src/jalview/gui/AlignFrame.java

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