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.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  64 import jalview.io.AlignmentProperties;
  65 import jalview.io.AnnotationFile;
  66 import jalview.io.BioJsHTMLOutput;
  67 import jalview.io.DataSourceType;
  68 import jalview.io.FileFormat;
  69 import jalview.io.FileFormatI;
  70 import jalview.io.FileFormats;
  71 import jalview.io.FileLoader;
  72 import jalview.io.FormatAdapter;
  73 import jalview.io.HtmlSvgOutput;
  74 import jalview.io.IdentifyFile;
  75 import jalview.io.JPredFile;
  76 import jalview.io.JalviewFileChooser;
  77 import jalview.io.JalviewFileView;
  78 import jalview.io.JnetAnnotationMaker;
  79 import jalview.io.NewickFile;
  80 import jalview.io.TCoffeeScoreFile;
  81 import jalview.jbgui.GAlignFrame;
  82 import jalview.schemes.ColourSchemeI;
  83 import jalview.schemes.ColourSchemes;
  84 import jalview.schemes.ResidueColourScheme;
  85 import jalview.schemes.ResidueProperties;
  86 import jalview.schemes.TCoffeeColourScheme;
  87 import jalview.util.MessageManager;
  88 import jalview.viewmodel.AlignmentViewport;
  89 import jalview.ws.DBRefFetcher;
  90 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  91 import jalview.ws.jws1.Discoverer;
  92 import jalview.ws.jws2.Jws2Discoverer;
  93 import jalview.ws.jws2.jabaws2.Jws2Instance;
  94 import jalview.ws.seqfetcher.DbSourceProxy;
  95
  96 import java.awt.BorderLayout;
  97 import java.awt.Component;
  98 import java.awt.Rectangle;
  99 import java.awt.Toolkit;
 100 import java.awt.datatransfer.Clipboard;
 101 import java.awt.datatransfer.DataFlavor;
 102 import java.awt.datatransfer.StringSelection;
 103 import java.awt.datatransfer.Transferable;
 104 import java.awt.dnd.DnDConstants;
 105 import java.awt.dnd.DropTargetDragEvent;
 106 import java.awt.dnd.DropTargetDropEvent;
 107 import java.awt.dnd.DropTargetEvent;
 108 import java.awt.dnd.DropTargetListener;
 109 import java.awt.event.ActionEvent;
 110 import java.awt.event.ActionListener;
 111 import java.awt.event.FocusAdapter;
 112 import java.awt.event.FocusEvent;
 113 import java.awt.event.ItemEvent;
 114 import java.awt.event.ItemListener;
 115 import java.awt.event.KeyAdapter;
 116 import java.awt.event.KeyEvent;
 117 import java.awt.event.MouseEvent;
 118 import java.awt.print.PageFormat;
 119 import java.awt.print.PrinterJob;
 120 import java.beans.PropertyChangeEvent;
 121 import java.io.File;
 122 import java.io.FileWriter;
 123 import java.io.PrintWriter;
 124 import java.net.URL;
 125 import java.util.ArrayList;
 126 import java.util.Arrays;
 127 import java.util.Deque;
 128 import java.util.Enumeration;
 129 import java.util.Hashtable;
 130 import java.util.List;
 131 import java.util.Vector;
 132
 133 import javax.swing.JCheckBoxMenuItem;
 134 import javax.swing.JEditorPane;
 135 import javax.swing.JInternalFrame;
 136 import javax.swing.JLayeredPane;
 137 import javax.swing.JMenu;
 138 import javax.swing.JMenuItem;
 139 import javax.swing.JScrollPane;
 140 import javax.swing.SwingUtilities;
 141
 142 /**
 143  * DOCUMENT ME!
 144  *
 145  * @author $author$
 146  * @version $Revision$
 147  */
 148 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 149         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 150 {
 151
 152   public static final int DEFAULT_WIDTH = 700;
 153
 154   public static final int DEFAULT_HEIGHT = 500;
 155
 156   /*
 157    * The currently displayed panel (selected tabbed view if more than one)
 158    */
 159   public AlignmentPanel alignPanel;
 160
 161   AlignViewport viewport;
 162
 163   public AlignViewControllerI avc;
 164
 165   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 166
 167   /**
 168    * Last format used to load or save alignments in this window
 169    */
 170   FileFormatI currentFileFormat = null;
 171
 172   /**
 173    * Current filename for this alignment
 174    */
 175   String fileName = null;
 176
 177   /**
 178    * Creates a new AlignFrame object with specific width and height.
 179    *
 180    * @param al
 181    * @param width
 182    * @param height
 183    */
 184   public AlignFrame(AlignmentI al, int width, int height)
 185   {
 186     this(al, null, width, height);
 187   }
 188
 189   /**
 190    * Creates a new AlignFrame object with specific width, height and
 191    * sequenceSetId
 192    *
 193    * @param al
 194    * @param width
 195    * @param height
 196    * @param sequenceSetId
 197    */
 198   public AlignFrame(AlignmentI al, int width, int height,
 199           String sequenceSetId)
 200   {
 201     this(al, null, width, height, sequenceSetId);
 202   }
 203
 204   /**
 205    * Creates a new AlignFrame object with specific width, height and
 206    * sequenceSetId
 207    *
 208    * @param al
 209    * @param width
 210    * @param height
 211    * @param sequenceSetId
 212    * @param viewId
 213    */
 214   public AlignFrame(AlignmentI al, int width, int height,
 215           String sequenceSetId, String viewId)
 216   {
 217     this(al, null, width, height, sequenceSetId, viewId);
 218   }
 219
 220   /**
 221    * new alignment window with hidden columns
 222    *
 223    * @param al
 224    *          AlignmentI
 225    * @param hiddenColumns
 226    *          ColumnSelection or null
 227    * @param width
 228    *          Width of alignment frame
 229    * @param height
 230    *          height of frame.
 231    */
 232   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 233           int width, int height)
 234   {
 235     this(al, hiddenColumns, width, height, null);
 236   }
 237
 238   /**
 239    * Create alignment frame for al with hiddenColumns, a specific width and
 240    * height, and specific sequenceId
 241    *
 242    * @param al
 243    * @param hiddenColumns
 244    * @param width
 245    * @param height
 246    * @param sequenceSetId
 247    *          (may be null)
 248    */
 249   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 250           int width, int height, String sequenceSetId)
 251   {
 252     this(al, hiddenColumns, width, height, sequenceSetId, null);
 253   }
 254
 255   /**
 256    * Create alignment frame for al with hiddenColumns, a specific width and
 257    * height, and specific sequenceId
 258    *
 259    * @param al
 260    * @param hiddenColumns
 261    * @param width
 262    * @param height
 263    * @param sequenceSetId
 264    *          (may be null)
 265    * @param viewId
 266    *          (may be null)
 267    */
 268   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 269           int width, int height, String sequenceSetId, String viewId)
 270   {
 271     setSize(width, height);
 272
 273     if (al.getDataset() == null)
 274     {
 275       al.setDataset(null);
 276     }
 277
 278     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 279
 280     alignPanel = new AlignmentPanel(this, viewport);
 281
 282     addAlignmentPanel(alignPanel, true);
 283     init();
 284   }
 285
 286   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 287           ColumnSelection hiddenColumns, int width, int height)
 288   {
 289     setSize(width, height);
 290
 291     if (al.getDataset() == null)
 292     {
 293       al.setDataset(null);
 294     }
 295
 296     viewport = new AlignViewport(al, hiddenColumns);
 297
 298     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 299     {
 300       viewport.hideSequence(hiddenSeqs);
 301     }
 302     alignPanel = new AlignmentPanel(this, viewport);
 303     addAlignmentPanel(alignPanel, true);
 304     init();
 305   }
 306
 307   /**
 308    * Make a new AlignFrame from existing alignmentPanels
 309    *
 310    * @param ap
 311    *          AlignmentPanel
 312    * @param av
 313    *          AlignViewport
 314    */
 315   public AlignFrame(AlignmentPanel ap)
 316   {
 317     viewport = ap.av;
 318     alignPanel = ap;
 319     addAlignmentPanel(ap, false);
 320     init();
 321   }
 322
 323   /**
 324    * initalise the alignframe from the underlying viewport data and the
 325    * configurations
 326    */
 327   void init()
 328   {
 329     if (!Jalview.isHeadlessMode())
 330     {
 331       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 332     }
 333
 334     avc = new jalview.controller.AlignViewController(this, viewport,
 335             alignPanel);
 336     if (viewport.getAlignmentConservationAnnotation() == null)
 337     {
 338       // BLOSUM62Colour.setEnabled(false);
 339       conservationMenuItem.setEnabled(false);
 340       modifyConservation.setEnabled(false);
 341       // PIDColour.setEnabled(false);
 342       // abovePIDThreshold.setEnabled(false);
 343       // modifyPID.setEnabled(false);
 344     }
 345
 346     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 347             "No sort");
 348
 349     if (sortby.equals("Id"))
 350     {
 351       sortIDMenuItem_actionPerformed(null);
 352     }
 353     else if (sortby.equals("Pairwise Identity"))
 354     {
 355       sortPairwiseMenuItem_actionPerformed(null);
 356     }
 357
 358     this.alignPanel.av
 359             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 360
 361     setMenusFromViewport(viewport);
 362     buildSortByAnnotationScoresMenu();
 363     buildTreeMenu();
 364     buildColourMenu();
 365
 366     if (Desktop.desktop != null)
 367     {
 368       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 369       addServiceListeners();
 370       setGUINucleotide();
 371     }
 372
 373     if (viewport.getWrapAlignment())
 374     {
 375       wrapMenuItem_actionPerformed(null);
 376     }
 377
 378     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 379     {
 380       this.overviewMenuItem_actionPerformed(null);
 381     }
 382
 383     addKeyListener();
 384
 385     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 386     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 387     final String menuLabel = MessageManager
 388             .getString("label.copy_format_from");
 389     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 390             new ViewSetProvider()
 391             {
 392
 393               @Override
 394               public AlignmentPanel[] getAllAlignmentPanels()
 395               {
 396                 origview.clear();
 397                 origview.add(alignPanel);
 398                 // make an array of all alignment panels except for this one
 399                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 400                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 401                 aps.remove(AlignFrame.this.alignPanel);
 402                 return aps.toArray(new AlignmentPanel[aps.size()]);
 403               }
 404             }, selviews, new ItemListener()
 405             {
 406
 407               @Override
 408               public void itemStateChanged(ItemEvent e)
 409               {
 410                 if (origview.size() > 0)
 411                 {
 412                   final AlignmentPanel ap = origview.get(0);
 413
 414                   /*
 415                    * Copy the ViewStyle of the selected panel to 'this one'.
 416                    * Don't change value of 'scaleProteinAsCdna' unless copying
 417                    * from a SplitFrame.
 418                    */
 419                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 420                           .getViewStyle();
 421                   boolean fromSplitFrame = selviews.get(0)
 422                           .getAlignViewport().getCodingComplement() != null;
 423                   if (!fromSplitFrame)
 424                   {
 425                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 426                             .getViewStyle().isScaleProteinAsCdna());
 427                   }
 428                   ap.getAlignViewport().setViewStyle(vs);
 429
 430                   /*
 431                    * Also rescale ViewStyle of SplitFrame complement if there is
 432                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 433                    * the whole ViewStyle (allow cDNA protein to have different
 434                    * fonts)
 435                    */
 436                   AlignViewportI complement = ap.getAlignViewport()
 437                           .getCodingComplement();
 438                   if (complement != null && vs.isScaleProteinAsCdna())
 439                   {
 440                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 441                     ((SplitFrame) af.getSplitViewContainer())
 442                             .adjustLayout();
 443                     af.setMenusForViewport();
 444                   }
 445
 446                   ap.updateLayout();
 447                   ap.setSelected(true);
 448                   ap.alignFrame.setMenusForViewport();
 449
 450                 }
 451               }
 452             });
 453     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 454             .indexOf("devel") > -1
 455             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 456                     .indexOf("test") > -1)
 457     {
 458       formatMenu.add(vsel);
 459     }
 460     addFocusListener(new FocusAdapter()
 461     {
 462       @Override
 463       public void focusGained(FocusEvent e)
 464       {
 465         Jalview.setCurrentAlignFrame(AlignFrame.this);
 466       }
 467     });
 468
 469   }
 470
 471   /**
 472    * Change the filename and format for the alignment, and enable the 'reload'
 473    * button functionality.
 474    *
 475    * @param file
 476    *          valid filename
 477    * @param format
 478    *          format of file
 479    */
 480   public void setFileName(String file, FileFormatI format)
 481   {
 482     fileName = file;
 483     setFileFormat(format);
 484     reload.setEnabled(true);
 485   }
 486
 487   /**
 488    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 489    * events
 490    */
 491   void addKeyListener()
 492   {
 493     addKeyListener(new KeyAdapter()
 494     {
 495       @Override
 496       public void keyPressed(KeyEvent evt)
 497       {
 498         if (viewport.cursorMode
 499                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 500                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 501                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 502                 && Character.isDigit(evt.getKeyChar()))
 503         {
 504           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 505         }
 506
 507         switch (evt.getKeyCode())
 508         {
 509
 510         case 27: // escape key
 511           deselectAllSequenceMenuItem_actionPerformed(null);
 512
 513           break;
 514
 515         case KeyEvent.VK_DOWN:
 516           if (evt.isAltDown() || !viewport.cursorMode)
 517           {
 518             moveSelectedSequences(false);
 519           }
 520           if (viewport.cursorMode)
 521           {
 522             alignPanel.getSeqPanel().moveCursor(0, 1);
 523           }
 524           break;
 525
 526         case KeyEvent.VK_UP:
 527           if (evt.isAltDown() || !viewport.cursorMode)
 528           {
 529             moveSelectedSequences(true);
 530           }
 531           if (viewport.cursorMode)
 532           {
 533             alignPanel.getSeqPanel().moveCursor(0, -1);
 534           }
 535
 536           break;
 537
 538         case KeyEvent.VK_LEFT:
 539           if (evt.isAltDown() || !viewport.cursorMode)
 540           {
 541             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 542           }
 543           else
 544           {
 545             alignPanel.getSeqPanel().moveCursor(-1, 0);
 546           }
 547
 548           break;
 549
 550         case KeyEvent.VK_RIGHT:
 551           if (evt.isAltDown() || !viewport.cursorMode)
 552           {
 553             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 554           }
 555           else
 556           {
 557             alignPanel.getSeqPanel().moveCursor(1, 0);
 558           }
 559           break;
 560
 561         case KeyEvent.VK_SPACE:
 562           if (viewport.cursorMode)
 563           {
 564             alignPanel.getSeqPanel().insertGapAtCursor(
 565                     evt.isControlDown() || evt.isShiftDown()
 566                             || evt.isAltDown());
 567           }
 568           break;
 569
 570         // case KeyEvent.VK_A:
 571         // if (viewport.cursorMode)
 572         // {
 573         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 574         // //System.out.println("A");
 575         // }
 576         // break;
 577         /*
 578          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 579          * System.out.println("closing bracket"); } break;
 580          */
 581         case KeyEvent.VK_DELETE:
 582         case KeyEvent.VK_BACK_SPACE:
 583           if (!viewport.cursorMode)
 584           {
 585             cut_actionPerformed(null);
 586           }
 587           else
 588           {
 589             alignPanel.getSeqPanel().deleteGapAtCursor(
 590                     evt.isControlDown() || evt.isShiftDown()
 591                             || evt.isAltDown());
 592           }
 593
 594           break;
 595
 596         case KeyEvent.VK_S:
 597           if (viewport.cursorMode)
 598           {
 599             alignPanel.getSeqPanel().setCursorRow();
 600           }
 601           break;
 602         case KeyEvent.VK_C:
 603           if (viewport.cursorMode && !evt.isControlDown())
 604           {
 605             alignPanel.getSeqPanel().setCursorColumn();
 606           }
 607           break;
 608         case KeyEvent.VK_P:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().setCursorPosition();
 612           }
 613           break;
 614
 615         case KeyEvent.VK_ENTER:
 616         case KeyEvent.VK_COMMA:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorRowAndColumn();
 620           }
 621           break;
 622
 623         case KeyEvent.VK_Q:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 627           }
 628           break;
 629         case KeyEvent.VK_M:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 633           }
 634           break;
 635
 636         case KeyEvent.VK_F2:
 637           viewport.cursorMode = !viewport.cursorMode;
 638           statusBar.setText(MessageManager.formatMessage(
 639                   "label.keyboard_editing_mode",
 640                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 644             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 645           }
 646           alignPanel.getSeqPanel().seqCanvas.repaint();
 647           break;
 648
 649         case KeyEvent.VK_F1:
 650           try
 651           {
 652             Help.showHelpWindow();
 653           } catch (Exception ex)
 654           {
 655             ex.printStackTrace();
 656           }
 657           break;
 658         case KeyEvent.VK_H:
 659         {
 660           boolean toggleSeqs = !evt.isControlDown();
 661           boolean toggleCols = !evt.isShiftDown();
 662           toggleHiddenRegions(toggleSeqs, toggleCols);
 663           break;
 664         }
 665         case KeyEvent.VK_B:
 666         {
 667           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 668           boolean modifyExisting = true; // always modify, don't clear
 669                                          // evt.isShiftDown();
 670           boolean invertHighlighted = evt.isAltDown();
 671           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 672                   toggleSel);
 673           break;
 674         }
 675         case KeyEvent.VK_PAGE_UP:
 676           if (viewport.getWrapAlignment())
 677           {
 678             alignPanel.scrollUp(true);
 679           }
 680           else
 681           {
 682             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 683                     - viewport.endSeq + viewport.startSeq);
 684           }
 685           break;
 686         case KeyEvent.VK_PAGE_DOWN:
 687           if (viewport.getWrapAlignment())
 688           {
 689             alignPanel.scrollUp(false);
 690           }
 691           else
 692           {
 693             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 694                     + viewport.endSeq - viewport.startSeq);
 695           }
 696           break;
 697         }
 698       }
 699
 700       @Override
 701       public void keyReleased(KeyEvent evt)
 702       {
 703         switch (evt.getKeyCode())
 704         {
 705         case KeyEvent.VK_LEFT:
 706           if (evt.isAltDown() || !viewport.cursorMode)
 707           {
 708             viewport.firePropertyChange("alignment", null, viewport
 709                     .getAlignment().getSequences());
 710           }
 711           break;
 712
 713         case KeyEvent.VK_RIGHT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null, viewport
 717                     .getAlignment().getSequences());
 718           }
 719           break;
 720         }
 721       }
 722     });
 723   }
 724
 725   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 726   {
 727     ap.alignFrame = this;
 728     avc = new jalview.controller.AlignViewController(this, viewport,
 729             alignPanel);
 730
 731     alignPanels.add(ap);
 732
 733     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 734
 735     int aSize = alignPanels.size();
 736
 737     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 738
 739     if (aSize == 1 && ap.av.viewName == null)
 740     {
 741       this.getContentPane().add(ap, BorderLayout.CENTER);
 742     }
 743     else
 744     {
 745       if (aSize == 2)
 746       {
 747         setInitialTabVisible();
 748       }
 749
 750       expandViews.setEnabled(true);
 751       gatherViews.setEnabled(true);
 752       tabbedPane.addTab(ap.av.viewName, ap);
 753
 754       ap.setVisible(false);
 755     }
 756
 757     if (newPanel)
 758     {
 759       if (ap.av.isPadGaps())
 760       {
 761         ap.av.getAlignment().padGaps();
 762       }
 763       ap.av.updateConservation(ap);
 764       ap.av.updateConsensus(ap);
 765       ap.av.updateStrucConsensus(ap);
 766     }
 767   }
 768
 769   public void setInitialTabVisible()
 770   {
 771     expandViews.setEnabled(true);
 772     gatherViews.setEnabled(true);
 773     tabbedPane.setVisible(true);
 774     AlignmentPanel first = alignPanels.get(0);
 775     tabbedPane.addTab(first.av.viewName, first);
 776     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 777   }
 778
 779   public AlignViewport getViewport()
 780   {
 781     return viewport;
 782   }
 783
 784   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 785   private void addServiceListeners()
 786   {
 787     final java.beans.PropertyChangeListener thisListener;
 788     Desktop.instance.addJalviewPropertyChangeListener("services",
 789             thisListener = new java.beans.PropertyChangeListener()
 790             {
 791               @Override
 792               public void propertyChange(PropertyChangeEvent evt)
 793               {
 794                 // // System.out.println("Discoverer property change.");
 795                 // if (evt.getPropertyName().equals("services"))
 796                 {
 797                   SwingUtilities.invokeLater(new Runnable()
 798                   {
 799
 800                     @Override
 801                     public void run()
 802                     {
 803                       System.err
 804                               .println("Rebuild WS Menu for service change");
 805                       BuildWebServiceMenu();
 806                     }
 807
 808                   });
 809                 }
 810               }
 811             });
 812     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 813     {
 814       @Override
 815       public void internalFrameClosed(
 816               javax.swing.event.InternalFrameEvent evt)
 817       {
 818         // System.out.println("deregistering discoverer listener");
 819         Desktop.instance.removeJalviewPropertyChangeListener("services",
 820                 thisListener);
 821         closeMenuItem_actionPerformed(true);
 822       };
 823     });
 824     // Finally, build the menu once to get current service state
 825     new Thread(new Runnable()
 826     {
 827       @Override
 828       public void run()
 829       {
 830         BuildWebServiceMenu();
 831       }
 832     }).start();
 833   }
 834
 835   /**
 836    * Configure menu items that vary according to whether the alignment is
 837    * nucleotide or protein
 838    */
 839   public void setGUINucleotide()
 840   {
 841     AlignmentI al = getViewport().getAlignment();
 842     boolean nucleotide = al.isNucleotide();
 843
 844     showTranslation.setVisible(nucleotide);
 845     showReverse.setVisible(nucleotide);
 846     showReverseComplement.setVisible(nucleotide);
 847     conservationMenuItem.setEnabled(!nucleotide);
 848     modifyConservation.setEnabled(!nucleotide
 849             && conservationMenuItem.isSelected());
 850     showGroupConservation.setEnabled(!nucleotide);
 851
 852     showComplementMenuItem.setText(nucleotide ? MessageManager
 853             .getString("label.protein") : MessageManager
 854             .getString("label.nucleotide"));
 855   }
 856
 857   /**
 858    * set up menus for the current viewport. This may be called after any
 859    * operation that affects the data in the current view (selection changed,
 860    * etc) to update the menus to reflect the new state.
 861    */
 862   @Override
 863   public void setMenusForViewport()
 864   {
 865     setMenusFromViewport(viewport);
 866   }
 867
 868   /**
 869    * Need to call this method when tabs are selected for multiple views, or when
 870    * loading from Jalview2XML.java
 871    *
 872    * @param av
 873    *          AlignViewport
 874    */
 875   void setMenusFromViewport(AlignViewport av)
 876   {
 877     padGapsMenuitem.setSelected(av.isPadGaps());
 878     colourTextMenuItem.setSelected(av.isShowColourText());
 879     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 880     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 881     conservationMenuItem.setSelected(av.getConservationSelected());
 882     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 883     seqLimits.setSelected(av.getShowJVSuffix());
 884     idRightAlign.setSelected(av.isRightAlignIds());
 885     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 886     renderGapsMenuItem.setSelected(av.isRenderGaps());
 887     wrapMenuItem.setSelected(av.getWrapAlignment());
 888     scaleAbove.setVisible(av.getWrapAlignment());
 889     scaleLeft.setVisible(av.getWrapAlignment());
 890     scaleRight.setVisible(av.getWrapAlignment());
 891     annotationPanelMenuItem.setState(av.isShowAnnotation());
 892     /*
 893      * Show/hide annotations only enabled if annotation panel is shown
 894      */
 895     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 900     viewTextMenuItem.setSelected(av.getShowText());
 901     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 902     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 903     showGroupConservation.setSelected(av.isShowGroupConservation());
 904     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 905     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 906     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 907
 908     ColourMenuHelper.setColourSelected(colourMenu,
 909             av.getGlobalColourScheme());
 910
 911     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 912     hiddenMarkers.setState(av.getShowHiddenMarkers());
 913     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 914     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 915     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 916     autoCalculate.setSelected(av.autoCalculateConsensus);
 917     sortByTree.setSelected(av.sortByTree);
 918     listenToViewSelections.setSelected(av.followSelection);
 919
 920     showProducts.setEnabled(canShowProducts());
 921     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 922
 923     updateEditMenuBar();
 924   }
 925
 926   /**
 927    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 928    *
 929    * @param b
 930    */
 931   public void setGroovyEnabled(boolean b)
 932   {
 933     runGroovy.setEnabled(b);
 934   }
 935
 936   private IProgressIndicator progressBar;
 937
 938   /*
 939    * (non-Javadoc)
 940    *
 941    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 942    */
 943   @Override
 944   public void setProgressBar(String message, long id)
 945   {
 946     progressBar.setProgressBar(message, id);
 947   }
 948
 949   @Override
 950   public void registerHandler(final long id,
 951           final IProgressIndicatorHandler handler)
 952   {
 953     progressBar.registerHandler(id, handler);
 954   }
 955
 956   /**
 957    *
 958    * @return true if any progress bars are still active
 959    */
 960   @Override
 961   public boolean operationInProgress()
 962   {
 963     return progressBar.operationInProgress();
 964   }
 965
 966   @Override
 967   public void setStatus(String text)
 968   {
 969     statusBar.setText(text);
 970   }
 971
 972   /*
 973    * Added so Castor Mapping file can obtain Jalview Version
 974    */
 975   public String getVersion()
 976   {
 977     return jalview.bin.Cache.getProperty("VERSION");
 978   }
 979
 980   public FeatureRenderer getFeatureRenderer()
 981   {
 982     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 983   }
 984
 985   @Override
 986   public void fetchSequence_actionPerformed(ActionEvent e)
 987   {
 988     new jalview.gui.SequenceFetcher(this);
 989   }
 990
 991   @Override
 992   public void addFromFile_actionPerformed(ActionEvent e)
 993   {
 994     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 995   }
 996
 997   @Override
 998   public void reload_actionPerformed(ActionEvent e)
 999   {
1000     if (fileName != null)
1001     {
1002       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003       // originating file's format
1004       // TODO: work out how to recover feature settings for correct view(s) when
1005       // file is reloaded.
1006       if (FileFormat.Jalview.equals(currentFileFormat))
1007       {
1008         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009         for (int i = 0; i < frames.length; i++)
1010         {
1011           if (frames[i] instanceof AlignFrame && frames[i] != this
1012                   && ((AlignFrame) frames[i]).fileName != null
1013                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1014           {
1015             try
1016             {
1017               frames[i].setSelected(true);
1018               Desktop.instance.closeAssociatedWindows();
1019             } catch (java.beans.PropertyVetoException ex)
1020             {
1021             }
1022           }
1023
1024         }
1025         Desktop.instance.closeAssociatedWindows();
1026
1027         FileLoader loader = new FileLoader();
1028         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1029                 : DataSourceType.FILE;
1030         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1031       }
1032       else
1033       {
1034         Rectangle bounds = this.getBounds();
1035
1036         FileLoader loader = new FileLoader();
1037         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1040                 protocol, currentFileFormat);
1041
1042         newframe.setBounds(bounds);
1043         if (featureSettings != null && featureSettings.isShowing())
1044         {
1045           final Rectangle fspos = featureSettings.frame.getBounds();
1046           // TODO: need a 'show feature settings' function that takes bounds -
1047           // need to refactor Desktop.addFrame
1048           newframe.featureSettings_actionPerformed(null);
1049           final FeatureSettings nfs = newframe.featureSettings;
1050           SwingUtilities.invokeLater(new Runnable()
1051           {
1052             @Override
1053             public void run()
1054             {
1055               nfs.frame.setBounds(fspos);
1056             }
1057           });
1058           this.featureSettings.close();
1059           this.featureSettings = null;
1060         }
1061         this.closeMenuItem_actionPerformed(true);
1062       }
1063     }
1064   }
1065
1066   @Override
1067   public void addFromText_actionPerformed(ActionEvent e)
1068   {
1069     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1070             .getAlignPanel());
1071   }
1072
1073   @Override
1074   public void addFromURL_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1077   }
1078
1079   @Override
1080   public void save_actionPerformed(ActionEvent e)
1081   {
1082     if (fileName == null || (currentFileFormat == null)
1083             || fileName.startsWith("http"))
1084     {
1085       saveAs_actionPerformed(null);
1086     }
1087     else
1088     {
1089       saveAlignment(fileName, currentFileFormat);
1090     }
1091   }
1092
1093   /**
1094    * DOCUMENT ME!
1095    *
1096    * @param e
1097    *          DOCUMENT ME!
1098    */
1099   @Override
1100   public void saveAs_actionPerformed(ActionEvent e)
1101   {
1102     String format = currentFileFormat == null ? null : currentFileFormat
1103             .getName();
1104     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1105             Cache.getProperty("LAST_DIRECTORY"), format);
1106
1107     chooser.setFileView(new JalviewFileView());
1108     chooser.setDialogTitle(MessageManager
1109             .getString("label.save_alignment_to_file"));
1110     chooser.setToolTipText(MessageManager.getString("action.save"));
1111
1112     int value = chooser.showSaveDialog(this);
1113
1114     if (value == JalviewFileChooser.APPROVE_OPTION)
1115     {
1116       currentFileFormat = chooser.getSelectedFormat();
1117       while (currentFileFormat == null)
1118       {
1119         JvOptionPane
1120                 .showInternalMessageDialog(
1121                         Desktop.desktop,
1122                         MessageManager
1123                                 .getString("label.select_file_format_before_saving"),
1124                         MessageManager
1125                                 .getString("label.file_format_not_specified"),
1126                         JvOptionPane.WARNING_MESSAGE);
1127         currentFileFormat = chooser.getSelectedFormat();
1128         value = chooser.showSaveDialog(this);
1129         if (value != JalviewFileChooser.APPROVE_OPTION)
1130         {
1131           return;
1132         }
1133       }
1134
1135       fileName = chooser.getSelectedFile().getPath();
1136
1137       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1138
1139       Cache.setProperty("LAST_DIRECTORY", fileName);
1140       saveAlignment(fileName, currentFileFormat);
1141     }
1142   }
1143
1144   public boolean saveAlignment(String file, FileFormatI format)
1145   {
1146     boolean success = true;
1147
1148     if (FileFormat.Jalview.equals(format))
1149     {
1150       String shortName = title;
1151
1152       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1153       {
1154         shortName = shortName.substring(shortName
1155                 .lastIndexOf(java.io.File.separatorChar) + 1);
1156       }
1157
1158       success = new Jalview2XML().saveAlignment(this, file, shortName);
1159
1160       statusBar.setText(MessageManager.formatMessage(
1161               "label.successfully_saved_to_file_in_format", new Object[] {
1162                   fileName, format }));
1163
1164     }
1165     else
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           PrintWriter out = new PrintWriter(new FileWriter(file));
1192
1193           out.print(output);
1194           out.close();
1195           this.setTitle(file);
1196           statusBar.setText(MessageManager.formatMessage(
1197                   "label.successfully_saved_to_file_in_format",
1198                   new Object[] { fileName, format.getName() }));
1199         } catch (Exception ex)
1200         {
1201           success = false;
1202           ex.printStackTrace();
1203         }
1204       }
1205     }
1206
1207     if (!success)
1208     {
1209       JvOptionPane.showInternalMessageDialog(this, MessageManager
1210               .formatMessage("label.couldnt_save_file",
1211                       new Object[] { fileName }), MessageManager
1212               .getString("label.error_saving_file"),
1213               JvOptionPane.WARNING_MESSAGE);
1214     }
1215
1216     return success;
1217   }
1218
1219   private void warningMessage(String warning, String title)
1220   {
1221     if (new jalview.util.Platform().isHeadless())
1222     {
1223       System.err.println("Warning: " + title + "\nWarning: " + warning);
1224
1225     }
1226     else
1227     {
1228       JvOptionPane.showInternalMessageDialog(this, warning, title,
1229               JvOptionPane.WARNING_MESSAGE);
1230     }
1231     return;
1232   }
1233
1234   /**
1235    * DOCUMENT ME!
1236    *
1237    * @param e
1238    *          DOCUMENT ME!
1239    */
1240   @Override
1241   protected void outputText_actionPerformed(ActionEvent e)
1242   {
1243     FileFormatI fileFormat = FileFormats.getInstance().forName(
1244             e.getActionCommand());
1245     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1246             viewport, null);
1247     if (exportData.getSettings().isCancelled())
1248     {
1249       return;
1250     }
1251     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252     cap.setForInput(null);
1253     try
1254     {
1255       FileFormatI format = fileFormat;
1256       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257               .formatSequences(format, 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           FileFormatI format, 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(), format);
1290     }
1291     // settings.isExportAnnotations();
1292
1293     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1294     {
1295       omitHidden = viewport.getViewAsString(false,
1296               settings.isExportHiddenSequences());
1297     }
1298
1299     int[] alignmentStartEnd = new int[2];
1300     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1301     {
1302       alignmentToExport = hiddenSeqs.getFullAlignment();
1303     }
1304     else
1305     {
1306       alignmentToExport = viewport.getAlignment();
1307     }
1308     alignmentStartEnd = alignmentToExport
1309             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1310                     .getHiddenColumns());
1311     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1312             omitHidden, alignmentStartEnd, settings);
1313     return ed;
1314   }
1315
1316   /**
1317    * DOCUMENT ME!
1318    *
1319    * @param e
1320    *          DOCUMENT ME!
1321    */
1322   @Override
1323   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1324   {
1325     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1326     htmlSVG.exportHTML(null);
1327   }
1328
1329   @Override
1330   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1331   {
1332     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1333     bjs.exportHTML(null);
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(FileFormat.Fasta,
1848             seqs, 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;
1935       FileFormatI format;
1936       try
1937       {
1938         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1939         if (str.length() < 1)
1940         {
1941           return;
1942         }
1943
1944         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1945
1946       } catch (OutOfMemoryError er)
1947       {
1948         new OOMWarning("Out of memory pasting sequences!!", er);
1949         return;
1950       }
1951
1952       SequenceI[] sequences;
1953       boolean annotationAdded = false;
1954       AlignmentI alignment = null;
1955
1956       if (Desktop.jalviewClipboard != null)
1957       {
1958         // The clipboard was filled from within Jalview, we must use the
1959         // sequences
1960         // And dataset from the copied alignment
1961         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1962         // be doubly sure that we create *new* sequence objects.
1963         sequences = new SequenceI[newseq.length];
1964         for (int i = 0; i < newseq.length; i++)
1965         {
1966           sequences[i] = new Sequence(newseq[i]);
1967         }
1968         alignment = new Alignment(sequences);
1969         externalPaste = false;
1970       }
1971       else
1972       {
1973         // parse the clipboard as an alignment.
1974         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1975                 format);
1976         sequences = alignment.getSequencesArray();
1977       }
1978
1979       int alwidth = 0;
1980       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1981       int fgroup = -1;
1982
1983       if (newAlignment)
1984       {
1985
1986         if (Desktop.jalviewClipboard != null)
1987         {
1988           // dataset is inherited
1989           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1990         }
1991         else
1992         {
1993           // new dataset is constructed
1994           alignment.setDataset(null);
1995         }
1996         alwidth = alignment.getWidth() + 1;
1997       }
1998       else
1999       {
2000         AlignmentI pastedal = alignment; // preserve pasted alignment object
2001         // Add pasted sequences and dataset into existing alignment.
2002         alignment = viewport.getAlignment();
2003         alwidth = alignment.getWidth() + 1;
2004         // decide if we need to import sequences from an existing dataset
2005         boolean importDs = Desktop.jalviewClipboard != null
2006                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2007         // importDs==true instructs us to copy over new dataset sequences from
2008         // an existing alignment
2009         Vector newDs = (importDs) ? new Vector() : null; // used to create
2010         // minimum dataset set
2011
2012         for (int i = 0; i < sequences.length; i++)
2013         {
2014           if (importDs)
2015           {
2016             newDs.addElement(null);
2017           }
2018           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2019           // paste
2020           if (importDs && ds != null)
2021           {
2022             if (!newDs.contains(ds))
2023             {
2024               newDs.setElementAt(ds, i);
2025               ds = new Sequence(ds);
2026               // update with new dataset sequence
2027               sequences[i].setDatasetSequence(ds);
2028             }
2029             else
2030             {
2031               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2032             }
2033           }
2034           else
2035           {
2036             // copy and derive new dataset sequence
2037             sequences[i] = sequences[i].deriveSequence();
2038             alignment.getDataset().addSequence(
2039                     sequences[i].getDatasetSequence());
2040             // TODO: avoid creation of duplicate dataset sequences with a
2041             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2042           }
2043           alignment.addSequence(sequences[i]); // merges dataset
2044         }
2045         if (newDs != null)
2046         {
2047           newDs.clear(); // tidy up
2048         }
2049         if (alignment.getAlignmentAnnotation() != null)
2050         {
2051           for (AlignmentAnnotation alan : alignment
2052                   .getAlignmentAnnotation())
2053           {
2054             if (alan.graphGroup > fgroup)
2055             {
2056               fgroup = alan.graphGroup;
2057             }
2058           }
2059         }
2060         if (pastedal.getAlignmentAnnotation() != null)
2061         {
2062           // Add any annotation attached to alignment.
2063           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2064           for (int i = 0; i < alann.length; i++)
2065           {
2066             annotationAdded = true;
2067             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2068             {
2069               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2070               if (newann.graphGroup > -1)
2071               {
2072                 if (newGraphGroups.size() <= newann.graphGroup
2073                         || newGraphGroups.get(newann.graphGroup) == null)
2074                 {
2075                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2076                   {
2077                     newGraphGroups.add(q, null);
2078                   }
2079                   newGraphGroups.set(newann.graphGroup, new Integer(
2080                           ++fgroup));
2081                 }
2082                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2083                         .intValue();
2084               }
2085
2086               newann.padAnnotation(alwidth);
2087               alignment.addAnnotation(newann);
2088             }
2089           }
2090         }
2091       }
2092       if (!newAlignment)
2093       {
2094         // /////
2095         // ADD HISTORY ITEM
2096         //
2097         addHistoryItem(new EditCommand(
2098                 MessageManager.getString("label.add_sequences"),
2099                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2100       }
2101       // Add any annotations attached to sequences
2102       for (int i = 0; i < sequences.length; i++)
2103       {
2104         if (sequences[i].getAnnotation() != null)
2105         {
2106           AlignmentAnnotation newann;
2107           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2108           {
2109             annotationAdded = true;
2110             newann = sequences[i].getAnnotation()[a];
2111             newann.adjustForAlignment();
2112             newann.padAnnotation(alwidth);
2113             if (newann.graphGroup > -1)
2114             {
2115               if (newann.graphGroup > -1)
2116               {
2117                 if (newGraphGroups.size() <= newann.graphGroup
2118                         || newGraphGroups.get(newann.graphGroup) == null)
2119                 {
2120                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2121                   {
2122                     newGraphGroups.add(q, null);
2123                   }
2124                   newGraphGroups.set(newann.graphGroup, new Integer(
2125                           ++fgroup));
2126                 }
2127                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2128                         .intValue();
2129               }
2130             }
2131             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2132             // was
2133             // duplicated
2134             // earlier
2135             alignment
2136                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2137           }
2138         }
2139       }
2140       if (!newAlignment)
2141       {
2142
2143         // propagate alignment changed.
2144         viewport.setEndSeq(alignment.getHeight());
2145         if (annotationAdded)
2146         {
2147           // Duplicate sequence annotation in all views.
2148           AlignmentI[] alview = this.getViewAlignments();
2149           for (int i = 0; i < sequences.length; i++)
2150           {
2151             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2152             if (sann == null)
2153             {
2154               continue;
2155             }
2156             for (int avnum = 0; avnum < alview.length; avnum++)
2157             {
2158               if (alview[avnum] != alignment)
2159               {
2160                 // duplicate in a view other than the one with input focus
2161                 int avwidth = alview[avnum].getWidth() + 1;
2162                 // this relies on sann being preserved after we
2163                 // modify the sequence's annotation array for each duplication
2164                 for (int a = 0; a < sann.length; a++)
2165                 {
2166                   AlignmentAnnotation newann = new AlignmentAnnotation(
2167                           sann[a]);
2168                   sequences[i].addAlignmentAnnotation(newann);
2169                   newann.padAnnotation(avwidth);
2170                   alview[avnum].addAnnotation(newann); // annotation was
2171                   // duplicated earlier
2172                   // TODO JAL-1145 graphGroups are not updated for sequence
2173                   // annotation added to several views. This may cause
2174                   // strangeness
2175                   alview[avnum].setAnnotationIndex(newann, a);
2176                 }
2177               }
2178             }
2179           }
2180           buildSortByAnnotationScoresMenu();
2181         }
2182         viewport.firePropertyChange("alignment", null,
2183                 alignment.getSequences());
2184         if (alignPanels != null)
2185         {
2186           for (AlignmentPanel ap : alignPanels)
2187           {
2188             ap.validateAnnotationDimensions(false);
2189           }
2190         }
2191         else
2192         {
2193           alignPanel.validateAnnotationDimensions(false);
2194         }
2195
2196       }
2197       else
2198       {
2199         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2200                 DEFAULT_HEIGHT);
2201         String newtitle = new String("Copied sequences");
2202
2203         if (Desktop.jalviewClipboard != null
2204                 && Desktop.jalviewClipboard[2] != null)
2205         {
2206           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2207           for (int[] region : hc)
2208           {
2209             af.viewport.hideColumns(region[0], region[1]);
2210           }
2211         }
2212
2213         // >>>This is a fix for the moment, until a better solution is
2214         // found!!<<<
2215         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2216                 .transferSettings(
2217                         alignPanel.getSeqPanel().seqCanvas
2218                                 .getFeatureRenderer());
2219
2220         // TODO: maintain provenance of an alignment, rather than just make the
2221         // title a concatenation of operations.
2222         if (!externalPaste)
2223         {
2224           if (title.startsWith("Copied sequences"))
2225           {
2226             newtitle = title;
2227           }
2228           else
2229           {
2230             newtitle = newtitle.concat("- from " + title);
2231           }
2232         }
2233         else
2234         {
2235           newtitle = new String("Pasted sequences");
2236         }
2237
2238         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2239                 DEFAULT_HEIGHT);
2240
2241       }
2242
2243     } catch (Exception ex)
2244     {
2245       ex.printStackTrace();
2246       System.out.println("Exception whilst pasting: " + ex);
2247       // could be anything being pasted in here
2248     }
2249
2250   }
2251
2252   @Override
2253   protected void expand_newalign(ActionEvent e)
2254   {
2255     try
2256     {
2257       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2258               .getAlignment(), -1);
2259       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2260               DEFAULT_HEIGHT);
2261       String newtitle = new String("Flanking alignment");
2262
2263       if (Desktop.jalviewClipboard != null
2264               && Desktop.jalviewClipboard[2] != null)
2265       {
2266         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2267         for (int region[] : hc)
2268         {
2269           af.viewport.hideColumns(region[0], region[1]);
2270         }
2271       }
2272
2273       // >>>This is a fix for the moment, until a better solution is
2274       // found!!<<<
2275       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2276               .transferSettings(
2277                       alignPanel.getSeqPanel().seqCanvas
2278                               .getFeatureRenderer());
2279
2280       // TODO: maintain provenance of an alignment, rather than just make the
2281       // title a concatenation of operations.
2282       {
2283         if (title.startsWith("Copied sequences"))
2284         {
2285           newtitle = title;
2286         }
2287         else
2288         {
2289           newtitle = newtitle.concat("- from " + title);
2290         }
2291       }
2292
2293       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2294
2295     } catch (Exception ex)
2296     {
2297       ex.printStackTrace();
2298       System.out.println("Exception whilst pasting: " + ex);
2299       // could be anything being pasted in here
2300     } catch (OutOfMemoryError oom)
2301     {
2302       new OOMWarning("Viewing flanking region of alignment", oom);
2303     }
2304   }
2305
2306   /**
2307    * DOCUMENT ME!
2308    *
2309    * @param e
2310    *          DOCUMENT ME!
2311    */
2312   @Override
2313   protected void cut_actionPerformed(ActionEvent e)
2314   {
2315     copy_actionPerformed(null);
2316     delete_actionPerformed(null);
2317   }
2318
2319   /**
2320    * DOCUMENT ME!
2321    *
2322    * @param e
2323    *          DOCUMENT ME!
2324    */
2325   @Override
2326   protected void delete_actionPerformed(ActionEvent evt)
2327   {
2328
2329     SequenceGroup sg = viewport.getSelectionGroup();
2330     if (sg == null)
2331     {
2332       return;
2333     }
2334
2335     /*
2336      * If the cut affects all sequences, warn, remove highlighted columns
2337      */
2338     if (sg.getSize() == viewport.getAlignment().getHeight())
2339     {
2340       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2341               .getAlignment().getWidth()) ? true : false;
2342       if (isEntireAlignWidth)
2343       {
2344         int confirm = JvOptionPane.showConfirmDialog(this,
2345                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2346                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2347                 JvOptionPane.OK_CANCEL_OPTION);
2348
2349         if (confirm == JvOptionPane.CANCEL_OPTION
2350                 || confirm == JvOptionPane.CLOSED_OPTION)
2351         {
2352           return;
2353         }
2354       }
2355       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2356               sg.getEndRes() + 1);
2357     }
2358     SequenceI[] cut = sg.getSequences()
2359             .toArray(new SequenceI[sg.getSize()]);
2360
2361     addHistoryItem(new EditCommand(
2362             MessageManager.getString("label.cut_sequences"), Action.CUT,
2363             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2364             viewport.getAlignment()));
2365
2366     viewport.setSelectionGroup(null);
2367     viewport.sendSelection();
2368     viewport.getAlignment().deleteGroup(sg);
2369
2370     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2371             .getSequences());
2372     if (viewport.getAlignment().getHeight() < 1)
2373     {
2374       try
2375       {
2376         this.setClosed(true);
2377       } catch (Exception ex)
2378       {
2379       }
2380     }
2381   }
2382
2383   /**
2384    * DOCUMENT ME!
2385    *
2386    * @param e
2387    *          DOCUMENT ME!
2388    */
2389   @Override
2390   protected void deleteGroups_actionPerformed(ActionEvent e)
2391   {
2392     if (avc.deleteGroups())
2393     {
2394       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2395       alignPanel.updateAnnotation();
2396       alignPanel.paintAlignment(true);
2397     }
2398   }
2399
2400   /**
2401    * DOCUMENT ME!
2402    *
2403    * @param e
2404    *          DOCUMENT ME!
2405    */
2406   @Override
2407   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2408   {
2409     SequenceGroup sg = new SequenceGroup();
2410
2411     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2412     {
2413       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2414     }
2415
2416     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2417     viewport.setSelectionGroup(sg);
2418     viewport.sendSelection();
2419     // JAL-2034 - should delegate to
2420     // alignPanel to decide if overview needs
2421     // updating.
2422     alignPanel.paintAlignment(false);
2423     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2424   }
2425
2426   /**
2427    * DOCUMENT ME!
2428    *
2429    * @param e
2430    *          DOCUMENT ME!
2431    */
2432   @Override
2433   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2434   {
2435     if (viewport.cursorMode)
2436     {
2437       alignPanel.getSeqPanel().keyboardNo1 = null;
2438       alignPanel.getSeqPanel().keyboardNo2 = null;
2439     }
2440     viewport.setSelectionGroup(null);
2441     viewport.getColumnSelection().clear();
2442     viewport.setSelectionGroup(null);
2443     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2444     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2445     // JAL-2034 - should delegate to
2446     // alignPanel to decide if overview needs
2447     // updating.
2448     alignPanel.paintAlignment(false);
2449     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2450     viewport.sendSelection();
2451   }
2452
2453   /**
2454    * DOCUMENT ME!
2455    *
2456    * @param e
2457    *          DOCUMENT ME!
2458    */
2459   @Override
2460   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2461   {
2462     SequenceGroup sg = viewport.getSelectionGroup();
2463
2464     if (sg == null)
2465     {
2466       selectAllSequenceMenuItem_actionPerformed(null);
2467
2468       return;
2469     }
2470
2471     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2472     {
2473       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2474     }
2475     // JAL-2034 - should delegate to
2476     // alignPanel to decide if overview needs
2477     // updating.
2478
2479     alignPanel.paintAlignment(true);
2480     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2481     viewport.sendSelection();
2482   }
2483
2484   @Override
2485   public void invertColSel_actionPerformed(ActionEvent e)
2486   {
2487     viewport.invertColumnSelection();
2488     alignPanel.paintAlignment(true);
2489     viewport.sendSelection();
2490   }
2491
2492   /**
2493    * DOCUMENT ME!
2494    *
2495    * @param e
2496    *          DOCUMENT ME!
2497    */
2498   @Override
2499   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2500   {
2501     trimAlignment(true);
2502   }
2503
2504   /**
2505    * DOCUMENT ME!
2506    *
2507    * @param e
2508    *          DOCUMENT ME!
2509    */
2510   @Override
2511   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2512   {
2513     trimAlignment(false);
2514   }
2515
2516   void trimAlignment(boolean trimLeft)
2517   {
2518     ColumnSelection colSel = viewport.getColumnSelection();
2519     int column;
2520
2521     if (!colSel.isEmpty())
2522     {
2523       if (trimLeft)
2524       {
2525         column = colSel.getMin();
2526       }
2527       else
2528       {
2529         column = colSel.getMax();
2530       }
2531
2532       SequenceI[] seqs;
2533       if (viewport.getSelectionGroup() != null)
2534       {
2535         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2536                 viewport.getHiddenRepSequences());
2537       }
2538       else
2539       {
2540         seqs = viewport.getAlignment().getSequencesArray();
2541       }
2542
2543       TrimRegionCommand trimRegion;
2544       if (trimLeft)
2545       {
2546         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2547                 column, viewport.getAlignment());
2548         viewport.setStartRes(0);
2549       }
2550       else
2551       {
2552         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2553                 column, viewport.getAlignment());
2554       }
2555
2556       statusBar.setText(MessageManager.formatMessage(
2557               "label.removed_columns",
2558               new String[] { Integer.valueOf(trimRegion.getSize())
2559                       .toString() }));
2560
2561       addHistoryItem(trimRegion);
2562
2563       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2564       {
2565         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2566                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2567         {
2568           viewport.getAlignment().deleteGroup(sg);
2569         }
2570       }
2571
2572       viewport.firePropertyChange("alignment", null, viewport
2573               .getAlignment().getSequences());
2574     }
2575   }
2576
2577   /**
2578    * DOCUMENT ME!
2579    *
2580    * @param e
2581    *          DOCUMENT ME!
2582    */
2583   @Override
2584   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2585   {
2586     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2587
2588     SequenceI[] seqs;
2589     if (viewport.getSelectionGroup() != null)
2590     {
2591       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2592               viewport.getHiddenRepSequences());
2593       start = viewport.getSelectionGroup().getStartRes();
2594       end = viewport.getSelectionGroup().getEndRes();
2595     }
2596     else
2597     {
2598       seqs = viewport.getAlignment().getSequencesArray();
2599     }
2600
2601     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2602             "Remove Gapped Columns", seqs, start, end,
2603             viewport.getAlignment());
2604
2605     addHistoryItem(removeGapCols);
2606
2607     statusBar.setText(MessageManager.formatMessage(
2608             "label.removed_empty_columns",
2609             new Object[] { Integer.valueOf(removeGapCols.getSize())
2610                     .toString() }));
2611
2612     // This is to maintain viewport position on first residue
2613     // of first sequence
2614     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2615     int startRes = seq.findPosition(viewport.startRes);
2616     // ShiftList shifts;
2617     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2618     // edit.alColumnChanges=shifts.getInverse();
2619     // if (viewport.hasHiddenColumns)
2620     // viewport.getColumnSelection().compensateForEdits(shifts);
2621     viewport.setStartRes(seq.findIndex(startRes) - 1);
2622     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2623             .getSequences());
2624
2625   }
2626
2627   /**
2628    * DOCUMENT ME!
2629    *
2630    * @param e
2631    *          DOCUMENT ME!
2632    */
2633   @Override
2634   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2635   {
2636     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2637
2638     SequenceI[] seqs;
2639     if (viewport.getSelectionGroup() != null)
2640     {
2641       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2642               viewport.getHiddenRepSequences());
2643       start = viewport.getSelectionGroup().getStartRes();
2644       end = viewport.getSelectionGroup().getEndRes();
2645     }
2646     else
2647     {
2648       seqs = viewport.getAlignment().getSequencesArray();
2649     }
2650
2651     // This is to maintain viewport position on first residue
2652     // of first sequence
2653     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2654     int startRes = seq.findPosition(viewport.startRes);
2655
2656     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2657             viewport.getAlignment()));
2658
2659     viewport.setStartRes(seq.findIndex(startRes) - 1);
2660
2661     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2662             .getSequences());
2663
2664   }
2665
2666   /**
2667    * DOCUMENT ME!
2668    *
2669    * @param e
2670    *          DOCUMENT ME!
2671    */
2672   @Override
2673   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2674   {
2675     viewport.setPadGaps(padGapsMenuitem.isSelected());
2676     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2677             .getSequences());
2678   }
2679
2680   /**
2681    * DOCUMENT ME!
2682    *
2683    * @param e
2684    *          DOCUMENT ME!
2685    */
2686   @Override
2687   public void findMenuItem_actionPerformed(ActionEvent e)
2688   {
2689     new Finder();
2690   }
2691
2692   /**
2693    * Create a new view of the current alignment.
2694    */
2695   @Override
2696   public void newView_actionPerformed(ActionEvent e)
2697   {
2698     newView(null, true);
2699   }
2700
2701   /**
2702    * Creates and shows a new view of the current alignment.
2703    *
2704    * @param viewTitle
2705    *          title of newly created view; if null, one will be generated
2706    * @param copyAnnotation
2707    *          if true then duplicate all annnotation, groups and settings
2708    * @return new alignment panel, already displayed.
2709    */
2710   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2711   {
2712     /*
2713      * Create a new AlignmentPanel (with its own, new Viewport)
2714      */
2715     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2716             true);
2717     if (!copyAnnotation)
2718     {
2719       /*
2720        * remove all groups and annotation except for the automatic stuff
2721        */
2722       newap.av.getAlignment().deleteAllGroups();
2723       newap.av.getAlignment().deleteAllAnnotations(false);
2724     }
2725
2726     newap.av.setGatherViewsHere(false);
2727
2728     if (viewport.viewName == null)
2729     {
2730       viewport.viewName = MessageManager
2731               .getString("label.view_name_original");
2732     }
2733
2734     /*
2735      * Views share the same edits undo and redo stacks
2736      */
2737     newap.av.setHistoryList(viewport.getHistoryList());
2738     newap.av.setRedoList(viewport.getRedoList());
2739
2740     /*
2741      * Views share the same mappings; need to deregister any new mappings
2742      * created by copyAlignPanel, and register the new reference to the shared
2743      * mappings
2744      */
2745     newap.av.replaceMappings(viewport.getAlignment());
2746
2747     newap.av.viewName = getNewViewName(viewTitle);
2748
2749     addAlignmentPanel(newap, true);
2750     newap.alignmentChanged();
2751
2752     if (alignPanels.size() == 2)
2753     {
2754       viewport.setGatherViewsHere(true);
2755     }
2756     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2757     return newap;
2758   }
2759
2760   /**
2761    * Make a new name for the view, ensuring it is unique within the current
2762    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2763    * these now use viewId. Unique view names are still desirable for usability.)
2764    *
2765    * @param viewTitle
2766    * @return
2767    */
2768   protected String getNewViewName(String viewTitle)
2769   {
2770     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2771     boolean addFirstIndex = false;
2772     if (viewTitle == null || viewTitle.trim().length() == 0)
2773     {
2774       viewTitle = MessageManager.getString("action.view");
2775       addFirstIndex = true;
2776     }
2777     else
2778     {
2779       index = 1;// we count from 1 if given a specific name
2780     }
2781     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2782
2783     List<Component> comps = PaintRefresher.components.get(viewport
2784             .getSequenceSetId());
2785
2786     List<String> existingNames = getExistingViewNames(comps);
2787
2788     while (existingNames.contains(newViewName))
2789     {
2790       newViewName = viewTitle + " " + (++index);
2791     }
2792     return newViewName;
2793   }
2794
2795   /**
2796    * Returns a list of distinct view names found in the given list of
2797    * components. View names are held on the viewport of an AlignmentPanel.
2798    *
2799    * @param comps
2800    * @return
2801    */
2802   protected List<String> getExistingViewNames(List<Component> comps)
2803   {
2804     List<String> existingNames = new ArrayList<String>();
2805     for (Component comp : comps)
2806     {
2807       if (comp instanceof AlignmentPanel)
2808       {
2809         AlignmentPanel ap = (AlignmentPanel) comp;
2810         if (!existingNames.contains(ap.av.viewName))
2811         {
2812           existingNames.add(ap.av.viewName);
2813         }
2814       }
2815     }
2816     return existingNames;
2817   }
2818
2819   /**
2820    * Explode tabbed views into separate windows.
2821    */
2822   @Override
2823   public void expandViews_actionPerformed(ActionEvent e)
2824   {
2825     Desktop.explodeViews(this);
2826   }
2827
2828   /**
2829    * Gather views in separate windows back into a tabbed presentation.
2830    */
2831   @Override
2832   public void gatherViews_actionPerformed(ActionEvent e)
2833   {
2834     Desktop.instance.gatherViews(this);
2835   }
2836
2837   /**
2838    * DOCUMENT ME!
2839    *
2840    * @param e
2841    *          DOCUMENT ME!
2842    */
2843   @Override
2844   public void font_actionPerformed(ActionEvent e)
2845   {
2846     new FontChooser(alignPanel);
2847   }
2848
2849   /**
2850    * DOCUMENT ME!
2851    *
2852    * @param e
2853    *          DOCUMENT ME!
2854    */
2855   @Override
2856   protected void seqLimit_actionPerformed(ActionEvent e)
2857   {
2858     viewport.setShowJVSuffix(seqLimits.isSelected());
2859
2860     alignPanel.getIdPanel().getIdCanvas()
2861             .setPreferredSize(alignPanel.calculateIdWidth());
2862     alignPanel.paintAlignment(true);
2863   }
2864
2865   @Override
2866   public void idRightAlign_actionPerformed(ActionEvent e)
2867   {
2868     viewport.setRightAlignIds(idRightAlign.isSelected());
2869     alignPanel.paintAlignment(true);
2870   }
2871
2872   @Override
2873   public void centreColumnLabels_actionPerformed(ActionEvent e)
2874   {
2875     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2876     alignPanel.paintAlignment(true);
2877   }
2878
2879   /*
2880    * (non-Javadoc)
2881    *
2882    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2883    */
2884   @Override
2885   protected void followHighlight_actionPerformed()
2886   {
2887     /*
2888      * Set the 'follow' flag on the Viewport (and scroll to position if now
2889      * true).
2890      */
2891     final boolean state = this.followHighlightMenuItem.getState();
2892     viewport.setFollowHighlight(state);
2893     if (state)
2894     {
2895       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2896     }
2897   }
2898
2899   /**
2900    * DOCUMENT ME!
2901    *
2902    * @param e
2903    *          DOCUMENT ME!
2904    */
2905   @Override
2906   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2907   {
2908     viewport.setColourText(colourTextMenuItem.isSelected());
2909     alignPanel.paintAlignment(true);
2910   }
2911
2912   /**
2913    * DOCUMENT ME!
2914    *
2915    * @param e
2916    *          DOCUMENT ME!
2917    */
2918   @Override
2919   public void wrapMenuItem_actionPerformed(ActionEvent e)
2920   {
2921     scaleAbove.setVisible(wrapMenuItem.isSelected());
2922     scaleLeft.setVisible(wrapMenuItem.isSelected());
2923     scaleRight.setVisible(wrapMenuItem.isSelected());
2924     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2925     alignPanel.updateLayout();
2926   }
2927
2928   @Override
2929   public void showAllSeqs_actionPerformed(ActionEvent e)
2930   {
2931     viewport.showAllHiddenSeqs();
2932   }
2933
2934   @Override
2935   public void showAllColumns_actionPerformed(ActionEvent e)
2936   {
2937     viewport.showAllHiddenColumns();
2938     repaint();
2939     viewport.sendSelection();
2940   }
2941
2942   @Override
2943   public void hideSelSequences_actionPerformed(ActionEvent e)
2944   {
2945     viewport.hideAllSelectedSeqs();
2946     // alignPanel.paintAlignment(true);
2947   }
2948
2949   /**
2950    * called by key handler and the hide all/show all menu items
2951    *
2952    * @param toggleSeqs
2953    * @param toggleCols
2954    */
2955   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2956   {
2957
2958     boolean hide = false;
2959     SequenceGroup sg = viewport.getSelectionGroup();
2960     if (!toggleSeqs && !toggleCols)
2961     {
2962       // Hide everything by the current selection - this is a hack - we do the
2963       // invert and then hide
2964       // first check that there will be visible columns after the invert.
2965       if (viewport.hasSelectedColumns()
2966               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2967                       .getEndRes()))
2968       {
2969         // now invert the sequence set, if required - empty selection implies
2970         // that no hiding is required.
2971         if (sg != null)
2972         {
2973           invertSequenceMenuItem_actionPerformed(null);
2974           sg = viewport.getSelectionGroup();
2975           toggleSeqs = true;
2976
2977         }
2978         viewport.expandColSelection(sg, true);
2979         // finally invert the column selection and get the new sequence
2980         // selection.
2981         invertColSel_actionPerformed(null);
2982         toggleCols = true;
2983       }
2984     }
2985
2986     if (toggleSeqs)
2987     {
2988       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2989       {
2990         hideSelSequences_actionPerformed(null);
2991         hide = true;
2992       }
2993       else if (!(toggleCols && viewport.hasSelectedColumns()))
2994       {
2995         showAllSeqs_actionPerformed(null);
2996       }
2997     }
2998
2999     if (toggleCols)
3000     {
3001       if (viewport.hasSelectedColumns())
3002       {
3003         hideSelColumns_actionPerformed(null);
3004         if (!toggleSeqs)
3005         {
3006           viewport.setSelectionGroup(sg);
3007         }
3008       }
3009       else if (!hide)
3010       {
3011         showAllColumns_actionPerformed(null);
3012       }
3013     }
3014   }
3015
3016   /*
3017    * (non-Javadoc)
3018    *
3019    * @see
3020    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3021    * event.ActionEvent)
3022    */
3023   @Override
3024   public void hideAllButSelection_actionPerformed(ActionEvent e)
3025   {
3026     toggleHiddenRegions(false, false);
3027     viewport.sendSelection();
3028   }
3029
3030   /*
3031    * (non-Javadoc)
3032    *
3033    * @see
3034    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3035    * .ActionEvent)
3036    */
3037   @Override
3038   public void hideAllSelection_actionPerformed(ActionEvent e)
3039   {
3040     SequenceGroup sg = viewport.getSelectionGroup();
3041     viewport.expandColSelection(sg, false);
3042     viewport.hideAllSelectedSeqs();
3043     viewport.hideSelectedColumns();
3044     alignPanel.paintAlignment(true);
3045     viewport.sendSelection();
3046   }
3047
3048   /*
3049    * (non-Javadoc)
3050    *
3051    * @see
3052    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3053    * ActionEvent)
3054    */
3055   @Override
3056   public void showAllhidden_actionPerformed(ActionEvent e)
3057   {
3058     viewport.showAllHiddenColumns();
3059     viewport.showAllHiddenSeqs();
3060     alignPanel.paintAlignment(true);
3061     viewport.sendSelection();
3062   }
3063
3064   @Override
3065   public void hideSelColumns_actionPerformed(ActionEvent e)
3066   {
3067     viewport.hideSelectedColumns();
3068     alignPanel.paintAlignment(true);
3069     viewport.sendSelection();
3070   }
3071
3072   @Override
3073   public void hiddenMarkers_actionPerformed(ActionEvent e)
3074   {
3075     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3076     repaint();
3077   }
3078
3079   /**
3080    * DOCUMENT ME!
3081    *
3082    * @param e
3083    *          DOCUMENT ME!
3084    */
3085   @Override
3086   protected void scaleAbove_actionPerformed(ActionEvent e)
3087   {
3088     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3089     alignPanel.paintAlignment(true);
3090   }
3091
3092   /**
3093    * DOCUMENT ME!
3094    *
3095    * @param e
3096    *          DOCUMENT ME!
3097    */
3098   @Override
3099   protected void scaleLeft_actionPerformed(ActionEvent e)
3100   {
3101     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3102     alignPanel.paintAlignment(true);
3103   }
3104
3105   /**
3106    * DOCUMENT ME!
3107    *
3108    * @param e
3109    *          DOCUMENT ME!
3110    */
3111   @Override
3112   protected void scaleRight_actionPerformed(ActionEvent e)
3113   {
3114     viewport.setScaleRightWrapped(scaleRight.isSelected());
3115     alignPanel.paintAlignment(true);
3116   }
3117
3118   /**
3119    * DOCUMENT ME!
3120    *
3121    * @param e
3122    *          DOCUMENT ME!
3123    */
3124   @Override
3125   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3126   {
3127     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3128     alignPanel.paintAlignment(true);
3129   }
3130
3131   /**
3132    * DOCUMENT ME!
3133    *
3134    * @param e
3135    *          DOCUMENT ME!
3136    */
3137   @Override
3138   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3139   {
3140     viewport.setShowText(viewTextMenuItem.isSelected());
3141     alignPanel.paintAlignment(true);
3142   }
3143
3144   /**
3145    * DOCUMENT ME!
3146    *
3147    * @param e
3148    *          DOCUMENT ME!
3149    */
3150   @Override
3151   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3152   {
3153     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3154     alignPanel.paintAlignment(true);
3155   }
3156
3157   public FeatureSettings featureSettings;
3158
3159   @Override
3160   public FeatureSettingsControllerI getFeatureSettingsUI()
3161   {
3162     return featureSettings;
3163   }
3164
3165   @Override
3166   public void featureSettings_actionPerformed(ActionEvent e)
3167   {
3168     if (featureSettings != null)
3169     {
3170       featureSettings.close();
3171       featureSettings = null;
3172     }
3173     if (!showSeqFeatures.isSelected())
3174     {
3175       // make sure features are actually displayed
3176       showSeqFeatures.setSelected(true);
3177       showSeqFeatures_actionPerformed(null);
3178     }
3179     featureSettings = new FeatureSettings(this);
3180   }
3181
3182   /**
3183    * Set or clear 'Show Sequence Features'
3184    *
3185    * @param evt
3186    *          DOCUMENT ME!
3187    */
3188   @Override
3189   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3190   {
3191     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3192     alignPanel.paintAlignment(true);
3193     if (alignPanel.getOverviewPanel() != null)
3194     {
3195       alignPanel.getOverviewPanel().updateOverviewImage();
3196     }
3197   }
3198
3199   /**
3200    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3201    * the annotations panel as a whole.
3202    *
3203    * The options to show/hide all annotations should be enabled when the panel
3204    * is shown, and disabled when the panel is hidden.
3205    *
3206    * @param e
3207    */
3208   @Override
3209   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3210   {
3211     final boolean setVisible = annotationPanelMenuItem.isSelected();
3212     viewport.setShowAnnotation(setVisible);
3213     this.showAllSeqAnnotations.setEnabled(setVisible);
3214     this.hideAllSeqAnnotations.setEnabled(setVisible);
3215     this.showAllAlAnnotations.setEnabled(setVisible);
3216     this.hideAllAlAnnotations.setEnabled(setVisible);
3217     alignPanel.updateLayout();
3218   }
3219
3220   @Override
3221   public void alignmentProperties()
3222   {
3223     JEditorPane editPane = new JEditorPane("text/html", "");
3224     editPane.setEditable(false);
3225     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3226             .formatAsHtml();
3227     editPane.setText(MessageManager.formatMessage("label.html_content",
3228             new Object[] { contents.toString() }));
3229     JInternalFrame frame = new JInternalFrame();
3230     frame.getContentPane().add(new JScrollPane(editPane));
3231
3232     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3233             "label.alignment_properties", new Object[] { getTitle() }),
3234             500, 400);
3235   }
3236
3237   /**
3238    * DOCUMENT ME!
3239    *
3240    * @param e
3241    *          DOCUMENT ME!
3242    */
3243   @Override
3244   public void overviewMenuItem_actionPerformed(ActionEvent e)
3245   {
3246     if (alignPanel.overviewPanel != null)
3247     {
3248       return;
3249     }
3250
3251     JInternalFrame frame = new JInternalFrame();
3252     OverviewPanel overview = new OverviewPanel(alignPanel);
3253     frame.setContentPane(overview);
3254     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3255             "label.overview_params", new Object[] { this.getTitle() }),
3256             frame.getWidth(), frame.getHeight());
3257     frame.pack();
3258     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3259     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3260     {
3261       @Override
3262       public void internalFrameClosed(
3263               javax.swing.event.InternalFrameEvent evt)
3264       {
3265         alignPanel.setOverviewPanel(null);
3266       };
3267     });
3268
3269     alignPanel.setOverviewPanel(overview);
3270   }
3271
3272   @Override
3273   public void textColour_actionPerformed()
3274   {
3275     new TextColourChooser().chooseColour(alignPanel, null);
3276   }
3277
3278   /*
3279    * public void covariationColour_actionPerformed() {
3280    * changeColour(new
3281    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3282    * ()[0])); }
3283    */
3284   @Override
3285   public void annotationColour_actionPerformed()
3286   {
3287     new AnnotationColourChooser(viewport, alignPanel);
3288   }
3289
3290   @Override
3291   public void annotationColumn_actionPerformed(ActionEvent e)
3292   {
3293     new AnnotationColumnChooser(viewport, alignPanel);
3294   }
3295
3296   /**
3297    * Action on the user checking or unchecking the option to apply the selected
3298    * colour scheme to all groups. If unchecked, groups may have their own
3299    * independent colour schemes.
3300    *
3301    * @param selected
3302    */
3303   @Override
3304   public void applyToAllGroups_actionPerformed(boolean selected)
3305   {
3306     viewport.setColourAppliesToAllGroups(selected);
3307   }
3308
3309   /**
3310    * Action on user selecting a colour from the colour menu
3311    *
3312    * @param name
3313    *          the name (not the menu item label!) of the colour scheme
3314    */
3315   @Override
3316   public void changeColour_actionPerformed(String name)
3317   {
3318     /*
3319      * 'User Defined' opens a panel to configure or load a
3320      * user-defined colour scheme
3321      */
3322     if (ResidueColourScheme.USER_DEFINED.equals(name))
3323     {
3324       new UserDefinedColours(alignPanel, null);
3325       return;
3326     }
3327
3328     /*
3329      * otherwise set the chosen colour scheme (or null for 'None')
3330      */
3331     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3332             viewport.getAlignment(), viewport.getHiddenRepSequences());
3333     changeColour(cs);
3334   }
3335
3336   /**
3337    * Actions on setting or changing the alignment colour scheme
3338    *
3339    * @param cs
3340    */
3341   @Override
3342   public void changeColour(ColourSchemeI cs)
3343   {
3344     // TODO: pull up to controller method
3345     if (cs != null)
3346     {
3347       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3348     }
3349
3350     viewport.setGlobalColourScheme(cs);
3351
3352     alignPanel.paintAlignment(true);
3353   }
3354
3355   /**
3356    * Show the PID threshold slider panel
3357    */
3358   @Override
3359   protected void modifyPID_actionPerformed()
3360   {
3361     SliderPanel.setPIDSliderSource(alignPanel,
3362             viewport.getViewportColourScheme(), alignPanel.getViewName());
3363     SliderPanel.showPIDSlider();
3364   }
3365
3366   /**
3367    * Show the Conservation slider panel
3368    */
3369   @Override
3370   protected void modifyConservation_actionPerformed()
3371   {
3372     SliderPanel.setConservationSlider(alignPanel,
3373             viewport.getViewportColourScheme(), alignPanel.getViewName());
3374     SliderPanel.showConservationSlider();
3375   }
3376
3377   /**
3378    * Action on selecting or deselecting (Colour) By Conservation
3379    */
3380   @Override
3381   public void conservationMenuItem_actionPerformed(boolean selected)
3382   {
3383     modifyConservation.setEnabled(selected);
3384     viewport.setConservationSelected(selected);
3385     viewport.getViewportColourScheme().setConservationApplied(selected);
3386
3387     changeColour(viewport.getGlobalColourScheme());
3388     if (selected)
3389     {
3390       modifyConservation_actionPerformed();
3391     }
3392     else
3393     {
3394       SliderPanel.hideConservationSlider();
3395     }
3396   }
3397
3398   /**
3399    * Action on selecting or deselecting (Colour) Above PID Threshold
3400    */
3401   @Override
3402   public void abovePIDThreshold_actionPerformed(boolean selected)
3403   {
3404     modifyPID.setEnabled(selected);
3405     viewport.setAbovePIDThreshold(selected);
3406     if (!selected)
3407     {
3408       viewport.getViewportColourScheme().setThreshold(0,
3409               viewport.isIgnoreGapsConsensus());
3410     }
3411
3412     changeColour(viewport.getGlobalColourScheme());
3413     if (selected)
3414     {
3415       modifyPID_actionPerformed();
3416     }
3417     else
3418     {
3419       SliderPanel.hidePIDSlider();
3420     }
3421   }
3422
3423   /**
3424    * DOCUMENT ME!
3425    *
3426    * @param e
3427    *          DOCUMENT ME!
3428    */
3429   @Override
3430   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3431   {
3432     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3433     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3434             .getAlignment().getSequenceAt(0), null);
3435     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3436             viewport.getAlignment()));
3437     alignPanel.paintAlignment(true);
3438   }
3439
3440   /**
3441    * DOCUMENT ME!
3442    *
3443    * @param e
3444    *          DOCUMENT ME!
3445    */
3446   @Override
3447   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3448   {
3449     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3450     AlignmentSorter.sortByID(viewport.getAlignment());
3451     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3452             viewport.getAlignment()));
3453     alignPanel.paintAlignment(true);
3454   }
3455
3456   /**
3457    * DOCUMENT ME!
3458    *
3459    * @param e
3460    *          DOCUMENT ME!
3461    */
3462   @Override
3463   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3464   {
3465     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3466     AlignmentSorter.sortByLength(viewport.getAlignment());
3467     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3468             viewport.getAlignment()));
3469     alignPanel.paintAlignment(true);
3470   }
3471
3472   /**
3473    * DOCUMENT ME!
3474    *
3475    * @param e
3476    *          DOCUMENT ME!
3477    */
3478   @Override
3479   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3480   {
3481     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3482     AlignmentSorter.sortByGroup(viewport.getAlignment());
3483     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3484             viewport.getAlignment()));
3485
3486     alignPanel.paintAlignment(true);
3487   }
3488
3489   /**
3490    * DOCUMENT ME!
3491    *
3492    * @param e
3493    *          DOCUMENT ME!
3494    */
3495   @Override
3496   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3497   {
3498     new RedundancyPanel(alignPanel, this);
3499   }
3500
3501   /**
3502    * DOCUMENT ME!
3503    *
3504    * @param e
3505    *          DOCUMENT ME!
3506    */
3507   @Override
3508   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3509   {
3510     if ((viewport.getSelectionGroup() == null)
3511             || (viewport.getSelectionGroup().getSize() < 2))
3512     {
3513       JvOptionPane.showInternalMessageDialog(this, MessageManager
3514               .getString("label.you_must_select_least_two_sequences"),
3515               MessageManager.getString("label.invalid_selection"),
3516               JvOptionPane.WARNING_MESSAGE);
3517     }
3518     else
3519     {
3520       JInternalFrame frame = new JInternalFrame();
3521       frame.setContentPane(new PairwiseAlignPanel(viewport));
3522       Desktop.addInternalFrame(frame,
3523               MessageManager.getString("action.pairwise_alignment"), 600,
3524               500);
3525     }
3526   }
3527
3528   /**
3529    * DOCUMENT ME!
3530    *
3531    * @param e
3532    *          DOCUMENT ME!
3533    */
3534   @Override
3535   public void PCAMenuItem_actionPerformed(ActionEvent e)
3536   {
3537     if (((viewport.getSelectionGroup() != null)
3538             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3539             .getSelectionGroup().getSize() > 0))
3540             || (viewport.getAlignment().getHeight() < 4))
3541     {
3542       JvOptionPane
3543               .showInternalMessageDialog(
3544                       this,
3545                       MessageManager
3546                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3547                       MessageManager
3548                               .getString("label.sequence_selection_insufficient"),
3549                       JvOptionPane.WARNING_MESSAGE);
3550
3551       return;
3552     }
3553
3554     new PCAPanel(alignPanel);
3555   }
3556
3557   @Override
3558   public void autoCalculate_actionPerformed(ActionEvent e)
3559   {
3560     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3561     if (viewport.autoCalculateConsensus)
3562     {
3563       viewport.firePropertyChange("alignment", null, viewport
3564               .getAlignment().getSequences());
3565     }
3566   }
3567
3568   @Override
3569   public void sortByTreeOption_actionPerformed(ActionEvent e)
3570   {
3571     viewport.sortByTree = sortByTree.isSelected();
3572   }
3573
3574   @Override
3575   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3576   {
3577     viewport.followSelection = listenToViewSelections.isSelected();
3578   }
3579
3580   /**
3581    * DOCUMENT ME!
3582    *
3583    * @param e
3584    *          DOCUMENT ME!
3585    */
3586   @Override
3587   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3588   {
3589     newTreePanel("AV", "PID", "Average distance tree using PID");
3590   }
3591
3592   /**
3593    * DOCUMENT ME!
3594    *
3595    * @param e
3596    *          DOCUMENT ME!
3597    */
3598   @Override
3599   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3600   {
3601     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3602   }
3603
3604   /**
3605    * DOCUMENT ME!
3606    *
3607    * @param e
3608    *          DOCUMENT ME!
3609    */
3610   @Override
3611   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3612   {
3613     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3614   }
3615
3616   /**
3617    * DOCUMENT ME!
3618    *
3619    * @param e
3620    *          DOCUMENT ME!
3621    */
3622   @Override
3623   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3624   {
3625     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3626   }
3627
3628   /**
3629    * DOCUMENT ME!
3630    *
3631    * @param type
3632    *          DOCUMENT ME!
3633    * @param pwType
3634    *          DOCUMENT ME!
3635    * @param title
3636    *          DOCUMENT ME!
3637    */
3638   void newTreePanel(String type, String pwType, String title)
3639   {
3640     TreePanel tp;
3641
3642     if (viewport.getSelectionGroup() != null
3643             && viewport.getSelectionGroup().getSize() > 0)
3644     {
3645       if (viewport.getSelectionGroup().getSize() < 3)
3646       {
3647         JvOptionPane
3648                 .showMessageDialog(
3649                         Desktop.desktop,
3650                         MessageManager
3651                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3652                         MessageManager
3653                                 .getString("label.not_enough_sequences"),
3654                         JvOptionPane.WARNING_MESSAGE);
3655         return;
3656       }
3657
3658       SequenceGroup sg = viewport.getSelectionGroup();
3659
3660       /* Decide if the selection is a column region */
3661       for (SequenceI _s : sg.getSequences())
3662       {
3663         if (_s.getLength() < sg.getEndRes())
3664         {
3665           JvOptionPane
3666                   .showMessageDialog(
3667                           Desktop.desktop,
3668                           MessageManager
3669                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3670                           MessageManager
3671                                   .getString("label.sequences_selection_not_aligned"),
3672                           JvOptionPane.WARNING_MESSAGE);
3673
3674           return;
3675         }
3676       }
3677
3678       title = title + " on region";
3679       tp = new TreePanel(alignPanel, type, pwType);
3680     }
3681     else
3682     {
3683       // are the visible sequences aligned?
3684       if (!viewport.getAlignment().isAligned(false))
3685       {
3686         JvOptionPane
3687                 .showMessageDialog(
3688                         Desktop.desktop,
3689                         MessageManager
3690                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3691                         MessageManager
3692                                 .getString("label.sequences_not_aligned"),
3693                         JvOptionPane.WARNING_MESSAGE);
3694
3695         return;
3696       }
3697
3698       if (viewport.getAlignment().getHeight() < 2)
3699       {
3700         return;
3701       }
3702
3703       tp = new TreePanel(alignPanel, type, pwType);
3704     }
3705
3706     title += " from ";
3707
3708     if (viewport.viewName != null)
3709     {
3710       title += viewport.viewName + " of ";
3711     }
3712
3713     title += this.title;
3714
3715     Desktop.addInternalFrame(tp, title, 600, 500);
3716   }
3717
3718   /**
3719    * DOCUMENT ME!
3720    *
3721    * @param title
3722    *          DOCUMENT ME!
3723    * @param order
3724    *          DOCUMENT ME!
3725    */
3726   public void addSortByOrderMenuItem(String title,
3727           final AlignmentOrder order)
3728   {
3729     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3730             "action.by_title_param", new Object[] { title }));
3731     sort.add(item);
3732     item.addActionListener(new java.awt.event.ActionListener()
3733     {
3734       @Override
3735       public void actionPerformed(ActionEvent e)
3736       {
3737         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3738
3739         // TODO: JBPNote - have to map order entries to curent SequenceI
3740         // pointers
3741         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3742
3743         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3744                 .getAlignment()));
3745
3746         alignPanel.paintAlignment(true);
3747       }
3748     });
3749   }
3750
3751   /**
3752    * Add a new sort by annotation score menu item
3753    *
3754    * @param sort
3755    *          the menu to add the option to
3756    * @param scoreLabel
3757    *          the label used to retrieve scores for each sequence on the
3758    *          alignment
3759    */
3760   public void addSortByAnnotScoreMenuItem(JMenu sort,
3761           final String scoreLabel)
3762   {
3763     final JMenuItem item = new JMenuItem(scoreLabel);
3764     sort.add(item);
3765     item.addActionListener(new java.awt.event.ActionListener()
3766     {
3767       @Override
3768       public void actionPerformed(ActionEvent e)
3769       {
3770         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3771         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3772                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3773         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3774                 viewport.getAlignment()));
3775         alignPanel.paintAlignment(true);
3776       }
3777     });
3778   }
3779
3780   /**
3781    * last hash for alignment's annotation array - used to minimise cost of
3782    * rebuild.
3783    */
3784   protected int _annotationScoreVectorHash;
3785
3786   /**
3787    * search the alignment and rebuild the sort by annotation score submenu the
3788    * last alignment annotation vector hash is stored to minimize cost of
3789    * rebuilding in subsequence calls.
3790    *
3791    */
3792   @Override
3793   public void buildSortByAnnotationScoresMenu()
3794   {
3795     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3796     {
3797       return;
3798     }
3799
3800     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3801     {
3802       sortByAnnotScore.removeAll();
3803       // almost certainly a quicker way to do this - but we keep it simple
3804       Hashtable scoreSorts = new Hashtable();
3805       AlignmentAnnotation aann[];
3806       for (SequenceI sqa : viewport.getAlignment().getSequences())
3807       {
3808         aann = sqa.getAnnotation();
3809         for (int i = 0; aann != null && i < aann.length; i++)
3810         {
3811           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3812           {
3813             scoreSorts.put(aann[i].label, aann[i].label);
3814           }
3815         }
3816       }
3817       Enumeration labels = scoreSorts.keys();
3818       while (labels.hasMoreElements())
3819       {
3820         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3821                 (String) labels.nextElement());
3822       }
3823       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3824       scoreSorts.clear();
3825
3826       _annotationScoreVectorHash = viewport.getAlignment()
3827               .getAlignmentAnnotation().hashCode();
3828     }
3829   }
3830
3831   /**
3832    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3833    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3834    * call. Listeners are added to remove the menu item when the treePanel is
3835    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3836    * modified.
3837    *
3838    * @param treePanel
3839    *          Displayed tree window.
3840    * @param title
3841    *          SortBy menu item title.
3842    */
3843   @Override
3844   public void buildTreeMenu()
3845   {
3846     calculateTree.removeAll();
3847     // build the calculate menu
3848
3849     for (final String type : new String[] { "NJ", "AV" })
3850     {
3851       String treecalcnm = MessageManager.getString("label.tree_calc_"
3852               + type.toLowerCase());
3853       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3854       {
3855         JMenuItem tm = new JMenuItem();
3856         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3857         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3858                 || sm.isProtein() == !viewport.getAlignment()
3859                         .isNucleotide())
3860         {
3861           String smn = MessageManager.getStringOrReturn(
3862                   "label.score_model_", sm.getName());
3863           final String title = MessageManager.formatMessage(
3864                   "label.treecalc_title", treecalcnm, smn);
3865           tm.setText(title);//
3866           tm.addActionListener(new java.awt.event.ActionListener()
3867           {
3868             @Override
3869             public void actionPerformed(ActionEvent e)
3870             {
3871               newTreePanel(type, pwtype, title);
3872             }
3873           });
3874           calculateTree.add(tm);
3875         }
3876
3877       }
3878     }
3879     sortByTreeMenu.removeAll();
3880
3881     List<Component> comps = PaintRefresher.components.get(viewport
3882             .getSequenceSetId());
3883     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3884     for (Component comp : comps)
3885     {
3886       if (comp instanceof TreePanel)
3887       {
3888         treePanels.add((TreePanel) comp);
3889       }
3890     }
3891
3892     if (treePanels.size() < 1)
3893     {
3894       sortByTreeMenu.setVisible(false);
3895       return;
3896     }
3897
3898     sortByTreeMenu.setVisible(true);
3899
3900     for (final TreePanel tp : treePanels)
3901     {
3902       final JMenuItem item = new JMenuItem(tp.getTitle());
3903       item.addActionListener(new java.awt.event.ActionListener()
3904       {
3905         @Override
3906         public void actionPerformed(ActionEvent e)
3907         {
3908           tp.sortByTree_actionPerformed();
3909           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3910
3911         }
3912       });
3913
3914       sortByTreeMenu.add(item);
3915     }
3916   }
3917
3918   public boolean sortBy(AlignmentOrder alorder, String undoname)
3919   {
3920     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3921     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3922     if (undoname != null)
3923     {
3924       addHistoryItem(new OrderCommand(undoname, oldOrder,
3925               viewport.getAlignment()));
3926     }
3927     alignPanel.paintAlignment(true);
3928     return true;
3929   }
3930
3931   /**
3932    * Work out whether the whole set of sequences or just the selected set will
3933    * be submitted for multiple alignment.
3934    *
3935    */
3936   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3937   {
3938     // Now, check we have enough sequences
3939     AlignmentView msa = null;
3940
3941     if ((viewport.getSelectionGroup() != null)
3942             && (viewport.getSelectionGroup().getSize() > 1))
3943     {
3944       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3945       // some common interface!
3946       /*
3947        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3948        * SequenceI[sz = seqs.getSize(false)];
3949        *
3950        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3951        * seqs.getSequenceAt(i); }
3952        */
3953       msa = viewport.getAlignmentView(true);
3954     }
3955     else if (viewport.getSelectionGroup() != null
3956             && viewport.getSelectionGroup().getSize() == 1)
3957     {
3958       int option = JvOptionPane.showConfirmDialog(this,
3959               MessageManager.getString("warn.oneseq_msainput_selection"),
3960               MessageManager.getString("label.invalid_selection"),
3961               JvOptionPane.OK_CANCEL_OPTION);
3962       if (option == JvOptionPane.OK_OPTION)
3963       {
3964         msa = viewport.getAlignmentView(false);
3965       }
3966     }
3967     else
3968     {
3969       msa = viewport.getAlignmentView(false);
3970     }
3971     return msa;
3972   }
3973
3974   /**
3975    * Decides what is submitted to a secondary structure prediction service: the
3976    * first sequence in the alignment, or in the current selection, or, if the
3977    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3978    * region or the whole alignment. (where the first sequence in the set is the
3979    * one that the prediction will be for).
3980    */
3981   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3982   {
3983     AlignmentView seqs = null;
3984
3985     if ((viewport.getSelectionGroup() != null)
3986             && (viewport.getSelectionGroup().getSize() > 0))
3987     {
3988       seqs = viewport.getAlignmentView(true);
3989     }
3990     else
3991     {
3992       seqs = viewport.getAlignmentView(false);
3993     }
3994     // limit sequences - JBPNote in future - could spawn multiple prediction
3995     // jobs
3996     // TODO: viewport.getAlignment().isAligned is a global state - the local
3997     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3998     if (!viewport.getAlignment().isAligned(false))
3999     {
4000       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4001       // TODO: if seqs.getSequences().length>1 then should really have warned
4002       // user!
4003
4004     }
4005     return seqs;
4006   }
4007
4008   /**
4009    * DOCUMENT ME!
4010    *
4011    * @param e
4012    *          DOCUMENT ME!
4013    */
4014   @Override
4015   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4016   {
4017     // Pick the tree file
4018     JalviewFileChooser chooser = new JalviewFileChooser(
4019             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4020     chooser.setFileView(new JalviewFileView());
4021     chooser.setDialogTitle(MessageManager
4022             .getString("label.select_newick_like_tree_file"));
4023     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4024
4025     int value = chooser.showOpenDialog(null);
4026
4027     if (value == JalviewFileChooser.APPROVE_OPTION)
4028     {
4029       String choice = chooser.getSelectedFile().getPath();
4030       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4031       jalview.io.NewickFile fin = null;
4032       try
4033       {
4034         fin = new NewickFile(choice, DataSourceType.FILE);
4035         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4036       } catch (Exception ex)
4037       {
4038         JvOptionPane
4039                 .showMessageDialog(
4040                         Desktop.desktop,
4041                         ex.getMessage(),
4042                         MessageManager
4043                                 .getString("label.problem_reading_tree_file"),
4044                         JvOptionPane.WARNING_MESSAGE);
4045         ex.printStackTrace();
4046       }
4047       if (fin != null && fin.hasWarningMessage())
4048       {
4049         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4050                 .getWarningMessage(), MessageManager
4051                 .getString("label.possible_problem_with_tree_file"),
4052                 JvOptionPane.WARNING_MESSAGE);
4053       }
4054     }
4055   }
4056
4057   public TreePanel ShowNewickTree(NewickFile nf, String title)
4058   {
4059     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4060   }
4061
4062   public TreePanel ShowNewickTree(NewickFile nf, String title,
4063           AlignmentView input)
4064   {
4065     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4066   }
4067
4068   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4069           int h, int x, int y)
4070   {
4071     return ShowNewickTree(nf, title, null, w, h, x, y);
4072   }
4073
4074   /**
4075    * Add a treeviewer for the tree extracted from a newick file object to the
4076    * current alignment view
4077    *
4078    * @param nf
4079    *          the tree
4080    * @param title
4081    *          tree viewer title
4082    * @param input
4083    *          Associated alignment input data (or null)
4084    * @param w
4085    *          width
4086    * @param h
4087    *          height
4088    * @param x
4089    *          position
4090    * @param y
4091    *          position
4092    * @return TreePanel handle
4093    */
4094   public TreePanel ShowNewickTree(NewickFile nf, String title,
4095           AlignmentView input, int w, int h, int x, int y)
4096   {
4097     TreePanel tp = null;
4098
4099     try
4100     {
4101       nf.parse();
4102
4103       if (nf.getTree() != null)
4104       {
4105         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4106
4107         tp.setSize(w, h);
4108
4109         if (x > 0 && y > 0)
4110         {
4111           tp.setLocation(x, y);
4112         }
4113
4114         Desktop.addInternalFrame(tp, title, w, h);
4115       }
4116     } catch (Exception ex)
4117     {
4118       ex.printStackTrace();
4119     }
4120
4121     return tp;
4122   }
4123
4124   private boolean buildingMenu = false;
4125
4126   /**
4127    * Generates menu items and listener event actions for web service clients
4128    *
4129    */
4130   public void BuildWebServiceMenu()
4131   {
4132     while (buildingMenu)
4133     {
4134       try
4135       {
4136         System.err.println("Waiting for building menu to finish.");
4137         Thread.sleep(10);
4138       } catch (Exception e)
4139       {
4140       }
4141     }
4142     final AlignFrame me = this;
4143     buildingMenu = true;
4144     new Thread(new Runnable()
4145     {
4146       @Override
4147       public void run()
4148       {
4149         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4150         try
4151         {
4152           // System.err.println("Building ws menu again "
4153           // + Thread.currentThread());
4154           // TODO: add support for context dependent disabling of services based
4155           // on
4156           // alignment and current selection
4157           // TODO: add additional serviceHandle parameter to specify abstract
4158           // handler
4159           // class independently of AbstractName
4160           // TODO: add in rediscovery GUI function to restart discoverer
4161           // TODO: group services by location as well as function and/or
4162           // introduce
4163           // object broker mechanism.
4164           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4165           final IProgressIndicator af = me;
4166
4167           /*
4168            * do not i18n these strings - they are hard-coded in class
4169            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4170            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4171            */
4172           final JMenu msawsmenu = new JMenu("Alignment");
4173           final JMenu secstrmenu = new JMenu(
4174                   "Secondary Structure Prediction");
4175           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4176           final JMenu analymenu = new JMenu("Analysis");
4177           final JMenu dismenu = new JMenu("Protein Disorder");
4178           // JAL-940 - only show secondary structure prediction services from
4179           // the legacy server
4180           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4181               // &&
4182           Discoverer.services != null && (Discoverer.services.size() > 0))
4183           {
4184             // TODO: refactor to allow list of AbstractName/Handler bindings to
4185             // be
4186             // stored or retrieved from elsewhere
4187             // No MSAWS used any more:
4188             // Vector msaws = null; // (Vector)
4189             // Discoverer.services.get("MsaWS");
4190             Vector secstrpr = (Vector) Discoverer.services
4191                     .get("SecStrPred");
4192             if (secstrpr != null)
4193             {
4194               // Add any secondary structure prediction services
4195               for (int i = 0, j = secstrpr.size(); i < j; i++)
4196               {
4197                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4198                         .get(i);
4199                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4200                         .getServiceClient(sh);
4201                 int p = secstrmenu.getItemCount();
4202                 impl.attachWSMenuEntry(secstrmenu, me);
4203                 int q = secstrmenu.getItemCount();
4204                 for (int litm = p; litm < q; litm++)
4205                 {
4206                   legacyItems.add(secstrmenu.getItem(litm));
4207                 }
4208               }
4209             }
4210           }
4211
4212           // Add all submenus in the order they should appear on the web
4213           // services menu
4214           wsmenu.add(msawsmenu);
4215           wsmenu.add(secstrmenu);
4216           wsmenu.add(dismenu);
4217           wsmenu.add(analymenu);
4218           // No search services yet
4219           // wsmenu.add(seqsrchmenu);
4220
4221           javax.swing.SwingUtilities.invokeLater(new Runnable()
4222           {
4223             @Override
4224             public void run()
4225             {
4226               try
4227               {
4228                 webService.removeAll();
4229                 // first, add discovered services onto the webservices menu
4230                 if (wsmenu.size() > 0)
4231                 {
4232                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4233                   {
4234                     webService.add(wsmenu.get(i));
4235                   }
4236                 }
4237                 else
4238                 {
4239                   webService.add(me.webServiceNoServices);
4240                 }
4241                 // TODO: move into separate menu builder class.
4242                 boolean new_sspred = false;
4243                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4244                 {
4245                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4246                   if (jws2servs != null)
4247                   {
4248                     if (jws2servs.hasServices())
4249                     {
4250                       jws2servs.attachWSMenuEntry(webService, me);
4251                       for (Jws2Instance sv : jws2servs.getServices())
4252                       {
4253                         if (sv.description.toLowerCase().contains("jpred"))
4254                         {
4255                           for (JMenuItem jmi : legacyItems)
4256                           {
4257                             jmi.setVisible(false);
4258                           }
4259                         }
4260                       }
4261
4262                     }
4263                     if (jws2servs.isRunning())
4264                     {
4265                       JMenuItem tm = new JMenuItem(
4266                               "Still discovering JABA Services");
4267                       tm.setEnabled(false);
4268                       webService.add(tm);
4269                     }
4270                   }
4271                 }
4272                 build_urlServiceMenu(me.webService);
4273                 build_fetchdbmenu(webService);
4274                 for (JMenu item : wsmenu)
4275                 {
4276                   if (item.getItemCount() == 0)
4277                   {
4278                     item.setEnabled(false);
4279                   }
4280                   else
4281                   {
4282                     item.setEnabled(true);
4283                   }
4284                 }
4285               } catch (Exception e)
4286               {
4287                 Cache.log
4288                         .debug("Exception during web service menu building process.",
4289                                 e);
4290               }
4291             }
4292           });
4293         } catch (Exception e)
4294         {
4295         }
4296         buildingMenu = false;
4297       }
4298     }).start();
4299
4300   }
4301
4302   /**
4303    * construct any groupURL type service menu entries.
4304    *
4305    * @param webService
4306    */
4307   private void build_urlServiceMenu(JMenu webService)
4308   {
4309     // TODO: remove this code when 2.7 is released
4310     // DEBUG - alignmentView
4311     /*
4312      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4313      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4314      *
4315      * @Override public void actionPerformed(ActionEvent e) {
4316      * jalview.datamodel.AlignmentView
4317      * .testSelectionViews(af.viewport.getAlignment(),
4318      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4319      *
4320      * }); webService.add(testAlView);
4321      */
4322     // TODO: refactor to RestClient discoverer and merge menu entries for
4323     // rest-style services with other types of analysis/calculation service
4324     // SHmmr test client - still being implemented.
4325     // DEBUG - alignmentView
4326
4327     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4328             .getRestClients())
4329     {
4330       client.attachWSMenuEntry(
4331               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4332               this);
4333     }
4334   }
4335
4336   /**
4337    * Searches the alignment sequences for xRefs and builds the Show
4338    * Cross-References menu (formerly called Show Products), with database
4339    * sources for which cross-references are found (protein sources for a
4340    * nucleotide alignment and vice versa)
4341    *
4342    * @return true if Show Cross-references menu should be enabled
4343    */
4344   public boolean canShowProducts()
4345   {
4346     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4347     AlignmentI dataset = viewport.getAlignment().getDataset();
4348
4349     showProducts.removeAll();
4350     final boolean dna = viewport.getAlignment().isNucleotide();
4351
4352     if (seqs == null || seqs.length == 0)
4353     {
4354       // nothing to see here.
4355       return false;
4356     }
4357
4358     boolean showp = false;
4359     try
4360     {
4361       List<String> ptypes = new CrossRef(seqs, dataset)
4362               .findXrefSourcesForSequences(dna);
4363
4364       for (final String source : ptypes)
4365       {
4366         showp = true;
4367         final AlignFrame af = this;
4368         JMenuItem xtype = new JMenuItem(source);
4369         xtype.addActionListener(new ActionListener()
4370         {
4371           @Override
4372           public void actionPerformed(ActionEvent e)
4373           {
4374             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4375           }
4376         });
4377         showProducts.add(xtype);
4378       }
4379       showProducts.setVisible(showp);
4380       showProducts.setEnabled(showp);
4381     } catch (Exception e)
4382     {
4383       Cache.log
4384               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4385                       e);
4386       return false;
4387     }
4388     return showp;
4389   }
4390
4391   /**
4392    * Finds and displays cross-references for the selected sequences (protein
4393    * products for nucleotide sequences, dna coding sequences for peptides).
4394    *
4395    * @param sel
4396    *          the sequences to show cross-references for
4397    * @param dna
4398    *          true if from a nucleotide alignment (so showing proteins)
4399    * @param source
4400    *          the database to show cross-references for
4401    */
4402   protected void showProductsFor(final SequenceI[] sel,
4403           final boolean _odna, final String source)
4404   {
4405     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4406             .start();
4407   }
4408
4409   /**
4410    * Construct and display a new frame containing the translation of this
4411    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4412    */
4413   @Override
4414   public void showTranslation_actionPerformed(ActionEvent e)
4415   {
4416     AlignmentI al = null;
4417     try
4418     {
4419       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4420
4421       al = dna.translateCdna();
4422     } catch (Exception ex)
4423     {
4424       jalview.bin.Cache.log.error(
4425               "Exception during translation. Please report this !", ex);
4426       final String msg = MessageManager
4427               .getString("label.error_when_translating_sequences_submit_bug_report");
4428       final String errorTitle = MessageManager
4429               .getString("label.implementation_error")
4430               + MessageManager.getString("label.translation_failed");
4431       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4432               JvOptionPane.ERROR_MESSAGE);
4433       return;
4434     }
4435     if (al == null || al.getHeight() == 0)
4436     {
4437       final String msg = MessageManager
4438               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4439       final String errorTitle = MessageManager
4440               .getString("label.translation_failed");
4441       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4442               JvOptionPane.WARNING_MESSAGE);
4443     }
4444     else
4445     {
4446       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4447       af.setFileFormat(this.currentFileFormat);
4448       final String newTitle = MessageManager.formatMessage(
4449               "label.translation_of_params",
4450               new Object[] { this.getTitle() });
4451       af.setTitle(newTitle);
4452       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4453       {
4454         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4455         viewport.openSplitFrame(af, new Alignment(seqs));
4456       }
4457       else
4458       {
4459         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4460                 DEFAULT_HEIGHT);
4461       }
4462     }
4463   }
4464
4465   /**
4466    * Set the file format
4467    *
4468    * @param format
4469    */
4470   public void setFileFormat(FileFormatI format)
4471   {
4472     this.currentFileFormat = format;
4473   }
4474
4475   /**
4476    * Try to load a features file onto the alignment.
4477    *
4478    * @param file
4479    *          contents or path to retrieve file
4480    * @param sourceType
4481    *          access mode of file (see jalview.io.AlignFile)
4482    * @return true if features file was parsed correctly.
4483    */
4484   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4485   {
4486     return avc.parseFeaturesFile(file, sourceType,
4487             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4488
4489   }
4490
4491   @Override
4492   public void refreshFeatureUI(boolean enableIfNecessary)
4493   {
4494     // note - currently this is only still here rather than in the controller
4495     // because of the featureSettings hard reference that is yet to be
4496     // abstracted
4497     if (enableIfNecessary)
4498     {
4499       viewport.setShowSequenceFeatures(true);
4500       showSeqFeatures.setSelected(true);
4501     }
4502
4503   }
4504
4505   @Override
4506   public void dragEnter(DropTargetDragEvent evt)
4507   {
4508   }
4509
4510   @Override
4511   public void dragExit(DropTargetEvent evt)
4512   {
4513   }
4514
4515   @Override
4516   public void dragOver(DropTargetDragEvent evt)
4517   {
4518   }
4519
4520   @Override
4521   public void dropActionChanged(DropTargetDragEvent evt)
4522   {
4523   }
4524
4525   @Override
4526   public void drop(DropTargetDropEvent evt)
4527   {
4528     // JAL-1552 - acceptDrop required before getTransferable call for
4529     // Java's Transferable for native dnd
4530     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4531     Transferable t = evt.getTransferable();
4532     List<String> files = new ArrayList<String>();
4533     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4534
4535     try
4536     {
4537       Desktop.transferFromDropTarget(files, protocols, evt, t);
4538     } catch (Exception e)
4539     {
4540       e.printStackTrace();
4541     }
4542     if (files != null)
4543     {
4544       try
4545       {
4546         // check to see if any of these files have names matching sequences in
4547         // the alignment
4548         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4549                 .getAlignment().getSequencesArray());
4550         /**
4551          * Object[] { String,SequenceI}
4552          */
4553         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4554         ArrayList<String> filesnotmatched = new ArrayList<String>();
4555         for (int i = 0; i < files.size(); i++)
4556         {
4557           String file = files.get(i).toString();
4558           String pdbfn = "";
4559           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4560           if (protocol == DataSourceType.FILE)
4561           {
4562             File fl = new File(file);
4563             pdbfn = fl.getName();
4564           }
4565           else if (protocol == DataSourceType.URL)
4566           {
4567             URL url = new URL(file);
4568             pdbfn = url.getFile();
4569           }
4570           if (pdbfn.length() > 0)
4571           {
4572             // attempt to find a match in the alignment
4573             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4574             int l = 0, c = pdbfn.indexOf(".");
4575             while (mtch == null && c != -1)
4576             {
4577               do
4578               {
4579                 l = c;
4580               } while ((c = pdbfn.indexOf(".", l)) > l);
4581               if (l > -1)
4582               {
4583                 pdbfn = pdbfn.substring(0, l);
4584               }
4585               mtch = idm.findAllIdMatches(pdbfn);
4586             }
4587             if (mtch != null)
4588             {
4589               FileFormatI type = null;
4590               try
4591               {
4592                 type = new IdentifyFile().identify(file, protocol);
4593               } catch (Exception ex)
4594               {
4595                 type = null;
4596               }
4597               if (type != null && type.isStructureFile())
4598               {
4599                 filesmatched.add(new Object[] { file, protocol, mtch });
4600                 continue;
4601               }
4602             }
4603             // File wasn't named like one of the sequences or wasn't a PDB file.
4604             filesnotmatched.add(file);
4605           }
4606         }
4607         int assocfiles = 0;
4608         if (filesmatched.size() > 0)
4609         {
4610           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4611                   || JvOptionPane
4612                           .showConfirmDialog(
4613                                   this,
4614                                   MessageManager
4615                                           .formatMessage(
4616                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4617                                                   new Object[] { Integer
4618                                                           .valueOf(
4619                                                                   filesmatched
4620                                                                           .size())
4621                                                           .toString() }),
4622                                   MessageManager
4623                                           .getString("label.automatically_associate_structure_files_by_name"),
4624                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4625
4626           {
4627             for (Object[] fm : filesmatched)
4628             {
4629               // try and associate
4630               // TODO: may want to set a standard ID naming formalism for
4631               // associating PDB files which have no IDs.
4632               for (SequenceI toassoc : (SequenceI[]) fm[2])
4633               {
4634                 PDBEntry pe = new AssociatePdbFileWithSeq()
4635                         .associatePdbWithSeq((String) fm[0],
4636                                 (DataSourceType) fm[1], toassoc, false,
4637                                 Desktop.instance);
4638                 if (pe != null)
4639                 {
4640                   System.err.println("Associated file : "
4641                           + ((String) fm[0]) + " with "
4642                           + toassoc.getDisplayId(true));
4643                   assocfiles++;
4644                 }
4645               }
4646               alignPanel.paintAlignment(true);
4647             }
4648           }
4649         }
4650         if (filesnotmatched.size() > 0)
4651         {
4652           if (assocfiles > 0
4653                   && (Cache.getDefault(
4654                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4655                           .showConfirmDialog(
4656                                   this,
4657                                   "<html>"
4658                                           + MessageManager
4659                                                   .formatMessage(
4660                                                           "label.ignore_unmatched_dropped_files_info",
4661                                                           new Object[] { Integer
4662                                                                   .valueOf(
4663                                                                           filesnotmatched
4664                                                                                   .size())
4665                                                                   .toString() })
4666                                           + "</html>",
4667                                   MessageManager
4668                                           .getString("label.ignore_unmatched_dropped_files"),
4669                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4670           {
4671             return;
4672           }
4673           for (String fn : filesnotmatched)
4674           {
4675             loadJalviewDataFile(fn, null, null, null);
4676           }
4677
4678         }
4679       } catch (Exception ex)
4680       {
4681         ex.printStackTrace();
4682       }
4683     }
4684   }
4685
4686   /**
4687    * Attempt to load a "dropped" file or URL string: First by testing whether
4688    * it's an Annotation file, then a JNet file, and finally a features file. If
4689    * all are false then the user may have dropped an alignment file onto this
4690    * AlignFrame.
4691    *
4692    * @param file
4693    *          either a filename or a URL string.
4694    */
4695   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4696           FileFormatI format, SequenceI assocSeq)
4697   {
4698     try
4699     {
4700       if (sourceType == null)
4701       {
4702         sourceType = FormatAdapter.checkProtocol(file);
4703       }
4704       // if the file isn't identified, or not positively identified as some
4705       // other filetype (PFAM is default unidentified alignment file type) then
4706       // try to parse as annotation.
4707       boolean isAnnotation = (format == null || FileFormat.Pfam
4708               .equals(format)) ? new AnnotationFile()
4709               .annotateAlignmentView(viewport, file, sourceType) : false;
4710
4711       if (!isAnnotation)
4712       {
4713         // first see if its a T-COFFEE score file
4714         TCoffeeScoreFile tcf = null;
4715         try
4716         {
4717           tcf = new TCoffeeScoreFile(file, sourceType);
4718           if (tcf.isValid())
4719           {
4720             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4721             {
4722               buildColourMenu();
4723               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4724               isAnnotation = true;
4725               statusBar
4726                       .setText(MessageManager
4727                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4728             }
4729             else
4730             {
4731               // some problem - if no warning its probable that the ID matching
4732               // process didn't work
4733               JvOptionPane
4734                       .showMessageDialog(
4735                               Desktop.desktop,
4736                               tcf.getWarningMessage() == null ? MessageManager
4737                                       .getString("label.check_file_matches_sequence_ids_alignment")
4738                                       : tcf.getWarningMessage(),
4739                               MessageManager
4740                                       .getString("label.problem_reading_tcoffee_score_file"),
4741                               JvOptionPane.WARNING_MESSAGE);
4742             }
4743           }
4744           else
4745           {
4746             tcf = null;
4747           }
4748         } catch (Exception x)
4749         {
4750           Cache.log
4751                   .debug("Exception when processing data source as T-COFFEE score file",
4752                           x);
4753           tcf = null;
4754         }
4755         if (tcf == null)
4756         {
4757           // try to see if its a JNet 'concise' style annotation file *before*
4758           // we
4759           // try to parse it as a features file
4760           if (format == null)
4761           {
4762             format = new IdentifyFile().identify(file, sourceType);
4763           }
4764           if (FileFormat.Jnet.equals(format))
4765           {
4766             JPredFile predictions = new JPredFile(file, sourceType);
4767             new JnetAnnotationMaker();
4768             JnetAnnotationMaker.add_annotation(predictions,
4769                     viewport.getAlignment(), 0, false);
4770             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4771             viewport.getAlignment().setSeqrep(repseq);
4772             ColumnSelection cs = new ColumnSelection();
4773             cs.hideInsertionsFor(repseq);
4774             viewport.setColumnSelection(cs);
4775             isAnnotation = true;
4776           }
4777           // else if (IdentifyFile.FeaturesFile.equals(format))
4778           else if (FileFormat.Features.equals(format))
4779           {
4780             if (parseFeaturesFile(file, sourceType))
4781             {
4782               alignPanel.paintAlignment(true);
4783             }
4784           }
4785           else
4786           {
4787             new FileLoader().LoadFile(viewport, file, sourceType, format);
4788           }
4789         }
4790       }
4791       if (isAnnotation)
4792       {
4793
4794         alignPanel.adjustAnnotationHeight();
4795         viewport.updateSequenceIdColours();
4796         buildSortByAnnotationScoresMenu();
4797         alignPanel.paintAlignment(true);
4798       }
4799     } catch (Exception ex)
4800     {
4801       ex.printStackTrace();
4802     } catch (OutOfMemoryError oom)
4803     {
4804       try
4805       {
4806         System.gc();
4807       } catch (Exception x)
4808       {
4809       }
4810       new OOMWarning(
4811               "loading data "
4812                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4813                               : "using " + sourceType + " from " + file)
4814                               : ".")
4815                       + (format != null ? "(parsing as '" + format
4816                               + "' file)" : ""), oom, Desktop.desktop);
4817     }
4818   }
4819
4820   /**
4821    * Method invoked by the ChangeListener on the tabbed pane, in other words
4822    * when a different tabbed pane is selected by the user or programmatically.
4823    */
4824   @Override
4825   public void tabSelectionChanged(int index)
4826   {
4827     if (index > -1)
4828     {
4829       alignPanel = alignPanels.get(index);
4830       viewport = alignPanel.av;
4831       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4832       setMenusFromViewport(viewport);
4833     }
4834
4835     /*
4836      * 'focus' any colour slider that is open to the selected viewport
4837      */
4838     if (viewport.getConservationSelected())
4839     {
4840       SliderPanel.setConservationSlider(alignPanel,
4841               viewport.getViewportColourScheme(), alignPanel.getViewName());
4842     }
4843     else
4844     {
4845       SliderPanel.hideConservationSlider();
4846     }
4847     if (viewport.getAbovePIDThreshold())
4848     {
4849       SliderPanel.setPIDSliderSource(alignPanel,
4850               viewport.getViewportColourScheme(), alignPanel.getViewName());
4851     }
4852     else
4853     {
4854       SliderPanel.hidePIDSlider();
4855     }
4856
4857     /*
4858      * If there is a frame linked to this one in a SplitPane, switch it to the
4859      * same view tab index. No infinite recursion of calls should happen, since
4860      * tabSelectionChanged() should not get invoked on setting the selected
4861      * index to an unchanged value. Guard against setting an invalid index
4862      * before the new view peer tab has been created.
4863      */
4864     final AlignViewportI peer = viewport.getCodingComplement();
4865     if (peer != null)
4866     {
4867       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4868       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4869       {
4870         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4871       }
4872     }
4873   }
4874
4875   /**
4876    * On right mouse click on view tab, prompt for and set new view name.
4877    */
4878   @Override
4879   public void tabbedPane_mousePressed(MouseEvent e)
4880   {
4881     if (e.isPopupTrigger())
4882     {
4883       String msg = MessageManager.getString("label.enter_view_name");
4884       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4885               JvOptionPane.QUESTION_MESSAGE);
4886
4887       if (reply != null)
4888       {
4889         viewport.viewName = reply;
4890         // TODO warn if reply is in getExistingViewNames()?
4891         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4892       }
4893     }
4894   }
4895
4896   public AlignViewport getCurrentView()
4897   {
4898     return viewport;
4899   }
4900
4901   /**
4902    * Open the dialog for regex description parsing.
4903    */
4904   @Override
4905   protected void extractScores_actionPerformed(ActionEvent e)
4906   {
4907     ParseProperties pp = new jalview.analysis.ParseProperties(
4908             viewport.getAlignment());
4909     // TODO: verify regex and introduce GUI dialog for version 2.5
4910     // if (pp.getScoresFromDescription("col", "score column ",
4911     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4912     // true)>0)
4913     if (pp.getScoresFromDescription("description column",
4914             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4915     {
4916       buildSortByAnnotationScoresMenu();
4917     }
4918   }
4919
4920   /*
4921    * (non-Javadoc)
4922    *
4923    * @see
4924    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4925    * )
4926    */
4927   @Override
4928   protected void showDbRefs_actionPerformed(ActionEvent e)
4929   {
4930     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4931   }
4932
4933   /*
4934    * (non-Javadoc)
4935    *
4936    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4937    * ActionEvent)
4938    */
4939   @Override
4940   protected void showNpFeats_actionPerformed(ActionEvent e)
4941   {
4942     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4943   }
4944
4945   /**
4946    * find the viewport amongst the tabs in this alignment frame and close that
4947    * tab
4948    *
4949    * @param av
4950    */
4951   public boolean closeView(AlignViewportI av)
4952   {
4953     if (viewport == av)
4954     {
4955       this.closeMenuItem_actionPerformed(false);
4956       return true;
4957     }
4958     Component[] comp = tabbedPane.getComponents();
4959     for (int i = 0; comp != null && i < comp.length; i++)
4960     {
4961       if (comp[i] instanceof AlignmentPanel)
4962       {
4963         if (((AlignmentPanel) comp[i]).av == av)
4964         {
4965           // close the view.
4966           closeView((AlignmentPanel) comp[i]);
4967           return true;
4968         }
4969       }
4970     }
4971     return false;
4972   }
4973
4974   protected void build_fetchdbmenu(JMenu webService)
4975   {
4976     // Temporary hack - DBRef Fetcher always top level ws entry.
4977     // TODO We probably want to store a sequence database checklist in
4978     // preferences and have checkboxes.. rather than individual sources selected
4979     // here
4980     final JMenu rfetch = new JMenu(
4981             MessageManager.getString("action.fetch_db_references"));
4982     rfetch.setToolTipText(MessageManager
4983             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4984     webService.add(rfetch);
4985
4986     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4987             MessageManager.getString("option.trim_retrieved_seqs"));
4988     trimrs.setToolTipText(MessageManager
4989             .getString("label.trim_retrieved_sequences"));
4990     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4991     trimrs.addActionListener(new ActionListener()
4992     {
4993       @Override
4994       public void actionPerformed(ActionEvent e)
4995       {
4996         trimrs.setSelected(trimrs.isSelected());
4997         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4998                 Boolean.valueOf(trimrs.isSelected()).toString());
4999       };
5000     });
5001     rfetch.add(trimrs);
5002     JMenuItem fetchr = new JMenuItem(
5003             MessageManager.getString("label.standard_databases"));
5004     fetchr.setToolTipText(MessageManager
5005             .getString("label.fetch_embl_uniprot"));
5006     fetchr.addActionListener(new ActionListener()
5007     {
5008
5009       @Override
5010       public void actionPerformed(ActionEvent e)
5011       {
5012         new Thread(new Runnable()
5013         {
5014           @Override
5015           public void run()
5016           {
5017             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5018                     .getAlignment().isNucleotide();
5019             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5020                     .getSequenceSelection(), alignPanel.alignFrame, null,
5021                     alignPanel.alignFrame.featureSettings, isNucleotide);
5022             dbRefFetcher.addListener(new FetchFinishedListenerI()
5023             {
5024               @Override
5025               public void finished()
5026               {
5027                 AlignFrame.this.setMenusForViewport();
5028               }
5029             });
5030             dbRefFetcher.fetchDBRefs(false);
5031           }
5032         }).start();
5033
5034       }
5035
5036     });
5037     rfetch.add(fetchr);
5038     final AlignFrame me = this;
5039     new Thread(new Runnable()
5040     {
5041       @Override
5042       public void run()
5043       {
5044         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5045                 .getSequenceFetcherSingleton(me);
5046         javax.swing.SwingUtilities.invokeLater(new Runnable()
5047         {
5048           @Override
5049           public void run()
5050           {
5051             String[] dbclasses = sf.getOrderedSupportedSources();
5052             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5053             // jalview.util.QuickSort.sort(otherdb, otherdb);
5054             List<DbSourceProxy> otherdb;
5055             JMenu dfetch = new JMenu();
5056             JMenu ifetch = new JMenu();
5057             JMenuItem fetchr = null;
5058             int comp = 0, icomp = 0, mcomp = 15;
5059             String mname = null;
5060             int dbi = 0;
5061             for (String dbclass : dbclasses)
5062             {
5063               otherdb = sf.getSourceProxy(dbclass);
5064               // add a single entry for this class, or submenu allowing 'fetch
5065               // all' or pick one
5066               if (otherdb == null || otherdb.size() < 1)
5067               {
5068                 continue;
5069               }
5070               // List<DbSourceProxy> dbs=otherdb;
5071               // otherdb=new ArrayList<DbSourceProxy>();
5072               // for (DbSourceProxy db:dbs)
5073               // {
5074               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5075               // }
5076               if (mname == null)
5077               {
5078                 mname = "From " + dbclass;
5079               }
5080               if (otherdb.size() == 1)
5081               {
5082                 final DbSourceProxy[] dassource = otherdb
5083                         .toArray(new DbSourceProxy[0]);
5084                 DbSourceProxy src = otherdb.get(0);
5085                 fetchr = new JMenuItem(src.getDbSource());
5086                 fetchr.addActionListener(new ActionListener()
5087                 {
5088
5089                   @Override
5090                   public void actionPerformed(ActionEvent e)
5091                   {
5092                     new Thread(new Runnable()
5093                     {
5094
5095                       @Override
5096                       public void run()
5097                       {
5098                         boolean isNucleotide = alignPanel.alignFrame
5099                                 .getViewport().getAlignment()
5100                                 .isNucleotide();
5101                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5102                                 alignPanel.av.getSequenceSelection(),
5103                                 alignPanel.alignFrame, dassource,
5104                                 alignPanel.alignFrame.featureSettings,
5105                                 isNucleotide);
5106                         dbRefFetcher
5107                                 .addListener(new FetchFinishedListenerI()
5108                                 {
5109                                   @Override
5110                                   public void finished()
5111                                   {
5112                                     AlignFrame.this.setMenusForViewport();
5113                                   }
5114                                 });
5115                         dbRefFetcher.fetchDBRefs(false);
5116                       }
5117                     }).start();
5118                   }
5119
5120                 });
5121                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5122                         MessageManager.formatMessage(
5123                                 "label.fetch_retrieve_from",
5124                                 new Object[] { src.getDbName() })));
5125                 dfetch.add(fetchr);
5126                 comp++;
5127               }
5128               else
5129               {
5130                 final DbSourceProxy[] dassource = otherdb
5131                         .toArray(new DbSourceProxy[0]);
5132                 // fetch all entry
5133                 DbSourceProxy src = otherdb.get(0);
5134                 fetchr = new JMenuItem(MessageManager.formatMessage(
5135                         "label.fetch_all_param",
5136                         new Object[] { src.getDbSource() }));
5137                 fetchr.addActionListener(new ActionListener()
5138                 {
5139                   @Override
5140                   public void actionPerformed(ActionEvent e)
5141                   {
5142                     new Thread(new Runnable()
5143                     {
5144
5145                       @Override
5146                       public void run()
5147                       {
5148                         boolean isNucleotide = alignPanel.alignFrame
5149                                 .getViewport().getAlignment()
5150                                 .isNucleotide();
5151                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5152                                 alignPanel.av.getSequenceSelection(),
5153                                 alignPanel.alignFrame, dassource,
5154                                 alignPanel.alignFrame.featureSettings,
5155                                 isNucleotide);
5156                         dbRefFetcher
5157                                 .addListener(new FetchFinishedListenerI()
5158                                 {
5159                                   @Override
5160                                   public void finished()
5161                                   {
5162                                     AlignFrame.this.setMenusForViewport();
5163                                   }
5164                                 });
5165                         dbRefFetcher.fetchDBRefs(false);
5166                       }
5167                     }).start();
5168                   }
5169                 });
5170
5171                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5172                         MessageManager.formatMessage(
5173                                 "label.fetch_retrieve_from_all_sources",
5174                                 new Object[] {
5175                                     Integer.valueOf(otherdb.size())
5176                                             .toString(), src.getDbSource(),
5177                                     src.getDbName() })));
5178                 dfetch.add(fetchr);
5179                 comp++;
5180                 // and then build the rest of the individual menus
5181                 ifetch = new JMenu(MessageManager.formatMessage(
5182                         "label.source_from_db_source",
5183                         new Object[] { src.getDbSource() }));
5184                 icomp = 0;
5185                 String imname = null;
5186                 int i = 0;
5187                 for (DbSourceProxy sproxy : otherdb)
5188                 {
5189                   String dbname = sproxy.getDbName();
5190                   String sname = dbname.length() > 5 ? dbname.substring(0,
5191                           5) + "..." : dbname;
5192                   String msname = dbname.length() > 10 ? dbname.substring(
5193                           0, 10) + "..." : dbname;
5194                   if (imname == null)
5195                   {
5196                     imname = MessageManager.formatMessage(
5197                             "label.from_msname", new Object[] { sname });
5198                   }
5199                   fetchr = new JMenuItem(msname);
5200                   final DbSourceProxy[] dassrc = { sproxy };
5201                   fetchr.addActionListener(new ActionListener()
5202                   {
5203
5204                     @Override
5205                     public void actionPerformed(ActionEvent e)
5206                     {
5207                       new Thread(new Runnable()
5208                       {
5209
5210                         @Override
5211                         public void run()
5212                         {
5213                           boolean isNucleotide = alignPanel.alignFrame
5214                                   .getViewport().getAlignment()
5215                                   .isNucleotide();
5216                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5217                                   alignPanel.av.getSequenceSelection(),
5218                                   alignPanel.alignFrame, dassrc,
5219                                   alignPanel.alignFrame.featureSettings,
5220                                   isNucleotide);
5221                           dbRefFetcher
5222                                   .addListener(new FetchFinishedListenerI()
5223                                   {
5224                                     @Override
5225                                     public void finished()
5226                                     {
5227                                       AlignFrame.this.setMenusForViewport();
5228                                     }
5229                                   });
5230                           dbRefFetcher.fetchDBRefs(false);
5231                         }
5232                       }).start();
5233                     }
5234
5235                   });
5236                   fetchr.setToolTipText("<html>"
5237                           + MessageManager.formatMessage(
5238                                   "label.fetch_retrieve_from", new Object[]
5239                                   { dbname }));
5240                   ifetch.add(fetchr);
5241                   ++i;
5242                   if (++icomp >= mcomp || i == (otherdb.size()))
5243                   {
5244                     ifetch.setText(MessageManager.formatMessage(
5245                             "label.source_to_target", imname, sname));
5246                     dfetch.add(ifetch);
5247                     ifetch = new JMenu();
5248                     imname = null;
5249                     icomp = 0;
5250                     comp++;
5251                   }
5252                 }
5253               }
5254               ++dbi;
5255               if (comp >= mcomp || dbi >= (dbclasses.length))
5256               {
5257                 dfetch.setText(MessageManager.formatMessage(
5258                         "label.source_to_target", mname, dbclass));
5259                 rfetch.add(dfetch);
5260                 dfetch = new JMenu();
5261                 mname = null;
5262                 comp = 0;
5263               }
5264             }
5265           }
5266         });
5267       }
5268     }).start();
5269
5270   }
5271
5272   /**
5273    * Left justify the whole alignment.
5274    */
5275   @Override
5276   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5277   {
5278     AlignmentI al = viewport.getAlignment();
5279     al.justify(false);
5280     viewport.firePropertyChange("alignment", null, al);
5281   }
5282
5283   /**
5284    * Right justify the whole alignment.
5285    */
5286   @Override
5287   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5288   {
5289     AlignmentI al = viewport.getAlignment();
5290     al.justify(true);
5291     viewport.firePropertyChange("alignment", null, al);
5292   }
5293
5294   @Override
5295   public void setShowSeqFeatures(boolean b)
5296   {
5297     showSeqFeatures.setSelected(b);
5298     viewport.setShowSequenceFeatures(b);
5299   }
5300
5301   /*
5302    * (non-Javadoc)
5303    *
5304    * @see
5305    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5306    * awt.event.ActionEvent)
5307    */
5308   @Override
5309   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5310   {
5311     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5312     alignPanel.paintAlignment(true);
5313   }
5314
5315   /*
5316    * (non-Javadoc)
5317    *
5318    * @see
5319    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5320    * .ActionEvent)
5321    */
5322   @Override
5323   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5324   {
5325     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5326     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5327
5328   }
5329
5330   /*
5331    * (non-Javadoc)
5332    *
5333    * @see
5334    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5335    * .event.ActionEvent)
5336    */
5337   @Override
5338   protected void showGroupConservation_actionPerformed(ActionEvent e)
5339   {
5340     viewport.setShowGroupConservation(showGroupConservation.getState());
5341     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5342   }
5343
5344   /*
5345    * (non-Javadoc)
5346    *
5347    * @see
5348    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5349    * .event.ActionEvent)
5350    */
5351   @Override
5352   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5353   {
5354     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5355     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5356   }
5357
5358   /*
5359    * (non-Javadoc)
5360    *
5361    * @see
5362    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5363    * .event.ActionEvent)
5364    */
5365   @Override
5366   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5367   {
5368     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5369     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5370   }
5371
5372   @Override
5373   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5374   {
5375     showSequenceLogo.setState(true);
5376     viewport.setShowSequenceLogo(true);
5377     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5378     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5379   }
5380
5381   @Override
5382   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5383   {
5384     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5385   }
5386
5387   /*
5388    * (non-Javadoc)
5389    *
5390    * @see
5391    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5392    * .event.ActionEvent)
5393    */
5394   @Override
5395   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5396   {
5397     if (avc.makeGroupsFromSelection())
5398     {
5399       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5400       alignPanel.updateAnnotation();
5401       alignPanel.paintAlignment(true);
5402     }
5403   }
5404
5405   public void clearAlignmentSeqRep()
5406   {
5407     // TODO refactor alignmentseqrep to controller
5408     if (viewport.getAlignment().hasSeqrep())
5409     {
5410       viewport.getAlignment().setSeqrep(null);
5411       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5412       alignPanel.updateAnnotation();
5413       alignPanel.paintAlignment(true);
5414     }
5415   }
5416
5417   @Override
5418   protected void createGroup_actionPerformed(ActionEvent e)
5419   {
5420     if (avc.createGroup())
5421     {
5422       alignPanel.alignmentChanged();
5423     }
5424   }
5425
5426   @Override
5427   protected void unGroup_actionPerformed(ActionEvent e)
5428   {
5429     if (avc.unGroup())
5430     {
5431       alignPanel.alignmentChanged();
5432     }
5433   }
5434
5435   /**
5436    * make the given alignmentPanel the currently selected tab
5437    *
5438    * @param alignmentPanel
5439    */
5440   public void setDisplayedView(AlignmentPanel alignmentPanel)
5441   {
5442     if (!viewport.getSequenceSetId().equals(
5443             alignmentPanel.av.getSequenceSetId()))
5444     {
5445       throw new Error(
5446               MessageManager
5447                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5448     }
5449     if (tabbedPane != null
5450             && tabbedPane.getTabCount() > 0
5451             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5452                     .getSelectedIndex())
5453     {
5454       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5455     }
5456   }
5457
5458   /**
5459    * Action on selection of menu options to Show or Hide annotations.
5460    *
5461    * @param visible
5462    * @param forSequences
5463    *          update sequence-related annotations
5464    * @param forAlignment
5465    *          update non-sequence-related annotations
5466    */
5467   @Override
5468   protected void setAnnotationsVisibility(boolean visible,
5469           boolean forSequences, boolean forAlignment)
5470   {
5471     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5472             .getAlignmentAnnotation();
5473     if (anns == null)
5474     {
5475       return;
5476     }
5477     for (AlignmentAnnotation aa : anns)
5478     {
5479       /*
5480        * don't display non-positional annotations on an alignment
5481        */
5482       if (aa.annotations == null)
5483       {
5484         continue;
5485       }
5486       boolean apply = (aa.sequenceRef == null && forAlignment)
5487               || (aa.sequenceRef != null && forSequences);
5488       if (apply)
5489       {
5490         aa.visible = visible;
5491       }
5492     }
5493     alignPanel.validateAnnotationDimensions(true);
5494     alignPanel.alignmentChanged();
5495   }
5496
5497   /**
5498    * Store selected annotation sort order for the view and repaint.
5499    */
5500   @Override
5501   protected void sortAnnotations_actionPerformed()
5502   {
5503     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5504     this.alignPanel.av
5505             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5506     alignPanel.paintAlignment(true);
5507   }
5508
5509   /**
5510    *
5511    * @return alignment panels in this alignment frame
5512    */
5513   public List<? extends AlignmentViewPanel> getAlignPanels()
5514   {
5515     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5516   }
5517
5518   /**
5519    * Open a new alignment window, with the cDNA associated with this (protein)
5520    * alignment, aligned as is the protein.
5521    */
5522   protected void viewAsCdna_actionPerformed()
5523   {
5524     // TODO no longer a menu action - refactor as required
5525     final AlignmentI alignment = getViewport().getAlignment();
5526     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5527     if (mappings == null)
5528     {
5529       return;
5530     }
5531     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5532     for (SequenceI aaSeq : alignment.getSequences())
5533     {
5534       for (AlignedCodonFrame acf : mappings)
5535       {
5536         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5537         if (dnaSeq != null)
5538         {
5539           /*
5540            * There is a cDNA mapping for this protein sequence - add to new
5541            * alignment. It will share the same dataset sequence as other mapped
5542            * cDNA (no new mappings need to be created).
5543            */
5544           final Sequence newSeq = new Sequence(dnaSeq);
5545           newSeq.setDatasetSequence(dnaSeq);
5546           cdnaSeqs.add(newSeq);
5547         }
5548       }
5549     }
5550     if (cdnaSeqs.size() == 0)
5551     {
5552       // show a warning dialog no mapped cDNA
5553       return;
5554     }
5555     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5556             .size()]));
5557     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5558             AlignFrame.DEFAULT_HEIGHT);
5559     cdna.alignAs(alignment);
5560     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5561             + this.title;
5562     Desktop.addInternalFrame(alignFrame, newtitle,
5563             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5564   }
5565
5566   /**
5567    * Set visibility of dna/protein complement view (available when shown in a
5568    * split frame).
5569    *
5570    * @param show
5571    */
5572   @Override
5573   protected void showComplement_actionPerformed(boolean show)
5574   {
5575     SplitContainerI sf = getSplitViewContainer();
5576     if (sf != null)
5577     {
5578       sf.setComplementVisible(this, show);
5579     }
5580   }
5581
5582   /**
5583    * Generate the reverse (optionally complemented) of the selected sequences,
5584    * and add them to the alignment
5585    */
5586   @Override
5587   protected void showReverse_actionPerformed(boolean complement)
5588   {
5589     AlignmentI al = null;
5590     try
5591     {
5592       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5593       al = dna.reverseCdna(complement);
5594       viewport.addAlignment(al, "");
5595       addHistoryItem(new EditCommand(
5596               MessageManager.getString("label.add_sequences"),
5597               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5598               viewport.getAlignment()));
5599     } catch (Exception ex)
5600     {
5601       System.err.println(ex.getMessage());
5602       return;
5603     }
5604   }
5605
5606   /**
5607    * Try to run a script in the Groovy console, having first ensured that this
5608    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5609    * be targeted at this alignment.
5610    */
5611   @Override
5612   protected void runGroovy_actionPerformed()
5613   {
5614     Jalview.setCurrentAlignFrame(this);
5615     groovy.ui.Console console = Desktop.getGroovyConsole();
5616     if (console != null)
5617     {
5618       try
5619       {
5620         console.runScript();
5621       } catch (Exception ex)
5622       {
5623         System.err.println((ex.toString()));
5624         JvOptionPane
5625                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5626                         .getString("label.couldnt_run_groovy_script"),
5627                         MessageManager
5628                                 .getString("label.groovy_support_failed"),
5629                         JvOptionPane.ERROR_MESSAGE);
5630       }
5631     }
5632     else
5633     {
5634       System.err.println("Can't run Groovy script as console not found");
5635     }
5636   }
5637
5638   /**
5639    * Hides columns containing (or not containing) a specified feature, provided
5640    * that would not leave all columns hidden
5641    *
5642    * @param featureType
5643    * @param columnsContaining
5644    * @return
5645    */
5646   public boolean hideFeatureColumns(String featureType,
5647           boolean columnsContaining)
5648   {
5649     boolean notForHiding = avc.markColumnsContainingFeatures(
5650             columnsContaining, false, false, featureType);
5651     if (notForHiding)
5652     {
5653       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5654               false, featureType))
5655       {
5656         getViewport().hideSelectedColumns();
5657         return true;
5658       }
5659     }
5660     return false;
5661   }
5662
5663   @Override
5664   protected void selectHighlightedColumns_actionPerformed(
5665           ActionEvent actionEvent)
5666   {
5667     // include key modifier check in case user selects from menu
5668     avc.markHighlightedColumns(
5669             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5670             true,
5671             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5672   }
5673
5674   /**
5675    * Rebuilds the Colour menu, including any user-defined colours which have
5676    * been loaded either on startup or during the session
5677    */
5678   public void buildColourMenu()
5679   {
5680     colourMenu.removeAll();
5681
5682     colourMenu.add(applyToAllGroups);
5683     colourMenu.add(textColour);
5684     colourMenu.addSeparator();
5685
5686     ColourMenuHelper.addMenuItems(colourMenu, this,
5687             viewport.getAlignment(), false);
5688
5689     colourMenu.addSeparator();
5690     colourMenu.add(conservationMenuItem);
5691     colourMenu.add(modifyConservation);
5692     colourMenu.add(abovePIDThreshold);
5693     colourMenu.add(modifyPID);
5694     colourMenu.add(annotationColour);
5695
5696     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5697     String schemeName = colourScheme == null ? null : colourScheme
5698             .getSchemeName();
5699
5700     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5701   }
5702 }
5703
5704 class PrintThread extends Thread
5705 {
5706   AlignmentPanel ap;
5707
5708   public PrintThread(AlignmentPanel ap)
5709   {
5710     this.ap = ap;
5711   }
5712
5713   static PageFormat pf;
5714
5715   @Override
5716   public void run()
5717   {
5718     PrinterJob printJob = PrinterJob.getPrinterJob();
5719
5720     if (pf != null)
5721     {
5722       printJob.setPrintable(ap, pf);
5723     }
5724     else
5725     {
5726       printJob.setPrintable(ap);
5727     }
5728
5729     if (printJob.printDialog())
5730     {
5731       try
5732       {
5733         printJob.print();
5734       } catch (Exception PrintException)
5735       {
5736         PrintException.printStackTrace();
5737       }
5738     }
5739   }
5740 }