
3404   /**
3405    * DOCUMENT ME!
3406    *
3407    * @param e
3408    *          DOCUMENT ME!
3409    */
3410   @Override
3411   public void strandColour_actionPerformed(ActionEvent e)
3412   {
3413     changeColour(new StrandColourScheme());
3414   }
3415
3416   /**
3417    * DOCUMENT ME!
3418    *
3419    * @param e
3420    *          DOCUMENT ME!
3421    */
3422   @Override
3423   public void turnColour_actionPerformed(ActionEvent e)
3424   {
3425     changeColour(new TurnColourScheme());
3426   }
3427
3428   /**
3429    * DOCUMENT ME!
3430    *
3431    * @param e
3432    *          DOCUMENT ME!
3433    */
3434   @Override
3435   public void buriedColour_actionPerformed(ActionEvent e)
3436   {
3437     changeColour(new BuriedColourScheme());
3438   }
3439
3440   /**
3441    * DOCUMENT ME!
3442    *
3443    * @param e
3444    *          DOCUMENT ME!
3445    */
3446   @Override
3447   public void nucleotideColour_actionPerformed(ActionEvent e)
3448   {
3449     changeColour(new NucleotideColourScheme());
3450   }
3451
3452   @Override
3453   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3454   {
3455     changeColour(new PurinePyrimidineColourScheme());
3456   }
3457
3458   /*
3459    * public void covariationColour_actionPerformed(ActionEvent e) {
3460    * changeColour(new
3461    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3462    * ()[0])); }
3463    */
3464   @Override
3465   public void annotationColour_actionPerformed(ActionEvent e)
3466   {
3467     new AnnotationColourChooser(viewport, alignPanel);
3468   }
3469
3470   @Override
3471   public void annotationColumn_actionPerformed(ActionEvent e)
3472   {
3473     new AnnotationColumnChooser(viewport, alignPanel);
3474   }
3475
3476   @Override
3477   public void rnahelicesColour_actionPerformed(ActionEvent e)
3478   {
3479     new RNAHelicesColourChooser(viewport, alignPanel);
3480   }
3481
3482   /**
3483    * DOCUMENT ME!
3484    *
3485    * @param e
3486    *          DOCUMENT ME!
3487    */
3488   @Override
3489   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3490   {
3491     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3492   }
3493
3494   /**
3495    * DOCUMENT ME!
3496    *
3497    * @param cs
3498    *          DOCUMENT ME!
3499    */
3500   public void changeColour(ColourSchemeI cs)
3501   {
3502     // TODO: pull up to controller method
3503
3504     if (cs != null)
3505     {
3506       // Make sure viewport is up to date w.r.t. any sliders
3507       if (viewport.getAbovePIDThreshold())
3508       {
3509         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3510                 "Background");
3511         viewport.setThreshold(threshold);
3512       }
3513
3514       if (viewport.getConservationSelected())
3515       {
3516         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3517                 cs, "Background"));
3518       }
3519       if (cs instanceof TCoffeeColourScheme)
3520       {
3521         tcoffeeColour.setEnabled(true);
3522         tcoffeeColour.setSelected(true);
3523       }
3524     }
3525
3526     viewport.setGlobalColourScheme(cs);
3527
3528     alignPanel.paintAlignment(true);
3529   }
3530
3531   /**
3532    * DOCUMENT ME!
3533    *
3534    * @param e
3535    *          DOCUMENT ME!
3536    */
3537   @Override
3538   protected void modifyPID_actionPerformed(ActionEvent e)
3539   {
3540     if (viewport.getAbovePIDThreshold()
3541             && viewport.getGlobalColourScheme() != null)
3542     {
3543       SliderPanel.setPIDSliderSource(alignPanel,
3544               viewport.getGlobalColourScheme(), "Background");
3545       SliderPanel.showPIDSlider();
3546     }
3547   }
3548
3549   /**
3550    * DOCUMENT ME!
3551    *
3552    * @param e
3553    *          DOCUMENT ME!
3554    */
3555   @Override
3556   protected void modifyConservation_actionPerformed(ActionEvent e)
3557   {
3558     if (viewport.getConservationSelected()
3559             && viewport.getGlobalColourScheme() != null)
3560     {
3561       SliderPanel.setConservationSlider(alignPanel,
3562               viewport.getGlobalColourScheme(), "Background");
3563       SliderPanel.showConservationSlider();
3564     }
3565   }
3566
3567   /**
3568    * DOCUMENT ME!
3569    *
3570    * @param e
3571    *          DOCUMENT ME!
3572    */
3573   @Override
3574   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3575   {
3576     viewport.setConservationSelected(conservationMenuItem.isSelected());
3577
3578     viewport.setAbovePIDThreshold(false);
3579     abovePIDThreshold.setSelected(false);
3580
3581     changeColour(viewport.getGlobalColourScheme());
3582
3583     modifyConservation_actionPerformed(null);
3584   }
3585
3586   /**
3587    * DOCUMENT ME!
3588    *
3589    * @param e
3590    *          DOCUMENT ME!
3591    */
3592   @Override
3593   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3594   {
3595     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3596
3597     conservationMenuItem.setSelected(false);
3598     viewport.setConservationSelected(false);
3599
3600     changeColour(viewport.getGlobalColourScheme());
3601
3602     modifyPID_actionPerformed(null);
3603   }
3604
3605   /**
3606    * DOCUMENT ME!
3607    *
3608    * @param e
3609    *          DOCUMENT ME!
3610    */
3611   @Override
3612   public void userDefinedColour_actionPerformed(ActionEvent e)
3613   {
3614     if (e.getActionCommand().equals(
3615             MessageManager.getString("action.user_defined")))
3616     {
3617       new UserDefinedColours(alignPanel, null);
3618     }
3619     else
3620     {
3621       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3622               .getUserColourSchemes().get(e.getActionCommand());
3623
3624       changeColour(udc);
3625     }
3626   }
3627
3628   public void updateUserColourMenu()
3629   {
3630
3631     Component[] menuItems = colourMenu.getMenuComponents();
3632     int iSize = menuItems.length;
3633     for (int i = 0; i < iSize; i++)
3634     {
3635       if (menuItems[i].getName() != null
3636               && menuItems[i].getName().equals("USER_DEFINED"))
3637       {
3638         colourMenu.remove(menuItems[i]);
3639         iSize--;
3640       }
3641     }
3642     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3643     {
3644       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3645               .getUserColourSchemes().keys();
3646
3647       while (userColours.hasMoreElements())
3648       {
3649         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3650                 userColours.nextElement().toString());
3651         radioItem.setName("USER_DEFINED");
3652         radioItem.addMouseListener(new MouseAdapter()
3653         {
3654           @Override
3655           public void mousePressed(MouseEvent evt)
3656           {
3657             if (evt.isControlDown()
3658                     || SwingUtilities.isRightMouseButton(evt))
3659             {
3660               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3661
3662               int option = JOptionPane.showInternalConfirmDialog(
3663                       jalview.gui.Desktop.desktop,
3664                       MessageManager
3665                               .getString("label.remove_from_default_list"),
3666                       MessageManager
3667                               .getString("label.remove_user_defined_colour"),
3668                       JOptionPane.YES_NO_OPTION);
3669               if (option == JOptionPane.YES_OPTION)
3670               {
3671                 jalview.gui.UserDefinedColours
3672                         .removeColourFromDefaults(radioItem.getText());
3673                 colourMenu.remove(radioItem);
3674               }
3675               else
3676               {
3677                 radioItem.addActionListener(new ActionListener()
3678                 {
3679                   @Override
3680                   public void actionPerformed(ActionEvent evt)
3681                   {
3682                     userDefinedColour_actionPerformed(evt);
3683                   }
3684                 });
3685               }
3686             }
3687           }
3688         });
3689         radioItem.addActionListener(new ActionListener()
3690         {
3691           @Override
3692           public void actionPerformed(ActionEvent evt)
3693           {
3694             userDefinedColour_actionPerformed(evt);
3695           }
3696         });
3697
3698         colourMenu.insert(radioItem, 15);
3699         colours.add(radioItem);
3700       }
3701     }
3702   }
3703
3704   /**
3705    * DOCUMENT ME!
3706    *
3707    * @param e
3708    *          DOCUMENT ME!
3709    */
3710   @Override
3711   public void PIDColour_actionPerformed(ActionEvent e)
3712   {
3713     changeColour(new PIDColourScheme());
3714   }
3715
3716   /**
3717    * DOCUMENT ME!
3718    *
3719    * @param e
3720    *          DOCUMENT ME!
3721    */
3722   @Override
3723   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3724   {
3725     changeColour(new Blosum62ColourScheme());
3726   }
3727
3728   /**
3729    * DOCUMENT ME!
3730    *
3731    * @param e
3732    *          DOCUMENT ME!
3733    */
3734   @Override
3735   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3736   {
3737     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3738     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3739             .getAlignment().getSequenceAt(0), null);
3740     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3741             viewport.getAlignment()));
3742     alignPanel.paintAlignment(true);
3743   }
3744
3745   /**
3746    * DOCUMENT ME!
3747    *
3748    * @param e
3749    *          DOCUMENT ME!
3750    */
3751   @Override
3752   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3753   {
3754     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3755     AlignmentSorter.sortByID(viewport.getAlignment());
3756     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3757             viewport.getAlignment()));
3758     alignPanel.paintAlignment(true);
3759   }
3760
3761   /**
3762    * DOCUMENT ME!
3763    *
3764    * @param e
3765    *          DOCUMENT ME!
3766    */
3767   @Override
3768   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3769   {
3770     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3771     AlignmentSorter.sortByLength(viewport.getAlignment());
3772     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3773             viewport.getAlignment()));
3774     alignPanel.paintAlignment(true);
3775   }
3776
3777   /**
3778    * DOCUMENT ME!
3779    *
3780    * @param e
3781    *          DOCUMENT ME!
3782    */
3783   @Override
3784   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3785   {
3786     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3787     AlignmentSorter.sortByGroup(viewport.getAlignment());
3788     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3789             viewport.getAlignment()));
3790
3791     alignPanel.paintAlignment(true);
3792   }
3793
3794   /**
3795    * DOCUMENT ME!
3796    *
3797    * @param e
3798    *          DOCUMENT ME!
3799    */
3800   @Override
3801   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3802   {
3803     new RedundancyPanel(alignPanel, this);
3804   }
3805
3806   /**
3807    * DOCUMENT ME!
3808    *
3809    * @param e
3810    *          DOCUMENT ME!
3811    */
3812   @Override
3813   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3814   {
3815     if ((viewport.getSelectionGroup() == null)
3816             || (viewport.getSelectionGroup().getSize() < 2))
3817     {
3818       JOptionPane.showInternalMessageDialog(this, MessageManager
3819               .getString("label.you_must_select_least_two_sequences"),
3820               MessageManager.getString("label.invalid_selection"),
3821               JOptionPane.WARNING_MESSAGE);
3822     }
3823     else
3824     {
3825       JInternalFrame frame = new JInternalFrame();
3826       frame.setContentPane(new PairwiseAlignPanel(viewport));
3827       Desktop.addInternalFrame(frame,
3828               MessageManager.getString("action.pairwise_alignment"), 600,
3829               500);
3830     }
3831   }
3832
3833   /**
3834    * DOCUMENT ME!
3835    *
3836    * @param e
3837    *          DOCUMENT ME!
3838    */
3839   @Override
3840   public void PCAMenuItem_actionPerformed(ActionEvent e)
3841   {
3842     if (((viewport.getSelectionGroup() != null)
3843             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3844             .getSelectionGroup().getSize() > 0))
3845             || (viewport.getAlignment().getHeight() < 4))
3846     {
3847       JOptionPane
3848               .showInternalMessageDialog(
3849                       this,
3850                       MessageManager
3851                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3852                       MessageManager
3853                               .getString("label.sequence_selection_insufficient"),
3854                       JOptionPane.WARNING_MESSAGE);
3855
3856       return;
3857     }
3858
3859     new PCAPanel(alignPanel);
3860   }
3861
3862   @Override
3863   public void autoCalculate_actionPerformed(ActionEvent e)
3864   {
3865     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3866     if (viewport.autoCalculateConsensus)
3867     {
3868       viewport.firePropertyChange("alignment", null, viewport
3869               .getAlignment().getSequences());
3870     }
3871   }
3872
3873   @Override
3874   public void sortByTreeOption_actionPerformed(ActionEvent e)
3875   {
3876     viewport.sortByTree = sortByTree.isSelected();
3877   }
3878
3879   @Override
3880   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3881   {
3882     viewport.followSelection = listenToViewSelections.isSelected();
3883   }
3884
3885   /**
3886    * DOCUMENT ME!
3887    *
3888    * @param e
3889    *          DOCUMENT ME!
3890    */
3891   @Override
3892   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3893   {
3894     newTreePanel("AV", "PID", "Average distance tree using PID");
3895   }
3896
3897   /**
3898    * DOCUMENT ME!
3899    *
3900    * @param e
3901    *          DOCUMENT ME!
3902    */
3903   @Override
3904   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3905   {
3906     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3907   }
3908
3909   /**
3910    * DOCUMENT ME!
3911    *
3912    * @param e
3913    *          DOCUMENT ME!
3914    */
3915   @Override
3916   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3917   {
3918     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3919   }
3920
3921   /**
3922    * DOCUMENT ME!
3923    *
3924    * @param e
3925    *          DOCUMENT ME!
3926    */
3927   @Override
3928   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3929   {
3930     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3931   }
3932
3933   /**
3934    * DOCUMENT ME!
3935    *
3936    * @param type
3937    *          DOCUMENT ME!
3938    * @param pwType
3939    *          DOCUMENT ME!
3940    * @param title
3941    *          DOCUMENT ME!
3942    */
3943   void newTreePanel(String type, String pwType, String title)
3944   {
3945     TreePanel tp;
3946
3947     if (viewport.getSelectionGroup() != null
3948             && viewport.getSelectionGroup().getSize() > 0)
3949     {
3950       if (viewport.getSelectionGroup().getSize() < 3)
3951       {
3952         JOptionPane
3953                 .showMessageDialog(
3954                         Desktop.desktop,
3955                         MessageManager
3956                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3957                         MessageManager
3958                                 .getString("label.not_enough_sequences"),
3959                         JOptionPane.WARNING_MESSAGE);
3960         return;
3961       }
3962
3963       SequenceGroup sg = viewport.getSelectionGroup();
3964
3965       /* Decide if the selection is a column region */
3966       for (SequenceI _s : sg.getSequences())
3967       {
3968         if (_s.getLength() < sg.getEndRes())
3969         {
3970           JOptionPane
3971                   .showMessageDialog(
3972                           Desktop.desktop,
3973                           MessageManager
3974                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3975                           MessageManager
3976                                   .getString("label.sequences_selection_not_aligned"),
3977                           JOptionPane.WARNING_MESSAGE);
3978
3979           return;
3980         }
3981       }
3982
3983       title = title + " on region";
3984       tp = new TreePanel(alignPanel, type, pwType);
3985     }
3986     else
3987     {
3988       // are the visible sequences aligned?
3989       if (!viewport.getAlignment().isAligned(false))
3990       {
3991         JOptionPane
3992                 .showMessageDialog(
3993                         Desktop.desktop,
3994                         MessageManager
3995                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3996                         MessageManager
3997                                 .getString("label.sequences_not_aligned"),
3998                         JOptionPane.WARNING_MESSAGE);
3999
4000         return;
4001       }
4002
4003       if (viewport.getAlignment().getHeight() < 2)
4004       {
4005         return;
4006       }
4007
4008       tp = new TreePanel(alignPanel, type, pwType);
4009     }
4010
4011     title += " from ";
4012
4013     if (viewport.viewName != null)
4014     {
4015       title += viewport.viewName + " of ";
4016     }
4017
4018     title += this.title;
4019
4020     Desktop.addInternalFrame(tp, title, 600, 500);
4021   }
4022
4023   /**
4024    * DOCUMENT ME!
4025    *
4026    * @param title
4027    *          DOCUMENT ME!
4028    * @param order
4029    *          DOCUMENT ME!
4030    */
4031   public void addSortByOrderMenuItem(String title,
4032           final AlignmentOrder order)
4033   {
4034     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4035             "action.by_title_param", new Object[] { title }));
4036     sort.add(item);
4037     item.addActionListener(new java.awt.event.ActionListener()
4038     {
4039       @Override
4040       public void actionPerformed(ActionEvent e)
4041       {
4042         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4043
4044         // TODO: JBPNote - have to map order entries to curent SequenceI
4045         // pointers
4046         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4047
4048         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4049                 .getAlignment()));
4050
4051         alignPanel.paintAlignment(true);
4052       }
4053     });
4054   }
4055
4056   /**
4057    * Add a new sort by annotation score menu item
4058    *
4059    * @param sort
4060    *          the menu to add the option to
4061    * @param scoreLabel
4062    *          the label used to retrieve scores for each sequence on the
4063    *          alignment
4064    */
4065   public void addSortByAnnotScoreMenuItem(JMenu sort,
4066           final String scoreLabel)
4067   {
4068     final JMenuItem item = new JMenuItem(scoreLabel);
4069     sort.add(item);
4070     item.addActionListener(new java.awt.event.ActionListener()
4071     {
4072       @Override
4073       public void actionPerformed(ActionEvent e)
4074       {
4075         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4076         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4077                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4078         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4079                 viewport.getAlignment()));
4080         alignPanel.paintAlignment(true);
4081       }
4082     });
4083   }
4084
4085   /**
4086    * last hash for alignment's annotation array - used to minimise cost of
4087    * rebuild.
4088    */
4089   protected int _annotationScoreVectorHash;
4090
4091   /**
4092    * search the alignment and rebuild the sort by annotation score submenu the
4093    * last alignment annotation vector hash is stored to minimize cost of
4094    * rebuilding in subsequence calls.
4095    *
4096    */
4097   @Override
4098   public void buildSortByAnnotationScoresMenu()
4099   {
4100     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4101     {
4102       return;
4103     }
4104
4105     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4106     {
4107       sortByAnnotScore.removeAll();
4108       // almost certainly a quicker way to do this - but we keep it simple
4109       Hashtable scoreSorts = new Hashtable();
4110       AlignmentAnnotation aann[];
4111       for (SequenceI sqa : viewport.getAlignment().getSequences())
4112       {
4113         aann = sqa.getAnnotation();
4114         for (int i = 0; aann != null && i < aann.length; i++)
4115         {
4116           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4117           {
4118             scoreSorts.put(aann[i].label, aann[i].label);
4119           }
4120         }
4121       }
4122       Enumeration labels = scoreSorts.keys();
4123       while (labels.hasMoreElements())
4124       {
4125         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4126                 (String) labels.nextElement());
4127       }
4128       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4129       scoreSorts.clear();
4130
4131       _annotationScoreVectorHash = viewport.getAlignment()
4132               .getAlignmentAnnotation().hashCode();
4133     }
4134   }
4135
4136   /**
4137    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4138    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4139    * call. Listeners are added to remove the menu item when the treePanel is
4140    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4141    * modified.
4142    *
4143    * @param treePanel
4144    *          Displayed tree window.
4145    * @param title
4146    *          SortBy menu item title.
4147    */
4148   @Override
4149   public void buildTreeMenu()
4150   {
4151     calculateTree.removeAll();
4152     // build the calculate menu
4153
4154     for (final String type : new String[] { "NJ", "AV" })
4155     {
4156       String treecalcnm = MessageManager.getString("label.tree_calc_"
4157               + type.toLowerCase());
4158       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4159       {
4160         JMenuItem tm = new JMenuItem();
4161         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4162         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4163         {
4164           String smn = MessageManager.getStringOrReturn(
4165                   "label.score_model_", sm.getName());
4166           final String title = MessageManager.formatMessage(
4167                   "label.treecalc_title", treecalcnm, smn);
4168           tm.setText(title);//
4169           tm.addActionListener(new java.awt.event.ActionListener()
4170           {
4171             @Override
4172             public void actionPerformed(ActionEvent e)
4173             {
4174               newTreePanel(type, pwtype, title);
4175             }
4176           });
4177           calculateTree.add(tm);
4178         }
4179
4180       }
4181     }
4182     sortByTreeMenu.removeAll();
4183
4184     List<Component> comps = PaintRefresher.components.get(viewport
4185             .getSequenceSetId());
4186     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4187     for (Component comp : comps)
4188     {
4189       if (comp instanceof TreePanel)
4190       {
4191         treePanels.add((TreePanel) comp);
4192       }
4193     }
4194
4195     if (treePanels.size() < 1)
4196     {
4197       sortByTreeMenu.setVisible(false);
4198       return;
4199     }
4200
4201     sortByTreeMenu.setVisible(true);
4202
4203     for (final TreePanel tp : treePanels)
4204     {
4205       final JMenuItem item = new JMenuItem(tp.getTitle());
4206       item.addActionListener(new java.awt.event.ActionListener()
4207       {
4208         @Override
4209         public void actionPerformed(ActionEvent e)
4210         {
4211           tp.sortByTree_actionPerformed();
4212           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4213
4214         }
4215       });
4216
4217       sortByTreeMenu.add(item);
4218     }
4219   }
4220
4221   public boolean sortBy(AlignmentOrder alorder, String undoname)
4222   {
4223     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4224     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4225     if (undoname != null)
4226     {
4227       addHistoryItem(new OrderCommand(undoname, oldOrder,
4228               viewport.getAlignment()));
4229     }
4230     alignPanel.paintAlignment(true);
4231     return true;
4232   }
4233
4234   /**
4235    * Work out whether the whole set of sequences or just the selected set will
4236    * be submitted for multiple alignment.
4237    *
4238    */
4239   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4240   {
4241     // Now, check we have enough sequences
4242     AlignmentView msa = null;
4243
4244     if ((viewport.getSelectionGroup() != null)
4245             && (viewport.getSelectionGroup().getSize() > 1))
4246     {
4247       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4248       // some common interface!
4249       /*
4250        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4251        * SequenceI[sz = seqs.getSize(false)];
4252        *
4253        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4254        * seqs.getSequenceAt(i); }
4255        */
4256       msa = viewport.getAlignmentView(true);
4257     }
4258     else if (viewport.getSelectionGroup() != null
4259             && viewport.getSelectionGroup().getSize() == 1)
4260     {
4261       int option = JOptionPane.showConfirmDialog(this,
4262               MessageManager.getString("warn.oneseq_msainput_selection"),
4263               MessageManager.getString("label.invalid_selection"),
4264               JOptionPane.OK_CANCEL_OPTION);
4265       if (option == JOptionPane.OK_OPTION)
4266       {
4267         msa = viewport.getAlignmentView(false);
4268       }
4269     }
4270     else
4271     {
4272       msa = viewport.getAlignmentView(false);
4273     }
4274     return msa;
4275   }
4276
4277   /**
4278    * Decides what is submitted to a secondary structure prediction service: the
4279    * first sequence in the alignment, or in the current selection, or, if the
4280    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4281    * region or the whole alignment. (where the first sequence in the set is the
4282    * one that the prediction will be for).
4283    */
4284   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4285   {
4286     AlignmentView seqs = null;
4287
4288     if ((viewport.getSelectionGroup() != null)
4289             && (viewport.getSelectionGroup().getSize() > 0))
4290     {
4291       seqs = viewport.getAlignmentView(true);
4292     }
4293     else
4294     {
4295       seqs = viewport.getAlignmentView(false);
4296     }
4297     // limit sequences - JBPNote in future - could spawn multiple prediction
4298     // jobs
4299     // TODO: viewport.getAlignment().isAligned is a global state - the local
4300     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4301     if (!viewport.getAlignment().isAligned(false))
4302     {
4303       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4304       // TODO: if seqs.getSequences().length>1 then should really have warned
4305       // user!
4306
4307     }
4308     return seqs;
4309   }
4310
4311   /**
4312    * DOCUMENT ME!
4313    *
4314    * @param e
4315    *          DOCUMENT ME!
4316    */
4317   @Override
4318   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4319   {
4320     // Pick the tree file
4321     JalviewFileChooser chooser = new JalviewFileChooser(
4322             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4323     chooser.setFileView(new JalviewFileView());
4324     chooser.setDialogTitle(MessageManager
4325             .getString("label.select_newick_like_tree_file"));
4326     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4327
4328     int value = chooser.showOpenDialog(null);
4329
4330     if (value == JalviewFileChooser.APPROVE_OPTION)
4331     {
4332       String choice = chooser.getSelectedFile().getPath();
4333       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4334       jalview.io.NewickFile fin = null;
4335       try
4336       {
4337         fin = new jalview.io.NewickFile(choice, "File");
4338         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4339       } catch (Exception ex)
4340       {
4341         JOptionPane
4342                 .showMessageDialog(
4343                         Desktop.desktop,
4344                         ex.getMessage(),
4345                         MessageManager
4346                                 .getString("label.problem_reading_tree_file"),
4347                         JOptionPane.WARNING_MESSAGE);
4348         ex.printStackTrace();
4349       }
4350       if (fin != null && fin.hasWarningMessage())
4351       {
4352         JOptionPane.showMessageDialog(Desktop.desktop, fin
4353                 .getWarningMessage(), MessageManager
4354                 .getString("label.possible_problem_with_tree_file"),
4355                 JOptionPane.WARNING_MESSAGE);
4356       }
4357     }
4358   }
4359
4360   @Override
4361   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4362   {
4363     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4364   }
4365
4366   public TreePanel ShowNewickTree(NewickFile nf, String title)
4367   {
4368     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4369   }
4370
4371   public TreePanel ShowNewickTree(NewickFile nf, String title,
4372           AlignmentView input)
4373   {
4374     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4375   }
4376
4377   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4378           int h, int x, int y)
4379   {
4380     return ShowNewickTree(nf, title, null, w, h, x, y);
4381   }
4382
4383   /**
4384    * Add a treeviewer for the tree extracted from a newick file object to the
4385    * current alignment view
4386    *
4387    * @param nf
4388    *          the tree
4389    * @param title
4390    *          tree viewer title
4391    * @param input
4392    *          Associated alignment input data (or null)
4393    * @param w
4394    *          width
4395    * @param h
4396    *          height
4397    * @param x
4398    *          position
4399    * @param y
4400    *          position
4401    * @return TreePanel handle
4402    */
4403   public TreePanel ShowNewickTree(NewickFile nf, String title,
4404           AlignmentView input, int w, int h, int x, int y)
4405   {
4406     TreePanel tp = null;
4407
4408     try
4409     {
4410       nf.parse();
4411
4412       if (nf.getTree() != null)
4413       {
4414         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4415
4416         tp.setSize(w, h);
4417
4418         if (x > 0 && y > 0)
4419         {
4420           tp.setLocation(x, y);
4421         }
4422
4423         Desktop.addInternalFrame(tp, title, w, h);
4424       }
4425     } catch (Exception ex)
4426     {
4427       ex.printStackTrace();
4428     }
4429
4430     return tp;
4431   }
4432
4433   private boolean buildingMenu = false;
4434
4435   /**
4436    * Generates menu items and listener event actions for web service clients
4437    *
4438    */
4439   public void BuildWebServiceMenu()
4440   {
4441     while (buildingMenu)
4442     {
4443       try
4444       {
4445         System.err.println("Waiting for building menu to finish.");
4446         Thread.sleep(10);
4447       } catch (Exception e)
4448       {
4449       }
4450     }
4451     final AlignFrame me = this;
4452     buildingMenu = true;
4453     new Thread(new Runnable()
4454     {
4455       @Override
4456       public void run()
4457       {
4458         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4459         try
4460         {
4461           // System.err.println("Building ws menu again "
4462           // + Thread.currentThread());
4463           // TODO: add support for context dependent disabling of services based
4464           // on
4465           // alignment and current selection
4466           // TODO: add additional serviceHandle parameter to specify abstract
4467           // handler
4468           // class independently of AbstractName
4469           // TODO: add in rediscovery GUI function to restart discoverer
4470           // TODO: group services by location as well as function and/or
4471           // introduce
4472           // object broker mechanism.
4473           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4474           final IProgressIndicator af = me;
4475           final JMenu msawsmenu = new JMenu("Alignment");
4476           final JMenu secstrmenu = new JMenu(
4477                   "Secondary Structure Prediction");
4478           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4479           final JMenu analymenu = new JMenu("Analysis");
4480           final JMenu dismenu = new JMenu("Protein Disorder");
4481           // final JMenu msawsmenu = new
4482           // JMenu(MessageManager.getString("label.alignment"));
4483           // final JMenu secstrmenu = new
4484           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4485           // final JMenu seqsrchmenu = new
4486           // JMenu(MessageManager.getString("label.sequence_database_search"));
4487           // final JMenu analymenu = new
4488           // JMenu(MessageManager.getString("label.analysis"));
4489           // final JMenu dismenu = new
4490           // JMenu(MessageManager.getString("label.protein_disorder"));
4491           // JAL-940 - only show secondary structure prediction services from
4492           // the legacy server
4493           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4494               // &&
4495           Discoverer.services != null && (Discoverer.services.size() > 0))
4496           {
4497             // TODO: refactor to allow list of AbstractName/Handler bindings to
4498             // be
4499             // stored or retrieved from elsewhere
4500             // No MSAWS used any more:
4501             // Vector msaws = null; // (Vector)
4502             // Discoverer.services.get("MsaWS");
4503             Vector secstrpr = (Vector) Discoverer.services
4504                     .get("SecStrPred");
4505             if (secstrpr != null)
4506             {
4507               // Add any secondary structure prediction services
4508               for (int i = 0, j = secstrpr.size(); i < j; i++)
4509               {
4510                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4511                         .get(i);
4512                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4513                         .getServiceClient(sh);
4514                 int p = secstrmenu.getItemCount();
4515                 impl.attachWSMenuEntry(secstrmenu, me);
4516                 int q = secstrmenu.getItemCount();
4517                 for (int litm = p; litm < q; litm++)
4518                 {
4519                   legacyItems.add(secstrmenu.getItem(litm));
4520                 }
4521               }
4522             }
4523           }
4524
4525           // Add all submenus in the order they should appear on the web
4526           // services menu
4527           wsmenu.add(msawsmenu);
4528           wsmenu.add(secstrmenu);
4529           wsmenu.add(dismenu);
4530           wsmenu.add(analymenu);
4531           // No search services yet
4532           // wsmenu.add(seqsrchmenu);
4533
4534           javax.swing.SwingUtilities.invokeLater(new Runnable()
4535           {
4536             @Override
4537             public void run()
4538             {
4539               try
4540               {
4541                 webService.removeAll();
4542                 // first, add discovered services onto the webservices menu
4543                 if (wsmenu.size() > 0)
4544                 {
4545                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4546                   {
4547                     webService.add(wsmenu.get(i));
4548                   }
4549                 }
4550                 else
4551                 {
4552                   webService.add(me.webServiceNoServices);
4553                 }
4554                 // TODO: move into separate menu builder class.
4555                 boolean new_sspred = false;
4556                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4557                 {
4558                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4559                   if (jws2servs != null)
4560                   {
4561                     if (jws2servs.hasServices())
4562                     {
4563                       jws2servs.attachWSMenuEntry(webService, me);
4564                       for (Jws2Instance sv : jws2servs.getServices())
4565                       {
4566                         if (sv.description.toLowerCase().contains("jpred"))
4567                         {
4568                           for (JMenuItem jmi : legacyItems)
4569                           {
4570                             jmi.setVisible(false);
4571                           }
4572                         }
4573                       }
4574
4575                     }
4576                     if (jws2servs.isRunning())
4577                     {
4578                       JMenuItem tm = new JMenuItem(
4579                               "Still discovering JABA Services");
4580                       tm.setEnabled(false);
4581                       webService.add(tm);
4582                     }
4583                   }
4584                 }
4585                 build_urlServiceMenu(me.webService);
4586                 build_fetchdbmenu(webService);
4587                 for (JMenu item : wsmenu)
4588                 {
4589                   if (item.getItemCount() == 0)
4590                   {
4591                     item.setEnabled(false);
4592                   }
4593                   else
4594                   {
4595                     item.setEnabled(true);
4596                   }
4597                 }
4598               } catch (Exception e)
4599               {
4600                 Cache.log
4601                         .debug("Exception during web service menu building process.",
4602                                 e);
4603               }
4604             }
4605           });
4606         } catch (Exception e)
4607         {
4608         }
4609         buildingMenu = false;
4610       }
4611     }).start();
4612
4613   }
4614
4615   /**
4616    * construct any groupURL type service menu entries.
4617    *
4618    * @param webService
4619    */
4620   private void build_urlServiceMenu(JMenu webService)
4621   {
4622     // TODO: remove this code when 2.7 is released
4623     // DEBUG - alignmentView
4624     /*
4625      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4626      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4627      *
4628      * @Override public void actionPerformed(ActionEvent e) {
4629      * jalview.datamodel.AlignmentView
4630      * .testSelectionViews(af.viewport.getAlignment(),
4631      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4632      *
4633      * }); webService.add(testAlView);
4634      */
4635     // TODO: refactor to RestClient discoverer and merge menu entries for
4636     // rest-style services with other types of analysis/calculation service
4637     // SHmmr test client - still being implemented.
4638     // DEBUG - alignmentView
4639
4640     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4641             .getRestClients())
4642     {
4643       client.attachWSMenuEntry(
4644               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4645               this);
4646     }
4647   }
4648
4649   /*
4650    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4651    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4652    * getProperty("LAST_DIRECTORY"));
4653    *
4654    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4655    * to Vamsas file"); chooser.setToolTipText("Export");
4656    *
4657    * int value = chooser.showSaveDialog(this);
4658    *
4659    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4660    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4661    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4662    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4663    */
4664   /**
4665    * prototype of an automatically enabled/disabled analysis function
4666    *
4667    */
4668   protected void setShowProductsEnabled()
4669   {
4670     SequenceI[] selection = viewport.getSequenceSelection();
4671     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4672             viewport.getAlignment().getDataset()))
4673     {
4674       showProducts.setEnabled(true);
4675
4676     }
4677     else
4678     {
4679       showProducts.setEnabled(false);
4680     }
4681   }
4682
4683   /**
4684    * search selection for sequence xRef products and build the show products
4685    * menu.
4686    *
4687    * @param selection
4688    * @param dataset
4689    * @return true if showProducts menu should be enabled.
4690    */
4691   public boolean canShowProducts(SequenceI[] selection,
4692           boolean isRegionSelection, Alignment dataset)
4693   {
4694     boolean showp = false;
4695     try
4696     {
4697       showProducts.removeAll();
4698       final boolean dna = viewport.getAlignment().isNucleotide();
4699       final Alignment ds = dataset;
4700       String[] ptypes = (selection == null || selection.length == 0) ? null
4701               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4702       // Object[] prods =
4703       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4704       // selection, dataset, true);
4705       final SequenceI[] sel = selection;
4706       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4707       {
4708         showp = true;
4709         final boolean isRegSel = isRegionSelection;
4710         final AlignFrame af = this;
4711         final String source = ptypes[t];
4712         JMenuItem xtype = new JMenuItem(ptypes[t]);
4713         xtype.addActionListener(new ActionListener()
4714         {
4715
4716           @Override
4717           public void actionPerformed(ActionEvent e)
4718           {
4719             // TODO: new thread for this call with vis-delay
4720             af.showProductsFor(af.viewport.getSequenceSelection(),
4721                     isRegSel, dna, source);
4722           }
4723
4724         });
4725         showProducts.add(xtype);
4726       }
4727       showProducts.setVisible(showp);
4728       showProducts.setEnabled(showp);
4729     } catch (Exception e)
4730     {
4731       jalview.bin.Cache.log
4732               .warn("canTranslate threw an exception - please report to help@jalview.org",
4733                       e);
4734       return false;
4735     }
4736     return showp;
4737   }
4738
4739   protected void showProductsFor(final SequenceI[] sel,
4740           final boolean isRegSel, final boolean dna, final String source)
4741   {
4742     Runnable foo = new Runnable()
4743     {
4744
4745       @Override
4746       public void run()
4747       {
4748         final long sttime = System.currentTimeMillis();
4749         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4750                 "status.searching_for_sequences_from",
4751                 new Object[] { source }), sttime);
4752         try
4753         {
4754           // update our local dataset reference
4755           Alignment ds = AlignFrame.this.getViewport().getAlignment()
4756                   .getDataset();
4757           Alignment prods = CrossRef
4758                   .findXrefSequences(sel, dna, source, ds);
4759           if (prods != null)
4760           {
4761             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4762             for (int s = 0; s < sprods.length; s++)
4763             {
4764               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4765               if (ds.getSequences() == null
4766                       || !ds.getSequences().contains(
4767                               sprods[s].getDatasetSequence()))
4768               {
4769                 ds.addSequence(sprods[s].getDatasetSequence());
4770               }
4771               sprods[s].updatePDBIds();
4772             }
4773             Alignment al = new Alignment(sprods);
4774             al.setDataset(ds);
4775
4776             /*
4777              * Copy dna-to-protein mappings to new alignment
4778              */
4779             // TODO 1: no mappings are set up for EMBL product
4780             // TODO 2: if they were, should add them to protein alignment, not
4781             // dna
4782             Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4783             for (AlignedCodonFrame acf : cf)
4784             {
4785               al.addCodonFrame(acf);
4786             }
4787             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4788                     DEFAULT_HEIGHT);
4789             String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4790                     + " for " + ((isRegSel) ? "selected region of " : "")
4791                     + getTitle();
4792             naf.setTitle(newtitle);
4793
4794             // temporary flag until SplitFrame is released
4795             boolean asSplitFrame = Cache.getDefault(
4796                     Preferences.ENABLE_SPLIT_FRAME, true);
4797             if (asSplitFrame)
4798             {
4799               /*
4800                * Make a copy of this alignment (sharing the same dataset
4801                * sequences). If we are DNA, drop introns and update mappings
4802                */
4803               AlignmentI copyAlignment = null;
4804               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4805                       .getSequenceSelection();
4806               if (dna)
4807               {
4808                 copyAlignment = AlignmentUtils.makeExonAlignment(
4809                         sequenceSelection, cf);
4810                 al.getCodonFrames().clear();
4811                 al.getCodonFrames().addAll(cf);
4812                 final StructureSelectionManager ssm = StructureSelectionManager
4813                         .getStructureSelectionManager(Desktop.instance);
4814                 ssm.registerMappings(cf);
4815               }
4816               else
4817               {
4818                 copyAlignment = new Alignment(new Alignment(
4819                         sequenceSelection));
4820               }
4821               AlignFrame copyThis = new AlignFrame(copyAlignment,
4822                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4823               copyThis.setTitle(AlignFrame.this.getTitle());
4824               // SplitFrame with dna above, protein below
4825               SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4826                       dna ? naf : copyThis);
4827               naf.setVisible(true);
4828               copyThis.setVisible(true);
4829               String linkedTitle = MessageManager
4830                       .getString("label.linked_view_title");
4831               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4832             }
4833             else
4834             {
4835               Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4836                       DEFAULT_HEIGHT);
4837             }
4838           }
4839           else
4840           {
4841             System.err.println("No Sequences generated for xRef type "
4842                     + source);
4843           }
4844         } catch (Exception e)
4845         {
4846           jalview.bin.Cache.log.error(
4847                   "Exception when finding crossreferences", e);
4848         } catch (OutOfMemoryError e)
4849         {
4850           new OOMWarning("whilst fetching crossreferences", e);
4851         } catch (Error e)
4852         {
4853           jalview.bin.Cache.log.error("Error when finding crossreferences",
4854                   e);
4855         }
4856         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4857                 "status.finished_searching_for_sequences_from",
4858                 new Object[] { source }), sttime);
4859       }
4860
4861     };
4862     Thread frunner = new Thread(foo);
4863     frunner.start();
4864   }
4865
4866   public boolean canShowTranslationProducts(SequenceI[] selection,
4867           AlignmentI alignment)
4868   {
4869     // old way
4870     try
4871     {
4872       return (jalview.analysis.Dna.canTranslate(selection,
4873               viewport.getViewAsVisibleContigs(true)));
4874     } catch (Exception e)
4875     {
4876       jalview.bin.Cache.log
4877               .warn("canTranslate threw an exception - please report to help@jalview.org",
4878                       e);
4879       return false;
4880     }
4881   }
4882
4883   /**
4884    * Construct and display a new frame containing the translation of this
4885    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4886    */
4887   @Override
4888   public void showTranslation_actionPerformed(ActionEvent e)
4889   {
4890     AlignmentI al = null;
4891     try
4892     {
4893       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4894
4895       al = dna.translateCdna();
4896     } catch (Exception ex)
4897     {
4898       jalview.bin.Cache.log.error(
4899               "Exception during translation. Please report this !", ex);
4900       final String msg = MessageManager
4901               .getString("label.error_when_translating_sequences_submit_bug_report");
4902       final String errorTitle = MessageManager
4903               .getString("label.implementation_error")
4904               + MessageManager.getString("translation_failed");
4905       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4906               JOptionPane.ERROR_MESSAGE);
4907       return;
4908     }
4909     if (al == null || al.getHeight() == 0)
4910     {
4911       final String msg = MessageManager
4912               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4913       final String errorTitle = MessageManager
4914               .getString("label.translation_failed");
4915       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4916               JOptionPane.WARNING_MESSAGE);
4917     }
4918     else
4919     {
4920       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4921       af.setFileFormat(this.currentFileFormat);
4922       final String newTitle = MessageManager.formatMessage(
4923               "label.translation_of_params",
4924               new Object[] { this.getTitle() });
4925       af.setTitle(newTitle);
4926       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4927       {
4928         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4929         viewport.openSplitFrame(af, new Alignment(seqs));
4930       }
4931       else
4932       {
4933         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4934                 DEFAULT_HEIGHT);
4935       }
4936     }
4937   }
4938
4939   /**
4940    * Set the file format
4941    *
4942    * @param fileFormat
4943    */
4944   public void setFileFormat(String fileFormat)
4945   {
4946     this.currentFileFormat = fileFormat;
4947   }
4948
4949   /**
4950    * Try to load a features file onto the alignment.
4951    *
4952    * @param file
4953    *          contents or path to retrieve file
4954    * @param type
4955    *          access mode of file (see jalview.io.AlignFile)
4956    * @return true if features file was parsed correctly.
4957    */
4958   public boolean parseFeaturesFile(String file, String type)
4959   {
4960     return avc.parseFeaturesFile(file, type,
4961             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4962
4963   }
4964
4965   @Override
4966   public void refreshFeatureUI(boolean enableIfNecessary)
4967   {
4968     // note - currently this is only still here rather than in the controller
4969     // because of the featureSettings hard reference that is yet to be
4970     // abstracted
4971     if (enableIfNecessary)
4972     {
4973       viewport.setShowSequenceFeatures(true);
4974       showSeqFeatures.setSelected(true);
4975     }
4976
4977   }
4978
4979   @Override
4980   public void dragEnter(DropTargetDragEvent evt)
4981   {
4982   }
4983
4984   @Override
4985   public void dragExit(DropTargetEvent evt)
4986   {
4987   }
4988
4989   @Override
4990   public void dragOver(DropTargetDragEvent evt)
4991   {
4992   }
4993
4994   @Override
4995   public void dropActionChanged(DropTargetDragEvent evt)
4996   {
4997   }
4998
4999   @Override
5000   public void drop(DropTargetDropEvent evt)
5001   {
5002     Transferable t = evt.getTransferable();
5003     java.util.List files = null;
5004
5005     try
5006     {
5007       DataFlavor uriListFlavor = new DataFlavor(
5008               "text/uri-list;class=java.lang.String");
5009       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5010       {
5011         // Works on Windows and MacOSX
5012         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5013         files = (java.util.List) t
5014                 .getTransferData(DataFlavor.javaFileListFlavor);
5015       }
5016       else if (t.isDataFlavorSupported(uriListFlavor))
5017       {
5018         // This is used by Unix drag system
5019         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5020         String data = (String) t.getTransferData(uriListFlavor);
5021         files = new java.util.ArrayList(1);
5022         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5023                 data, "\r\n"); st.hasMoreTokens();)
5024         {
5025           String s = st.nextToken();
5026           if (s.startsWith("#"))
5027           {
5028             // the line is a comment (as per the RFC 2483)
5029             continue;
5030           }
5031
5032           java.net.URI uri = new java.net.URI(s);
5033           // check to see if we can handle this kind of URI
5034           if (uri.getScheme().toLowerCase().startsWith("http"))
5035           {
5036             files.add(uri.toString());
5037           }
5038           else
5039           {
5040             // otherwise preserve old behaviour: catch all for file objects
5041             java.io.File file = new java.io.File(uri);
5042             files.add(file.toString());
5043           }
5044         }
5045       }
5046     } catch (Exception e)
5047     {
5048       e.printStackTrace();
5049     }
5050     if (files != null)
5051     {
5052       try
5053       {
5054         // check to see if any of these files have names matching sequences in
5055         // the alignment
5056         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5057                 .getAlignment().getSequencesArray());
5058         /**
5059          * Object[] { String,SequenceI}
5060          */
5061         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5062         ArrayList<String> filesnotmatched = new ArrayList<String>();
5063         for (int i = 0; i < files.size(); i++)
5064         {
5065           String file = files.get(i).toString();
5066           String pdbfn = "";
5067           String protocol = FormatAdapter.checkProtocol(file);
5068           if (protocol == jalview.io.FormatAdapter.FILE)
5069           {
5070             File fl = new File(file);
5071             pdbfn = fl.getName();
5072           }
5073           else if (protocol == jalview.io.FormatAdapter.URL)
5074           {
5075             URL url = new URL(file);
5076             pdbfn = url.getFile();
5077           }
5078           if (pdbfn.length() > 0)
5079           {
5080             // attempt to find a match in the alignment
5081             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5082             int l = 0, c = pdbfn.indexOf(".");
5083             while (mtch == null && c != -1)
5084             {
5085               do
5086               {
5087                 l = c;
5088               } while ((c = pdbfn.indexOf(".", l)) > l);
5089               if (l > -1)
5090               {
5091                 pdbfn = pdbfn.substring(0, l);
5092               }
5093               mtch = idm.findAllIdMatches(pdbfn);
5094             }
5095             if (mtch != null)
5096             {
5097               String type = null;
5098               try
5099               {
5100                 type = new IdentifyFile().Identify(file, protocol);
5101               } catch (Exception ex)
5102               {
5103                 type = null;
5104               }
5105               if (type != null)
5106               {
5107                 if (type.equalsIgnoreCase("PDB"))
5108                 {
5109                   filesmatched.add(new Object[] { file, protocol, mtch });
5110                   continue;
5111                 }
5112               }
5113             }
5114             // File wasn't named like one of the sequences or wasn't a PDB file.
5115             filesnotmatched.add(file);
5116           }
5117         }
5118         int assocfiles = 0;
5119         if (filesmatched.size() > 0)
5120         {
5121           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5122                   || JOptionPane
5123                           .showConfirmDialog(
5124                                   this,
5125                                   MessageManager
5126                                           .formatMessage(
5127                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5128                                                   new Object[] { Integer
5129                                                           .valueOf(
5130                                                                   filesmatched
5131                                                                           .size())
5132                                                           .toString() }),
5133                                   MessageManager
5134                                           .getString("label.automatically_associate_pdb_files_by_name"),
5135                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5136
5137           {
5138             for (Object[] fm : filesmatched)
5139             {
5140               // try and associate
5141               // TODO: may want to set a standard ID naming formalism for
5142               // associating PDB files which have no IDs.
5143               for (SequenceI toassoc : (SequenceI[]) fm[2])
5144               {
5145                 PDBEntry pe = new AssociatePdbFileWithSeq()
5146                         .associatePdbWithSeq((String) fm[0],
5147                                 (String) fm[1], toassoc, false,
5148                                 Desktop.instance);
5149                 if (pe != null)
5150                 {
5151                   System.err.println("Associated file : "
5152                           + ((String) fm[0]) + " with "
5153                           + toassoc.getDisplayId(true));
5154                   assocfiles++;
5155                 }
5156               }
5157               alignPanel.paintAlignment(true);
5158             }
5159           }
5160         }
5161         if (filesnotmatched.size() > 0)
5162         {
5163           if (assocfiles > 0
5164                   && (Cache.getDefault(
5165                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5166                           .showConfirmDialog(
5167                                   this,
5168                                   "<html>"
5169                                           + MessageManager
5170                                                   .formatMessage(
5171                                                           "label.ignore_unmatched_dropped_files_info",
5172                                                           new Object[] { Integer
5173                                                                   .valueOf(
5174                                                                           filesnotmatched
5175                                                                                   .size())
5176                                                                   .toString() })
5177                                           + "</html>",
5178                                   MessageManager
5179                                           .getString("label.ignore_unmatched_dropped_files"),
5180                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5181           {
5182             return;
5183           }
5184           for (String fn : filesnotmatched)
5185           {
5186             loadJalviewDataFile(fn, null, null, null);
5187           }
5188
5189         }
5190       } catch (Exception ex)
5191       {
5192         ex.printStackTrace();
5193       }
5194     }
5195   }
5196
5197   /**
5198    * Attempt to load a "dropped" file or URL string: First by testing whether
5199    * it's and Annotation file, then a JNet file, and finally a features file. If
5200    * all are false then the user may have dropped an alignment file onto this
5201    * AlignFrame.
5202    *
5203    * @param file
5204    *          either a filename or a URL string.
5205    */
5206   public void loadJalviewDataFile(String file, String protocol,
5207           String format, SequenceI assocSeq)
5208   {
5209     try
5210     {
5211       if (protocol == null)
5212       {
5213         protocol = jalview.io.FormatAdapter.checkProtocol(file);
5214       }
5215       // if the file isn't identified, or not positively identified as some
5216       // other filetype (PFAM is default unidentified alignment file type) then
5217       // try to parse as annotation.
5218       boolean isAnnotation = (format == null || format
5219               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5220               .annotateAlignmentView(viewport, file, protocol) : false;
5221
5222       if (!isAnnotation)
5223       {
5224         // first see if its a T-COFFEE score file
5225         TCoffeeScoreFile tcf = null;
5226         try
5227         {
5228           tcf = new TCoffeeScoreFile(file, protocol);
5229           if (tcf.isValid())
5230           {
5231             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5232             {
5233               tcoffeeColour.setEnabled(true);
5234               tcoffeeColour.setSelected(true);
5235               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5236               isAnnotation = true;
5237               statusBar
5238                       .setText(MessageManager
5239                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5240             }
5241             else
5242             {
5243               // some problem - if no warning its probable that the ID matching
5244               // process didn't work
5245               JOptionPane
5246                       .showMessageDialog(
5247                               Desktop.desktop,
5248                               tcf.getWarningMessage() == null ? MessageManager
5249                                       .getString("label.check_file_matches_sequence_ids_alignment")
5250                                       : tcf.getWarningMessage(),
5251                               MessageManager
5252                                       .getString("label.problem_reading_tcoffee_score_file"),
5253                               JOptionPane.WARNING_MESSAGE);
5254             }
5255           }
5256           else
5257           {
5258             tcf = null;
5259           }
5260         } catch (Exception x)
5261         {
5262           Cache.log
5263                   .debug("Exception when processing data source as T-COFFEE score file",
5264                           x);
5265           tcf = null;
5266         }
5267         if (tcf == null)
5268         {
5269           // try to see if its a JNet 'concise' style annotation file *before*
5270           // we
5271           // try to parse it as a features file
5272           if (format == null)
5273           {
5274             format = new IdentifyFile().Identify(file, protocol);
5275           }
5276           if (format.equalsIgnoreCase("JnetFile"))
5277           {
5278             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5279                     file, protocol);
5280             new JnetAnnotationMaker();
5281             JnetAnnotationMaker.add_annotation(predictions,
5282                     viewport.getAlignment(), 0, false);
5283             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5284             viewport.getAlignment().setSeqrep(repseq);
5285             ColumnSelection cs = new ColumnSelection();
5286             cs.hideInsertionsFor(repseq);
5287             viewport.setColumnSelection(cs);
5288             isAnnotation = true;
5289           }
5290           else
5291           {
5292             /*
5293              * if (format.equalsIgnoreCase("PDB")) {
5294              *
5295              * String pdbfn = ""; // try to match up filename with sequence id
5296              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5297              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5298              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5299              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5300              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5301              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5302              * // attempt to find a match in the alignment SequenceI mtch =
5303              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5304              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5305              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5306              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5307              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5308              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5309              * { System.err.println("Associated file : " + file + " with " +
5310              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5311              * TODO: maybe need to load as normal otherwise return; } }
5312              */
5313             // try to parse it as a features file
5314             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5315             // if it wasn't a features file then we just treat it as a general
5316             // alignment file to load into the current view.
5317             if (!isGroupsFile)
5318             {
5319               new FileLoader().LoadFile(viewport, file, protocol, format);
5320             }
5321             else
5322             {
5323               alignPanel.paintAlignment(true);
5324             }
5325           }
5326         }
5327       }
5328       if (isAnnotation)
5329       {
5330
5331         alignPanel.adjustAnnotationHeight();
5332         viewport.updateSequenceIdColours();
5333         buildSortByAnnotationScoresMenu();
5334         alignPanel.paintAlignment(true);
5335       }
5336     } catch (Exception ex)
5337     {
5338       ex.printStackTrace();
5339     } catch (OutOfMemoryError oom)
5340     {
5341       try
5342       {
5343         System.gc();
5344       } catch (Exception x)
5345       {
5346       }
5347       ;
5348       new OOMWarning(
5349               "loading data "
5350                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5351                               : "using " + protocol + " from " + file)
5352                               : ".")
5353                       + (format != null ? "(parsing as '" + format
5354                               + "' file)" : ""), oom, Desktop.desktop);
5355     }
5356   }
5357
5358   /**
5359    * Method invoked by the ChangeListener on the tabbed pane, in other words
5360    * when a different tabbed pane is selected by the user or programmatically.
5361    */
5362   @Override
5363   public void tabSelectionChanged(int index)
5364   {
5365     if (index > -1)
5366     {
5367       alignPanel = alignPanels.get(index);
5368       viewport = alignPanel.av;
5369       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5370       setMenusFromViewport(viewport);
5371     }
5372
5373     /*
5374      * If there is a frame linked to this one in a SplitPane, switch it to the
5375      * same view tab index. No infinite recursion of calls should happen, since
5376      * tabSelectionChanged() should not get invoked on setting the selected
5377      * index to an unchanged value. Guard against setting an invalid index
5378      * before the new view peer tab has been created.
5379      */
5380     final AlignViewportI peer = viewport.getCodingComplement();
5381     if (peer != null)
5382     {
5383       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5384       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5385       {
5386         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5387       }
5388     }
5389   }
5390
5391   /**
5392    * On right mouse click on view tab, prompt for and set new view name.
5393    */
5394   @Override
5395   public void tabbedPane_mousePressed(MouseEvent e)
5396   {
5397     if (SwingUtilities.isRightMouseButton(e))
5398     {
5399       String msg = MessageManager.getString("label.enter_view_name");
5400       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5401               JOptionPane.QUESTION_MESSAGE);
5402
5403       if (reply != null)
5404       {
5405         viewport.viewName = reply;
5406         // TODO warn if reply is in getExistingViewNames()?
5407         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5408       }
5409     }
5410   }
5411
5412   public AlignViewport getCurrentView()
5413   {
5414     return viewport;
5415   }
5416
5417   /**
5418    * Open the dialog for regex description parsing.
5419    */
5420   @Override
5421   protected void extractScores_actionPerformed(ActionEvent e)
5422   {
5423     ParseProperties pp = new jalview.analysis.ParseProperties(
5424             viewport.getAlignment());
5425     // TODO: verify regex and introduce GUI dialog for version 2.5
5426     // if (pp.getScoresFromDescription("col", "score column ",
5427     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5428     // true)>0)
5429     if (pp.getScoresFromDescription("description column",
5430             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5431     {
5432       buildSortByAnnotationScoresMenu();
5433     }
5434   }
5435
5436   /*
5437    * (non-Javadoc)
5438    *
5439    * @see
5440    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5441    * )
5442    */
5443   @Override
5444   protected void showDbRefs_actionPerformed(ActionEvent e)
5445   {
5446     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5447   }
5448
5449   /*
5450    * (non-Javadoc)
5451    *
5452    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5453    * ActionEvent)
5454    */
5455   @Override
5456   protected void showNpFeats_actionPerformed(ActionEvent e)
5457   {
5458     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5459   }
5460
5461   /**
5462    * find the viewport amongst the tabs in this alignment frame and close that
5463    * tab
5464    *
5465    * @param av
5466    */
5467   public boolean closeView(AlignViewportI av)
5468   {
5469     if (viewport == av)
5470     {
5471       this.closeMenuItem_actionPerformed(false);
5472       return true;
5473     }
5474     Component[] comp = tabbedPane.getComponents();
5475     for (int i = 0; comp != null && i < comp.length; i++)
5476     {
5477       if (comp[i] instanceof AlignmentPanel)
5478       {
5479         if (((AlignmentPanel) comp[i]).av == av)
5480         {
5481           // close the view.
5482           closeView((AlignmentPanel) comp[i]);
5483           return true;
5484         }
5485       }
5486     }
5487     return false;
5488   }
5489
5490   protected void build_fetchdbmenu(JMenu webService)
5491   {
5492     // Temporary hack - DBRef Fetcher always top level ws entry.
5493     // TODO We probably want to store a sequence database checklist in
5494     // preferences and have checkboxes.. rather than individual sources selected
5495     // here
5496     final JMenu rfetch = new JMenu(
5497             MessageManager.getString("action.fetch_db_references"));
5498     rfetch.setToolTipText(MessageManager
5499             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5500     webService.add(rfetch);
5501
5502     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5503             MessageManager.getString("option.trim_retrieved_seqs"));
5504     trimrs.setToolTipText(MessageManager
5505             .getString("label.trim_retrieved_sequences"));
5506     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5507     trimrs.addActionListener(new ActionListener()
5508     {
5509       @Override
5510       public void actionPerformed(ActionEvent e)
5511       {
5512         trimrs.setSelected(trimrs.isSelected());
5513         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5514                 Boolean.valueOf(trimrs.isSelected()).toString());
5515       };
5516     });
5517     rfetch.add(trimrs);
5518     JMenuItem fetchr = new JMenuItem(
5519             MessageManager.getString("label.standard_databases"));
5520     fetchr.setToolTipText(MessageManager
5521             .getString("label.fetch_embl_uniprot"));
5522     fetchr.addActionListener(new ActionListener()
5523     {
5524
5525       @Override
5526       public void actionPerformed(ActionEvent e)
5527       {
5528         new Thread(new Runnable()
5529         {
5530
5531           @Override
5532           public void run()
5533           {
5534             new jalview.ws.DBRefFetcher(alignPanel.av
5535                     .getSequenceSelection(), alignPanel.alignFrame)
5536                     .fetchDBRefs(false);
5537           }
5538         }).start();
5539
5540       }
5541
5542     });
5543     rfetch.add(fetchr);
5544     final AlignFrame me = this;
5545     new Thread(new Runnable()
5546     {
5547       @Override
5548       public void run()
5549       {
5550         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5551                 .getSequenceFetcherSingleton(me);
5552         javax.swing.SwingUtilities.invokeLater(new Runnable()
5553         {
5554           @Override
5555           public void run()
5556           {
5557             String[] dbclasses = sf.getOrderedSupportedSources();
5558             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5559             // jalview.util.QuickSort.sort(otherdb, otherdb);
5560             List<DbSourceProxy> otherdb;
5561             JMenu dfetch = new JMenu();
5562             JMenu ifetch = new JMenu();
5563             JMenuItem fetchr = null;
5564             int comp = 0, icomp = 0, mcomp = 15;
5565             String mname = null;
5566             int dbi = 0;
5567             for (String dbclass : dbclasses)
5568             {
5569               otherdb = sf.getSourceProxy(dbclass);
5570               // add a single entry for this class, or submenu allowing 'fetch
5571               // all' or pick one
5572               if (otherdb == null || otherdb.size() < 1)
5573               {
5574                 continue;
5575               }
5576               // List<DbSourceProxy> dbs=otherdb;
5577               // otherdb=new ArrayList<DbSourceProxy>();
5578               // for (DbSourceProxy db:dbs)
5579               // {
5580               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5581               // }
5582               if (mname == null)
5583               {
5584                 mname = "From " + dbclass;
5585               }
5586               if (otherdb.size() == 1)
5587               {
5588                 final DbSourceProxy[] dassource = otherdb
5589                         .toArray(new DbSourceProxy[0]);
5590                 DbSourceProxy src = otherdb.get(0);
5591                 fetchr = new JMenuItem(src.getDbSource());
5592                 fetchr.addActionListener(new ActionListener()
5593                 {
5594
5595                   @Override
5596                   public void actionPerformed(ActionEvent e)
5597                   {
5598                     new Thread(new Runnable()
5599                     {
5600
5601                       @Override
5602                       public void run()
5603                       {
5604                         new jalview.ws.DBRefFetcher(alignPanel.av
5605                                 .getSequenceSelection(),
5606                                 alignPanel.alignFrame, dassource)
5607                                 .fetchDBRefs(false);
5608                       }
5609                     }).start();
5610                   }
5611
5612                 });
5613                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5614                         MessageManager.formatMessage(
5615                                 "label.fetch_retrieve_from",
5616                                 new Object[] { src.getDbName() })));
5617                 dfetch.add(fetchr);
5618                 comp++;
5619               }
5620               else
5621               {
5622                 final DbSourceProxy[] dassource = otherdb
5623                         .toArray(new DbSourceProxy[0]);
5624                 // fetch all entry
5625                 DbSourceProxy src = otherdb.get(0);
5626                 fetchr = new JMenuItem(MessageManager.formatMessage(
5627                         "label.fetch_all_param",
5628                         new Object[] { src.getDbSource() }));
5629                 fetchr.addActionListener(new ActionListener()
5630                 {
5631                   @Override
5632                   public void actionPerformed(ActionEvent e)
5633                   {
5634                     new Thread(new Runnable()
5635                     {
5636
5637                       @Override
5638                       public void run()
5639                       {
5640                         new jalview.ws.DBRefFetcher(alignPanel.av
5641                                 .getSequenceSelection(),
5642                                 alignPanel.alignFrame, dassource)
5643                                 .fetchDBRefs(false);
5644                       }
5645                     }).start();
5646                   }
5647                 });
5648
5649                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5650                         MessageManager.formatMessage(
5651                                 "label.fetch_retrieve_from_all_sources",
5652                                 new Object[] {
5653                                     Integer.valueOf(otherdb.size())
5654                                             .toString(), src.getDbSource(),
5655                                     src.getDbName() })));
5656                 dfetch.add(fetchr);
5657                 comp++;
5658                 // and then build the rest of the individual menus
5659                 ifetch = new JMenu(MessageManager.formatMessage(
5660                         "label.source_from_db_source",
5661                         new Object[] { src.getDbSource() }));
5662                 icomp = 0;
5663                 String imname = null;
5664                 int i = 0;
5665                 for (DbSourceProxy sproxy : otherdb)
5666                 {
5667                   String dbname = sproxy.getDbName();
5668                   String sname = dbname.length() > 5 ? dbname.substring(0,
5669                           5) + "..." : dbname;
5670                   String msname = dbname.length() > 10 ? dbname.substring(
5671                           0, 10) + "..." : dbname;
5672                   if (imname == null)
5673                   {
5674                     imname = MessageManager.formatMessage(
5675                             "label.from_msname", new Object[] { sname });
5676                   }
5677                   fetchr = new JMenuItem(msname);
5678                   final DbSourceProxy[] dassrc = { sproxy };
5679                   fetchr.addActionListener(new ActionListener()
5680                   {
5681
5682                     @Override
5683                     public void actionPerformed(ActionEvent e)
5684                     {
5685                       new Thread(new Runnable()
5686                       {
5687
5688                         @Override
5689                         public void run()
5690                         {
5691                           new jalview.ws.DBRefFetcher(alignPanel.av
5692                                   .getSequenceSelection(),
5693                                   alignPanel.alignFrame, dassrc)
5694                                   .fetchDBRefs(false);
5695                         }
5696                       }).start();
5697                     }
5698
5699                   });
5700                   fetchr.setToolTipText("<html>"
5701                           + MessageManager.formatMessage(
5702                                   "label.fetch_retrieve_from", new Object[]
5703                                   { dbname }));
5704                   ifetch.add(fetchr);
5705                   ++i;
5706                   if (++icomp >= mcomp || i == (otherdb.size()))
5707                   {
5708                     ifetch.setText(MessageManager.formatMessage(
5709                             "label.source_to_target", imname, sname));
5710                     dfetch.add(ifetch);
5711                     ifetch = new JMenu();
5712                     imname = null;
5713                     icomp = 0;
5714                     comp++;
5715                   }
5716                 }
5717               }
5718               ++dbi;
5719               if (comp >= mcomp || dbi >= (dbclasses.length))
5720               {
5721                 dfetch.setText(MessageManager.formatMessage(
5722                         "label.source_to_target", mname, dbclass));
5723                 rfetch.add(dfetch);
5724                 dfetch = new JMenu();
5725                 mname = null;
5726                 comp = 0;
5727               }
5728             }
5729           }
5730         });
5731       }
5732     }).start();
5733
5734   }
5735
5736   /**
5737    * Left justify the whole alignment.
5738    */
5739   @Override
5740   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5741   {
5742     AlignmentI al = viewport.getAlignment();
5743     al.justify(false);
5744     viewport.firePropertyChange("alignment", null, al);
5745   }
5746
5747   /**
5748    * Right justify the whole alignment.
5749    */
5750   @Override
5751   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5752   {
5753     AlignmentI al = viewport.getAlignment();
5754     al.justify(true);
5755     viewport.firePropertyChange("alignment", null, al);
5756   }
5757
5758   public void setShowSeqFeatures(boolean b)
5759   {
5760     showSeqFeatures.setSelected(b);
5761     viewport.setShowSequenceFeatures(b);
5762   }
5763
5764   /*
5765    * (non-Javadoc)
5766    *
5767    * @see
5768    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5769    * awt.event.ActionEvent)
5770    */
5771   @Override
5772   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5773   {
5774     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5775     alignPanel.paintAlignment(true);
5776   }
5777
5778   /*
5779    * (non-Javadoc)
5780    *
5781    * @see
5782    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5783    * .ActionEvent)
5784    */
5785   @Override
5786   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5787   {
5788     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5789     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5790
5791   }
5792
5793   /*
5794    * (non-Javadoc)
5795    *
5796    * @see
5797    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5798    * .event.ActionEvent)
5799    */
5800   @Override
5801   protected void showGroupConservation_actionPerformed(ActionEvent e)
5802   {
5803     viewport.setShowGroupConservation(showGroupConservation.getState());
5804     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5805   }
5806
5807   /*
5808    * (non-Javadoc)
5809    *
5810    * @see
5811    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5812    * .event.ActionEvent)
5813    */
5814   @Override
5815   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5816   {
5817     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5818     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5819   }
5820
5821   /*
5822    * (non-Javadoc)
5823    *
5824    * @see
5825    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5826    * .event.ActionEvent)
5827    */
5828   @Override
5829   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5830   {
5831     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5832     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5833   }
5834
5835   @Override
5836   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5837   {
5838     showSequenceLogo.setState(true);
5839     viewport.setShowSequenceLogo(true);
5840     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5841     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5842   }
5843
5844   @Override
5845   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5846   {
5847     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5848   }
5849
5850   /*
5851    * (non-Javadoc)
5852    *
5853    * @see
5854    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5855    * .event.ActionEvent)
5856    */
5857   @Override
5858   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5859   {
5860     if (avc.makeGroupsFromSelection())
5861     {
5862       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5863       alignPanel.updateAnnotation();
5864       alignPanel.paintAlignment(true);
5865     }
5866   }
5867
5868   public void clearAlignmentSeqRep()
5869   {
5870     // TODO refactor alignmentseqrep to controller
5871     if (viewport.getAlignment().hasSeqrep())
5872     {
5873       viewport.getAlignment().setSeqrep(null);
5874       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5875       alignPanel.updateAnnotation();
5876       alignPanel.paintAlignment(true);
5877     }
5878   }
5879
5880   @Override
5881   protected void createGroup_actionPerformed(ActionEvent e)
5882   {
5883     if (avc.createGroup())
5884     {
5885       alignPanel.alignmentChanged();
5886     }
5887   }
5888
5889   @Override
5890   protected void unGroup_actionPerformed(ActionEvent e)
5891   {
5892     if (avc.unGroup())
5893     {
5894       alignPanel.alignmentChanged();
5895     }
5896   }
5897
5898   /**
5899    * make the given alignmentPanel the currently selected tab
5900    *
5901    * @param alignmentPanel
5902    */
5903   public void setDisplayedView(AlignmentPanel alignmentPanel)
5904   {
5905     if (!viewport.getSequenceSetId().equals(
5906             alignmentPanel.av.getSequenceSetId()))
5907     {
5908       throw new Error(
5909               MessageManager
5910                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5911     }
5912     if (tabbedPane != null
5913             && tabbedPane.getTabCount() > 0
5914             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5915                     .getSelectedIndex())
5916     {
5917       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5918     }
5919   }
5920
5921   /**
5922    * Action on selection of menu options to Show or Hide annotations.
5923    *
5924    * @param visible
5925    * @param forSequences
5926    *          update sequence-related annotations
5927    * @param forAlignment
5928    *          update non-sequence-related annotations
5929    */
5930   @Override
5931   protected void setAnnotationsVisibility(boolean visible,
5932           boolean forSequences, boolean forAlignment)
5933   {
5934     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5935             .getAlignmentAnnotation())
5936     {
5937       /*
5938        * don't display non-positional annotations on an alignment
5939        */
5940       if (aa.annotations == null)
5941       {
5942         continue;
5943       }
5944       boolean apply = (aa.sequenceRef == null && forAlignment)
5945               || (aa.sequenceRef != null && forSequences);
5946       if (apply)
5947       {
5948         aa.visible = visible;
5949       }
5950     }
5951     alignPanel.validateAnnotationDimensions(true);
5952     alignPanel.alignmentChanged();
5953   }
5954
5955   /**
5956    * Store selected annotation sort order for the view and repaint.
5957    */
5958   @Override
5959   protected void sortAnnotations_actionPerformed()
5960   {
5961     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5962     this.alignPanel.av
5963             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5964     alignPanel.paintAlignment(true);
5965   }
5966
5967   /**
5968    *
5969    * @return alignment panels in this alignment frame
5970    */
5971   public List<? extends AlignmentViewPanel> getAlignPanels()
5972   {
5973     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5974   }
5975
5976   /**
5977    * Open a new alignment window, with the cDNA associated with this (protein)
5978    * alignment, aligned as is the protein.
5979    */
5980   protected void viewAsCdna_actionPerformed()
5981   {
5982     // TODO no longer a menu action - refactor as required
5983     final AlignmentI alignment = getViewport().getAlignment();
5984     Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5985     if (mappings == null)
5986     {
5987       return;
5988     }
5989     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5990     for (SequenceI aaSeq : alignment.getSequences())
5991     {
5992       for (AlignedCodonFrame acf : mappings)
5993       {
5994         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5995         if (dnaSeq != null)
5996         {
5997           /*
5998            * There is a cDNA mapping for this protein sequence - add to new
5999            * alignment. It will share the same dataset sequence as other mapped
6000            * cDNA (no new mappings need to be created).
6001            */
6002           final Sequence newSeq = new Sequence(dnaSeq);
6003           newSeq.setDatasetSequence(dnaSeq);
6004           cdnaSeqs.add(newSeq);
6005         }
6006       }
6007     }
6008     if (cdnaSeqs.size() == 0)
6009     {
6010       // show a warning dialog no mapped cDNA
6011       return;
6012     }
6013     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6014             .size()]));
6015     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6016             AlignFrame.DEFAULT_HEIGHT);
6017     cdna.alignAs(alignment);
6018     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6019             + this.title;
6020     Desktop.addInternalFrame(alignFrame, newtitle,
6021             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6022   }
6023
6024   /**
6025    * Set visibility of dna/protein complement view (available when shown in a
6026    * split frame).
6027    *
6028    * @param show
6029    */
6030   @Override
6031   protected void showComplement_actionPerformed(boolean show)
6032   {
6033     SplitContainerI sf = getSplitViewContainer();
6034     if (sf != null)
6035     {
6036       sf.setComplementVisible(this, show);
6037     }
6038   }
6039 }
6040
6041 class PrintThread extends Thread
6042 {
6043   AlignmentPanel ap;
6044
6045   public PrintThread(AlignmentPanel ap)
6046   {
6047     this.ap = ap;
6048   }
6049
6050   static PageFormat pf;
6051
6052   @Override
6053   public void run()
6054   {
6055     PrinterJob printJob = PrinterJob.getPrinterJob();
6056
6057     if (pf != null)
6058     {
6059       printJob.setPrintable(ap, pf);
6060     }
6061     else
6062     {
6063       printJob.setPrintable(ap);
6064     }
6065
6066     if (printJob.printDialog())
6067     {
6068       try
6069       {
6070         printJob.print();
6071       } catch (Exception PrintException)
6072       {
6073         PrintException.printStackTrace();
6074       }
6075     }
6076   }
6077 }