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.TCoffeeColourScheme;
  86 import jalview.util.MessageManager;
  87 import jalview.viewmodel.AlignmentViewport;
  88 import jalview.ws.DBRefFetcher;
  89 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  90 import jalview.ws.jws1.Discoverer;
  91 import jalview.ws.jws2.Jws2Discoverer;
  92 import jalview.ws.jws2.jabaws2.Jws2Instance;
  93 import jalview.ws.seqfetcher.DbSourceProxy;
  94
  95 import java.awt.BorderLayout;
  96 import java.awt.Component;
  97 import java.awt.Rectangle;
  98 import java.awt.Toolkit;
  99 import java.awt.datatransfer.Clipboard;
 100 import java.awt.datatransfer.DataFlavor;
 101 import java.awt.datatransfer.StringSelection;
 102 import java.awt.datatransfer.Transferable;
 103 import java.awt.dnd.DnDConstants;
 104 import java.awt.dnd.DropTargetDragEvent;
 105 import java.awt.dnd.DropTargetDropEvent;
 106 import java.awt.dnd.DropTargetEvent;
 107 import java.awt.dnd.DropTargetListener;
 108 import java.awt.event.ActionEvent;
 109 import java.awt.event.ActionListener;
 110 import java.awt.event.FocusAdapter;
 111 import java.awt.event.FocusEvent;
 112 import java.awt.event.ItemEvent;
 113 import java.awt.event.ItemListener;
 114 import java.awt.event.KeyAdapter;
 115 import java.awt.event.KeyEvent;
 116 import java.awt.event.MouseEvent;
 117 import java.awt.print.PageFormat;
 118 import java.awt.print.PrinterJob;
 119 import java.beans.PropertyChangeEvent;
 120 import java.io.File;
 121 import java.io.FileWriter;
 122 import java.io.PrintWriter;
 123 import java.net.URL;
 124 import java.util.ArrayList;
 125 import java.util.Arrays;
 126 import java.util.Deque;
 127 import java.util.Enumeration;
 128 import java.util.Hashtable;
 129 import java.util.List;
 130 import java.util.Vector;
 131
 132 import javax.swing.JCheckBoxMenuItem;
 133 import javax.swing.JEditorPane;
 134 import javax.swing.JInternalFrame;
 135 import javax.swing.JLayeredPane;
 136 import javax.swing.JMenu;
 137 import javax.swing.JMenuItem;
 138 import javax.swing.JScrollPane;
 139 import javax.swing.SwingUtilities;
 140
 141 /**
 142  * DOCUMENT ME!
 143  *
 144  * @author $author$
 145  * @version $Revision$
 146  */
 147 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 148         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 149 {
 150
 151   public static final int DEFAULT_WIDTH = 700;
 152
 153   public static final int DEFAULT_HEIGHT = 500;
 154
 155   /*
 156    * The currently displayed panel (selected tabbed view if more than one)
 157    */
 158   public AlignmentPanel alignPanel;
 159
 160   AlignViewport viewport;
 161
 162   public AlignViewControllerI avc;
 163
 164   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 165
 166   /**
 167    * Last format used to load or save alignments in this window
 168    */
 169   FileFormatI currentFileFormat = null;
 170
 171   /**
 172    * Current filename for this alignment
 173    */
 174   String fileName = null;
 175
 176   /**
 177    * Creates a new AlignFrame object with specific width and height.
 178    *
 179    * @param al
 180    * @param width
 181    * @param height
 182    */
 183   public AlignFrame(AlignmentI al, int width, int height)
 184   {
 185     this(al, null, width, height);
 186   }
 187
 188   /**
 189    * Creates a new AlignFrame object with specific width, height and
 190    * sequenceSetId
 191    *
 192    * @param al
 193    * @param width
 194    * @param height
 195    * @param sequenceSetId
 196    */
 197   public AlignFrame(AlignmentI al, int width, int height,
 198           String sequenceSetId)
 199   {
 200     this(al, null, width, height, sequenceSetId);
 201   }
 202
 203   /**
 204    * Creates a new AlignFrame object with specific width, height and
 205    * sequenceSetId
 206    *
 207    * @param al
 208    * @param width
 209    * @param height
 210    * @param sequenceSetId
 211    * @param viewId
 212    */
 213   public AlignFrame(AlignmentI al, int width, int height,
 214           String sequenceSetId, String viewId)
 215   {
 216     this(al, null, width, height, sequenceSetId, viewId);
 217   }
 218
 219   /**
 220    * new alignment window with hidden columns
 221    *
 222    * @param al
 223    *          AlignmentI
 224    * @param hiddenColumns
 225    *          ColumnSelection or null
 226    * @param width
 227    *          Width of alignment frame
 228    * @param height
 229    *          height of frame.
 230    */
 231   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 232           int width, int height)
 233   {
 234     this(al, hiddenColumns, width, height, null);
 235   }
 236
 237   /**
 238    * Create alignment frame for al with hiddenColumns, a specific width and
 239    * height, and specific sequenceId
 240    *
 241    * @param al
 242    * @param hiddenColumns
 243    * @param width
 244    * @param height
 245    * @param sequenceSetId
 246    *          (may be null)
 247    */
 248   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 249           int width, int height, String sequenceSetId)
 250   {
 251     this(al, hiddenColumns, width, height, sequenceSetId, null);
 252   }
 253
 254   /**
 255    * Create alignment frame for al with hiddenColumns, a specific width and
 256    * height, and specific sequenceId
 257    *
 258    * @param al
 259    * @param hiddenColumns
 260    * @param width
 261    * @param height
 262    * @param sequenceSetId
 263    *          (may be null)
 264    * @param viewId
 265    *          (may be null)
 266    */
 267   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 268           int width, int height, String sequenceSetId, String viewId)
 269   {
 270     setSize(width, height);
 271
 272     if (al.getDataset() == null)
 273     {
 274       al.setDataset(null);
 275     }
 276
 277     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 278
 279     alignPanel = new AlignmentPanel(this, viewport);
 280
 281     addAlignmentPanel(alignPanel, true);
 282     init();
 283   }
 284
 285   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 286           ColumnSelection hiddenColumns, int width, int height)
 287   {
 288     setSize(width, height);
 289
 290     if (al.getDataset() == null)
 291     {
 292       al.setDataset(null);
 293     }
 294
 295     viewport = new AlignViewport(al, hiddenColumns);
 296
 297     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 298     {
 299       viewport.hideSequence(hiddenSeqs);
 300     }
 301     alignPanel = new AlignmentPanel(this, viewport);
 302     addAlignmentPanel(alignPanel, true);
 303     init();
 304   }
 305
 306   /**
 307    * Make a new AlignFrame from existing alignmentPanels
 308    *
 309    * @param ap
 310    *          AlignmentPanel
 311    * @param av
 312    *          AlignViewport
 313    */
 314   public AlignFrame(AlignmentPanel ap)
 315   {
 316     viewport = ap.av;
 317     alignPanel = ap;
 318     addAlignmentPanel(ap, false);
 319     init();
 320   }
 321
 322   /**
 323    * initalise the alignframe from the underlying viewport data and the
 324    * configurations
 325    */
 326   void init()
 327   {
 328     if (!Jalview.isHeadlessMode())
 329     {
 330       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 331     }
 332
 333     avc = new jalview.controller.AlignViewController(this, viewport,
 334             alignPanel);
 335     if (viewport.getAlignmentConservationAnnotation() == null)
 336     {
 337       // BLOSUM62Colour.setEnabled(false);
 338       conservationMenuItem.setEnabled(false);
 339       modifyConservation.setEnabled(false);
 340       // PIDColour.setEnabled(false);
 341       // abovePIDThreshold.setEnabled(false);
 342       // modifyPID.setEnabled(false);
 343     }
 344
 345     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 346             "No sort");
 347
 348     if (sortby.equals("Id"))
 349     {
 350       sortIDMenuItem_actionPerformed(null);
 351     }
 352     else if (sortby.equals("Pairwise Identity"))
 353     {
 354       sortPairwiseMenuItem_actionPerformed(null);
 355     }
 356
 357     this.alignPanel.av
 358             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 359
 360     setMenusFromViewport(viewport);
 361     buildSortByAnnotationScoresMenu();
 362     calculateTree.addActionListener(new ActionListener()
 363     {
 364
 365       @Override
 366       public void actionPerformed(ActionEvent e)
 367       {
 368         new TreeChooser(AlignFrame.this);
 369       }
 370     });
 371     buildColourMenu();
 372
 373     if (Desktop.desktop != null)
 374     {
 375       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 376       addServiceListeners();
 377       setGUINucleotide();
 378     }
 379
 380     if (viewport.getWrapAlignment())
 381     {
 382       wrapMenuItem_actionPerformed(null);
 383     }
 384
 385     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 386     {
 387       this.overviewMenuItem_actionPerformed(null);
 388     }
 389
 390     addKeyListener();
 391
 392     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 393     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 394     final String menuLabel = MessageManager
 395             .getString("label.copy_format_from");
 396     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 397             new ViewSetProvider()
 398             {
 399
 400               @Override
 401               public AlignmentPanel[] getAllAlignmentPanels()
 402               {
 403                 origview.clear();
 404                 origview.add(alignPanel);
 405                 // make an array of all alignment panels except for this one
 406                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 407                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 408                 aps.remove(AlignFrame.this.alignPanel);
 409                 return aps.toArray(new AlignmentPanel[aps.size()]);
 410               }
 411             }, selviews, new ItemListener()
 412             {
 413
 414               @Override
 415               public void itemStateChanged(ItemEvent e)
 416               {
 417                 if (origview.size() > 0)
 418                 {
 419                   final AlignmentPanel ap = origview.get(0);
 420
 421                   /*
 422                    * Copy the ViewStyle of the selected panel to 'this one'.
 423                    * Don't change value of 'scaleProteinAsCdna' unless copying
 424                    * from a SplitFrame.
 425                    */
 426                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 427                           .getViewStyle();
 428                   boolean fromSplitFrame = selviews.get(0)
 429                           .getAlignViewport().getCodingComplement() != null;
 430                   if (!fromSplitFrame)
 431                   {
 432                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 433                             .getViewStyle().isScaleProteinAsCdna());
 434                   }
 435                   ap.getAlignViewport().setViewStyle(vs);
 436
 437                   /*
 438                    * Also rescale ViewStyle of SplitFrame complement if there is
 439                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 440                    * the whole ViewStyle (allow cDNA protein to have different
 441                    * fonts)
 442                    */
 443                   AlignViewportI complement = ap.getAlignViewport()
 444                           .getCodingComplement();
 445                   if (complement != null && vs.isScaleProteinAsCdna())
 446                   {
 447                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 448                     ((SplitFrame) af.getSplitViewContainer())
 449                             .adjustLayout();
 450                     af.setMenusForViewport();
 451                   }
 452
 453                   ap.updateLayout();
 454                   ap.setSelected(true);
 455                   ap.alignFrame.setMenusForViewport();
 456
 457                 }
 458               }
 459             });
 460     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 461             .indexOf("devel") > -1
 462             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 463                     .indexOf("test") > -1)
 464     {
 465       formatMenu.add(vsel);
 466     }
 467     addFocusListener(new FocusAdapter()
 468     {
 469       @Override
 470       public void focusGained(FocusEvent e)
 471       {
 472         Jalview.setCurrentAlignFrame(AlignFrame.this);
 473       }
 474     });
 475
 476   }
 477
 478   /**
 479    * Change the filename and format for the alignment, and enable the 'reload'
 480    * button functionality.
 481    *
 482    * @param file
 483    *          valid filename
 484    * @param format
 485    *          format of file
 486    */
 487   public void setFileName(String file, FileFormatI format)
 488   {
 489     fileName = file;
 490     setFileFormat(format);
 491     reload.setEnabled(true);
 492   }
 493
 494   /**
 495    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 496    * events
 497    */
 498   void addKeyListener()
 499   {
 500     addKeyListener(new KeyAdapter()
 501     {
 502       @Override
 503       public void keyPressed(KeyEvent evt)
 504       {
 505         if (viewport.cursorMode
 506                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 507                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 508                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 509                 && Character.isDigit(evt.getKeyChar()))
 510         {
 511           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 512         }
 513
 514         switch (evt.getKeyCode())
 515         {
 516
 517         case 27: // escape key
 518           deselectAllSequenceMenuItem_actionPerformed(null);
 519
 520           break;
 521
 522         case KeyEvent.VK_DOWN:
 523           if (evt.isAltDown() || !viewport.cursorMode)
 524           {
 525             moveSelectedSequences(false);
 526           }
 527           if (viewport.cursorMode)
 528           {
 529             alignPanel.getSeqPanel().moveCursor(0, 1);
 530           }
 531           break;
 532
 533         case KeyEvent.VK_UP:
 534           if (evt.isAltDown() || !viewport.cursorMode)
 535           {
 536             moveSelectedSequences(true);
 537           }
 538           if (viewport.cursorMode)
 539           {
 540             alignPanel.getSeqPanel().moveCursor(0, -1);
 541           }
 542
 543           break;
 544
 545         case KeyEvent.VK_LEFT:
 546           if (evt.isAltDown() || !viewport.cursorMode)
 547           {
 548             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 549           }
 550           else
 551           {
 552             alignPanel.getSeqPanel().moveCursor(-1, 0);
 553           }
 554
 555           break;
 556
 557         case KeyEvent.VK_RIGHT:
 558           if (evt.isAltDown() || !viewport.cursorMode)
 559           {
 560             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 561           }
 562           else
 563           {
 564             alignPanel.getSeqPanel().moveCursor(1, 0);
 565           }
 566           break;
 567
 568         case KeyEvent.VK_SPACE:
 569           if (viewport.cursorMode)
 570           {
 571             alignPanel.getSeqPanel().insertGapAtCursor(
 572                     evt.isControlDown() || evt.isShiftDown()
 573                             || evt.isAltDown());
 574           }
 575           break;
 576
 577         // case KeyEvent.VK_A:
 578         // if (viewport.cursorMode)
 579         // {
 580         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 581         // //System.out.println("A");
 582         // }
 583         // break;
 584         /*
 585          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 586          * System.out.println("closing bracket"); } break;
 587          */
 588         case KeyEvent.VK_DELETE:
 589         case KeyEvent.VK_BACK_SPACE:
 590           if (!viewport.cursorMode)
 591           {
 592             cut_actionPerformed(null);
 593           }
 594           else
 595           {
 596             alignPanel.getSeqPanel().deleteGapAtCursor(
 597                     evt.isControlDown() || evt.isShiftDown()
 598                             || evt.isAltDown());
 599           }
 600
 601           break;
 602
 603         case KeyEvent.VK_S:
 604           if (viewport.cursorMode)
 605           {
 606             alignPanel.getSeqPanel().setCursorRow();
 607           }
 608           break;
 609         case KeyEvent.VK_C:
 610           if (viewport.cursorMode && !evt.isControlDown())
 611           {
 612             alignPanel.getSeqPanel().setCursorColumn();
 613           }
 614           break;
 615         case KeyEvent.VK_P:
 616           if (viewport.cursorMode)
 617           {
 618             alignPanel.getSeqPanel().setCursorPosition();
 619           }
 620           break;
 621
 622         case KeyEvent.VK_ENTER:
 623         case KeyEvent.VK_COMMA:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setCursorRowAndColumn();
 627           }
 628           break;
 629
 630         case KeyEvent.VK_Q:
 631           if (viewport.cursorMode)
 632           {
 633             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 634           }
 635           break;
 636         case KeyEvent.VK_M:
 637           if (viewport.cursorMode)
 638           {
 639             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 640           }
 641           break;
 642
 643         case KeyEvent.VK_F2:
 644           viewport.cursorMode = !viewport.cursorMode;
 645           statusBar.setText(MessageManager.formatMessage(
 646                   "label.keyboard_editing_mode",
 647                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 651             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 652           }
 653           alignPanel.getSeqPanel().seqCanvas.repaint();
 654           break;
 655
 656         case KeyEvent.VK_F1:
 657           try
 658           {
 659             Help.showHelpWindow();
 660           } catch (Exception ex)
 661           {
 662             ex.printStackTrace();
 663           }
 664           break;
 665         case KeyEvent.VK_H:
 666         {
 667           boolean toggleSeqs = !evt.isControlDown();
 668           boolean toggleCols = !evt.isShiftDown();
 669           toggleHiddenRegions(toggleSeqs, toggleCols);
 670           break;
 671         }
 672         case KeyEvent.VK_B:
 673         {
 674           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 675           boolean modifyExisting = true; // always modify, don't clear
 676                                          // evt.isShiftDown();
 677           boolean invertHighlighted = evt.isAltDown();
 678           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 679                   toggleSel);
 680           break;
 681         }
 682         case KeyEvent.VK_PAGE_UP:
 683           if (viewport.getWrapAlignment())
 684           {
 685             alignPanel.scrollUp(true);
 686           }
 687           else
 688           {
 689             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 690                     - viewport.endSeq + viewport.startSeq);
 691           }
 692           break;
 693         case KeyEvent.VK_PAGE_DOWN:
 694           if (viewport.getWrapAlignment())
 695           {
 696             alignPanel.scrollUp(false);
 697           }
 698           else
 699           {
 700             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 701                     + viewport.endSeq - viewport.startSeq);
 702           }
 703           break;
 704         }
 705       }
 706
 707       @Override
 708       public void keyReleased(KeyEvent evt)
 709       {
 710         switch (evt.getKeyCode())
 711         {
 712         case KeyEvent.VK_LEFT:
 713           if (evt.isAltDown() || !viewport.cursorMode)
 714           {
 715             viewport.firePropertyChange("alignment", null, viewport
 716                     .getAlignment().getSequences());
 717           }
 718           break;
 719
 720         case KeyEvent.VK_RIGHT:
 721           if (evt.isAltDown() || !viewport.cursorMode)
 722           {
 723             viewport.firePropertyChange("alignment", null, viewport
 724                     .getAlignment().getSequences());
 725           }
 726           break;
 727         }
 728       }
 729     });
 730   }
 731
 732   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 733   {
 734     ap.alignFrame = this;
 735     avc = new jalview.controller.AlignViewController(this, viewport,
 736             alignPanel);
 737
 738     alignPanels.add(ap);
 739
 740     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 741
 742     int aSize = alignPanels.size();
 743
 744     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 745
 746     if (aSize == 1 && ap.av.viewName == null)
 747     {
 748       this.getContentPane().add(ap, BorderLayout.CENTER);
 749     }
 750     else
 751     {
 752       if (aSize == 2)
 753       {
 754         setInitialTabVisible();
 755       }
 756
 757       expandViews.setEnabled(true);
 758       gatherViews.setEnabled(true);
 759       tabbedPane.addTab(ap.av.viewName, ap);
 760
 761       ap.setVisible(false);
 762     }
 763
 764     if (newPanel)
 765     {
 766       if (ap.av.isPadGaps())
 767       {
 768         ap.av.getAlignment().padGaps();
 769       }
 770       ap.av.updateConservation(ap);
 771       ap.av.updateConsensus(ap);
 772       ap.av.updateStrucConsensus(ap);
 773     }
 774   }
 775
 776   public void setInitialTabVisible()
 777   {
 778     expandViews.setEnabled(true);
 779     gatherViews.setEnabled(true);
 780     tabbedPane.setVisible(true);
 781     AlignmentPanel first = alignPanels.get(0);
 782     tabbedPane.addTab(first.av.viewName, first);
 783     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 784   }
 785
 786   public AlignViewport getViewport()
 787   {
 788     return viewport;
 789   }
 790
 791   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 792   private void addServiceListeners()
 793   {
 794     final java.beans.PropertyChangeListener thisListener;
 795     Desktop.instance.addJalviewPropertyChangeListener("services",
 796             thisListener = new java.beans.PropertyChangeListener()
 797             {
 798               @Override
 799               public void propertyChange(PropertyChangeEvent evt)
 800               {
 801                 // // System.out.println("Discoverer property change.");
 802                 // if (evt.getPropertyName().equals("services"))
 803                 {
 804                   SwingUtilities.invokeLater(new Runnable()
 805                   {
 806
 807                     @Override
 808                     public void run()
 809                     {
 810                       System.err
 811                               .println("Rebuild WS Menu for service change");
 812                       BuildWebServiceMenu();
 813                     }
 814
 815                   });
 816                 }
 817               }
 818             });
 819     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 820     {
 821       @Override
 822       public void internalFrameClosed(
 823               javax.swing.event.InternalFrameEvent evt)
 824       {
 825         // System.out.println("deregistering discoverer listener");
 826         Desktop.instance.removeJalviewPropertyChangeListener("services",
 827                 thisListener);
 828         closeMenuItem_actionPerformed(true);
 829       };
 830     });
 831     // Finally, build the menu once to get current service state
 832     new Thread(new Runnable()
 833     {
 834       @Override
 835       public void run()
 836       {
 837         BuildWebServiceMenu();
 838       }
 839     }).start();
 840   }
 841
 842   /**
 843    * Configure menu items that vary according to whether the alignment is
 844    * nucleotide or protein
 845    */
 846   public void setGUINucleotide()
 847   {
 848     AlignmentI al = getViewport().getAlignment();
 849     boolean nucleotide = al.isNucleotide();
 850
 851     showTranslation.setVisible(nucleotide);
 852     showReverse.setVisible(nucleotide);
 853     showReverseComplement.setVisible(nucleotide);
 854     conservationMenuItem.setEnabled(!nucleotide);
 855     modifyConservation.setEnabled(!nucleotide
 856             && conservationMenuItem.isSelected());
 857     showGroupConservation.setEnabled(!nucleotide);
 858
 859     showComplementMenuItem.setText(nucleotide ? MessageManager
 860             .getString("label.protein") : MessageManager
 861             .getString("label.nucleotide"));
 862   }
 863
 864   /**
 865    * set up menus for the current viewport. This may be called after any
 866    * operation that affects the data in the current view (selection changed,
 867    * etc) to update the menus to reflect the new state.
 868    */
 869   @Override
 870   public void setMenusForViewport()
 871   {
 872     setMenusFromViewport(viewport);
 873   }
 874
 875   /**
 876    * Need to call this method when tabs are selected for multiple views, or when
 877    * loading from Jalview2XML.java
 878    *
 879    * @param av
 880    *          AlignViewport
 881    */
 882   void setMenusFromViewport(AlignViewport av)
 883   {
 884     padGapsMenuitem.setSelected(av.isPadGaps());
 885     colourTextMenuItem.setSelected(av.isShowColourText());
 886     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 887     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 888     conservationMenuItem.setSelected(av.getConservationSelected());
 889     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 890     seqLimits.setSelected(av.getShowJVSuffix());
 891     idRightAlign.setSelected(av.isRightAlignIds());
 892     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 893     renderGapsMenuItem.setSelected(av.isRenderGaps());
 894     wrapMenuItem.setSelected(av.getWrapAlignment());
 895     scaleAbove.setVisible(av.getWrapAlignment());
 896     scaleLeft.setVisible(av.getWrapAlignment());
 897     scaleRight.setVisible(av.getWrapAlignment());
 898     annotationPanelMenuItem.setState(av.isShowAnnotation());
 899     /*
 900      * Show/hide annotations only enabled if annotation panel is shown
 901      */
 902     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 904     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 905     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 906     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 907     viewTextMenuItem.setSelected(av.getShowText());
 908     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 909     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 910     showGroupConservation.setSelected(av.isShowGroupConservation());
 911     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 912     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 913     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 914
 915     ColourMenuHelper.setColourSelected(colourMenu,
 916             av.getGlobalColourScheme());
 917
 918     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 919     hiddenMarkers.setState(av.getShowHiddenMarkers());
 920     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 921     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 922     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 923     autoCalculate.setSelected(av.autoCalculateConsensus);
 924     sortByTree.setSelected(av.sortByTree);
 925     listenToViewSelections.setSelected(av.followSelection);
 926
 927     showProducts.setEnabled(canShowProducts());
 928     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 929
 930     updateEditMenuBar();
 931   }
 932
 933   /**
 934    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 935    *
 936    * @param b
 937    */
 938   public void setGroovyEnabled(boolean b)
 939   {
 940     runGroovy.setEnabled(b);
 941   }
 942
 943   private IProgressIndicator progressBar;
 944
 945   /*
 946    * (non-Javadoc)
 947    *
 948    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 949    */
 950   @Override
 951   public void setProgressBar(String message, long id)
 952   {
 953     progressBar.setProgressBar(message, id);
 954   }
 955
 956   @Override
 957   public void registerHandler(final long id,
 958           final IProgressIndicatorHandler handler)
 959   {
 960     progressBar.registerHandler(id, handler);
 961   }
 962
 963   /**
 964    *
 965    * @return true if any progress bars are still active
 966    */
 967   @Override
 968   public boolean operationInProgress()
 969   {
 970     return progressBar.operationInProgress();
 971   }
 972
 973   @Override
 974   public void setStatus(String text)
 975   {
 976     statusBar.setText(text);
 977   }
 978
 979   /*
 980    * Added so Castor Mapping file can obtain Jalview Version
 981    */
 982   public String getVersion()
 983   {
 984     return jalview.bin.Cache.getProperty("VERSION");
 985   }
 986
 987   public FeatureRenderer getFeatureRenderer()
 988   {
 989     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 990   }
 991
 992   @Override
 993   public void fetchSequence_actionPerformed(ActionEvent e)
 994   {
 995     new jalview.gui.SequenceFetcher(this);
 996   }
 997
 998   @Override
 999   public void addFromFile_actionPerformed(ActionEvent e)
1000   {
1001     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1002   }
1003
1004   @Override
1005   public void reload_actionPerformed(ActionEvent e)
1006   {
1007     if (fileName != null)
1008     {
1009       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1010       // originating file's format
1011       // TODO: work out how to recover feature settings for correct view(s) when
1012       // file is reloaded.
1013       if (FileFormat.Jalview.equals(currentFileFormat))
1014       {
1015         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1016         for (int i = 0; i < frames.length; i++)
1017         {
1018           if (frames[i] instanceof AlignFrame && frames[i] != this
1019                   && ((AlignFrame) frames[i]).fileName != null
1020                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1021           {
1022             try
1023             {
1024               frames[i].setSelected(true);
1025               Desktop.instance.closeAssociatedWindows();
1026             } catch (java.beans.PropertyVetoException ex)
1027             {
1028             }
1029           }
1030
1031         }
1032         Desktop.instance.closeAssociatedWindows();
1033
1034         FileLoader loader = new FileLoader();
1035         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1036                 : DataSourceType.FILE;
1037         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1038       }
1039       else
1040       {
1041         Rectangle bounds = this.getBounds();
1042
1043         FileLoader loader = new FileLoader();
1044         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1045                 : DataSourceType.FILE;
1046         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1047                 protocol, currentFileFormat);
1048
1049         newframe.setBounds(bounds);
1050         if (featureSettings != null && featureSettings.isShowing())
1051         {
1052           final Rectangle fspos = featureSettings.frame.getBounds();
1053           // TODO: need a 'show feature settings' function that takes bounds -
1054           // need to refactor Desktop.addFrame
1055           newframe.featureSettings_actionPerformed(null);
1056           final FeatureSettings nfs = newframe.featureSettings;
1057           SwingUtilities.invokeLater(new Runnable()
1058           {
1059             @Override
1060             public void run()
1061             {
1062               nfs.frame.setBounds(fspos);
1063             }
1064           });
1065           this.featureSettings.close();
1066           this.featureSettings = null;
1067         }
1068         this.closeMenuItem_actionPerformed(true);
1069       }
1070     }
1071   }
1072
1073   @Override
1074   public void addFromText_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1077             .getAlignPanel());
1078   }
1079
1080   @Override
1081   public void addFromURL_actionPerformed(ActionEvent e)
1082   {
1083     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1084   }
1085
1086   @Override
1087   public void save_actionPerformed(ActionEvent e)
1088   {
1089     if (fileName == null || (currentFileFormat == null)
1090             || fileName.startsWith("http"))
1091     {
1092       saveAs_actionPerformed(null);
1093     }
1094     else
1095     {
1096       saveAlignment(fileName, currentFileFormat);
1097     }
1098   }
1099
1100   /**
1101    * DOCUMENT ME!
1102    *
1103    * @param e
1104    *          DOCUMENT ME!
1105    */
1106   @Override
1107   public void saveAs_actionPerformed(ActionEvent e)
1108   {
1109     String format = currentFileFormat == null ? null : currentFileFormat
1110             .getName();
1111     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1112             Cache.getProperty("LAST_DIRECTORY"), format);
1113
1114     chooser.setFileView(new JalviewFileView());
1115     chooser.setDialogTitle(MessageManager
1116             .getString("label.save_alignment_to_file"));
1117     chooser.setToolTipText(MessageManager.getString("action.save"));
1118
1119     int value = chooser.showSaveDialog(this);
1120
1121     if (value == JalviewFileChooser.APPROVE_OPTION)
1122     {
1123       currentFileFormat = chooser.getSelectedFormat();
1124       while (currentFileFormat == null)
1125       {
1126         JvOptionPane
1127                 .showInternalMessageDialog(
1128                         Desktop.desktop,
1129                         MessageManager
1130                                 .getString("label.select_file_format_before_saving"),
1131                         MessageManager
1132                                 .getString("label.file_format_not_specified"),
1133                         JvOptionPane.WARNING_MESSAGE);
1134         currentFileFormat = chooser.getSelectedFormat();
1135         value = chooser.showSaveDialog(this);
1136         if (value != JalviewFileChooser.APPROVE_OPTION)
1137         {
1138           return;
1139         }
1140       }
1141
1142       fileName = chooser.getSelectedFile().getPath();
1143
1144       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1145
1146       Cache.setProperty("LAST_DIRECTORY", fileName);
1147       saveAlignment(fileName, currentFileFormat);
1148     }
1149   }
1150
1151   public boolean saveAlignment(String file, FileFormatI format)
1152   {
1153     boolean success = true;
1154
1155     if (FileFormat.Jalview.equals(format))
1156     {
1157       String shortName = title;
1158
1159       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160       {
1161         shortName = shortName.substring(shortName
1162                 .lastIndexOf(java.io.File.separatorChar) + 1);
1163       }
1164
1165       success = new Jalview2XML().saveAlignment(this, file, shortName);
1166
1167       statusBar.setText(MessageManager.formatMessage(
1168               "label.successfully_saved_to_file_in_format", new Object[] {
1169                   fileName, format }));
1170
1171     }
1172     else
1173     {
1174       AlignmentExportData exportData = getAlignmentForExport(format,
1175               viewport, null);
1176       if (exportData.getSettings().isCancelled())
1177       {
1178         return false;
1179       }
1180       FormatAdapter f = new FormatAdapter(alignPanel,
1181               exportData.getSettings());
1182       String output = f.formatSequences(
1183               format,
1184               exportData.getAlignment(), // class cast exceptions will
1185               // occur in the distant future
1186               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1187               f.getCacheSuffixDefault(format),
1188               viewport.getColumnSelection());
1189
1190       if (output == null)
1191       {
1192         success = false;
1193       }
1194       else
1195       {
1196         try
1197         {
1198           PrintWriter out = new PrintWriter(new FileWriter(file));
1199
1200           out.print(output);
1201           out.close();
1202           this.setTitle(file);
1203           statusBar.setText(MessageManager.formatMessage(
1204                   "label.successfully_saved_to_file_in_format",
1205                   new Object[] { fileName, format.getName() }));
1206         } catch (Exception ex)
1207         {
1208           success = false;
1209           ex.printStackTrace();
1210         }
1211       }
1212     }
1213
1214     if (!success)
1215     {
1216       JvOptionPane.showInternalMessageDialog(this, MessageManager
1217               .formatMessage("label.couldnt_save_file",
1218                       new Object[] { fileName }), MessageManager
1219               .getString("label.error_saving_file"),
1220               JvOptionPane.WARNING_MESSAGE);
1221     }
1222
1223     return success;
1224   }
1225
1226   private void warningMessage(String warning, String title)
1227   {
1228     if (new jalview.util.Platform().isHeadless())
1229     {
1230       System.err.println("Warning: " + title + "\nWarning: " + warning);
1231
1232     }
1233     else
1234     {
1235       JvOptionPane.showInternalMessageDialog(this, warning, title,
1236               JvOptionPane.WARNING_MESSAGE);
1237     }
1238     return;
1239   }
1240
1241   /**
1242    * DOCUMENT ME!
1243    *
1244    * @param e
1245    *          DOCUMENT ME!
1246    */
1247   @Override
1248   protected void outputText_actionPerformed(ActionEvent e)
1249   {
1250     FileFormatI fileFormat = FileFormats.getInstance().forName(
1251             e.getActionCommand());
1252     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1253             viewport, null);
1254     if (exportData.getSettings().isCancelled())
1255     {
1256       return;
1257     }
1258     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1259     cap.setForInput(null);
1260     try
1261     {
1262       FileFormatI format = fileFormat;
1263       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1264               .formatSequences(format, exportData.getAlignment(),
1265                       exportData.getOmitHidden(),
1266                       exportData.getStartEndPostions(),
1267                       viewport.getColumnSelection()));
1268       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1269               "label.alignment_output_command",
1270               new Object[] { e.getActionCommand() }), 600, 500);
1271     } catch (OutOfMemoryError oom)
1272     {
1273       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1274       cap.dispose();
1275     }
1276
1277   }
1278
1279   public static AlignmentExportData getAlignmentForExport(
1280           FileFormatI format, AlignViewportI viewport,
1281           AlignExportSettingI exportSettings)
1282   {
1283     AlignmentI alignmentToExport = null;
1284     AlignExportSettingI settings = exportSettings;
1285     String[] omitHidden = null;
1286
1287     HiddenSequences hiddenSeqs = viewport.getAlignment()
1288             .getHiddenSequences();
1289
1290     alignmentToExport = viewport.getAlignment();
1291
1292     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1293     if (settings == null)
1294     {
1295       settings = new AlignExportSettings(hasHiddenSeqs,
1296               viewport.hasHiddenColumns(), format);
1297     }
1298     // settings.isExportAnnotations();
1299
1300     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1301     {
1302       omitHidden = viewport.getViewAsString(false,
1303               settings.isExportHiddenSequences());
1304     }
1305
1306     int[] alignmentStartEnd = new int[2];
1307     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1308     {
1309       alignmentToExport = hiddenSeqs.getFullAlignment();
1310     }
1311     else
1312     {
1313       alignmentToExport = viewport.getAlignment();
1314     }
1315     alignmentStartEnd = alignmentToExport
1316             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1317                     .getHiddenColumns());
1318     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1319             omitHidden, alignmentStartEnd, settings);
1320     return ed;
1321   }
1322
1323   /**
1324    * DOCUMENT ME!
1325    *
1326    * @param e
1327    *          DOCUMENT ME!
1328    */
1329   @Override
1330   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1331   {
1332     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1333     htmlSVG.exportHTML(null);
1334   }
1335
1336   @Override
1337   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1338   {
1339     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1340     bjs.exportHTML(null);
1341   }
1342
1343   public void createImageMap(File file, String image)
1344   {
1345     alignPanel.makePNGImageMap(file, image);
1346   }
1347
1348   /**
1349    * DOCUMENT ME!
1350    *
1351    * @param e
1352    *          DOCUMENT ME!
1353    */
1354   @Override
1355   public void createPNG(File f)
1356   {
1357     alignPanel.makePNG(f);
1358   }
1359
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   @Override
1367   public void createEPS(File f)
1368   {
1369     alignPanel.makeEPS(f);
1370   }
1371
1372   @Override
1373   public void createSVG(File f)
1374   {
1375     alignPanel.makeSVG(f);
1376   }
1377
1378   @Override
1379   public void pageSetup_actionPerformed(ActionEvent e)
1380   {
1381     PrinterJob printJob = PrinterJob.getPrinterJob();
1382     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1383   }
1384
1385   /**
1386    * DOCUMENT ME!
1387    *
1388    * @param e
1389    *          DOCUMENT ME!
1390    */
1391   @Override
1392   public void printMenuItem_actionPerformed(ActionEvent e)
1393   {
1394     // Putting in a thread avoids Swing painting problems
1395     PrintThread thread = new PrintThread(alignPanel);
1396     thread.start();
1397   }
1398
1399   @Override
1400   public void exportFeatures_actionPerformed(ActionEvent e)
1401   {
1402     new AnnotationExporter().exportFeatures(alignPanel);
1403   }
1404
1405   @Override
1406   public void exportAnnotations_actionPerformed(ActionEvent e)
1407   {
1408     new AnnotationExporter().exportAnnotations(alignPanel);
1409   }
1410
1411   @Override
1412   public void associatedData_actionPerformed(ActionEvent e)
1413   {
1414     // Pick the tree file
1415     JalviewFileChooser chooser = new JalviewFileChooser(
1416             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1417     chooser.setFileView(new JalviewFileView());
1418     chooser.setDialogTitle(MessageManager
1419             .getString("label.load_jalview_annotations"));
1420     chooser.setToolTipText(MessageManager
1421             .getString("label.load_jalview_annotations"));
1422
1423     int value = chooser.showOpenDialog(null);
1424
1425     if (value == JalviewFileChooser.APPROVE_OPTION)
1426     {
1427       String choice = chooser.getSelectedFile().getPath();
1428       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1429       loadJalviewDataFile(choice, null, null, null);
1430     }
1431
1432   }
1433
1434   /**
1435    * Close the current view or all views in the alignment frame. If the frame
1436    * only contains one view then the alignment will be removed from memory.
1437    *
1438    * @param closeAllTabs
1439    */
1440   @Override
1441   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1442   {
1443     if (alignPanels != null && alignPanels.size() < 2)
1444     {
1445       closeAllTabs = true;
1446     }
1447
1448     try
1449     {
1450       if (alignPanels != null)
1451       {
1452         if (closeAllTabs)
1453         {
1454           if (this.isClosed())
1455           {
1456             // really close all the windows - otherwise wait till
1457             // setClosed(true) is called
1458             for (int i = 0; i < alignPanels.size(); i++)
1459             {
1460               AlignmentPanel ap = alignPanels.get(i);
1461               ap.closePanel();
1462             }
1463           }
1464         }
1465         else
1466         {
1467           closeView(alignPanel);
1468         }
1469       }
1470
1471       if (closeAllTabs)
1472       {
1473         /*
1474          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1475          * be called recursively, with the frame now in 'closed' state
1476          */
1477         this.setClosed(true);
1478       }
1479     } catch (Exception ex)
1480     {
1481       ex.printStackTrace();
1482     }
1483   }
1484
1485   /**
1486    * Close the specified panel and close up tabs appropriately.
1487    *
1488    * @param panelToClose
1489    */
1490   public void closeView(AlignmentPanel panelToClose)
1491   {
1492     int index = tabbedPane.getSelectedIndex();
1493     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1494     alignPanels.remove(panelToClose);
1495     panelToClose.closePanel();
1496     panelToClose = null;
1497
1498     tabbedPane.removeTabAt(closedindex);
1499     tabbedPane.validate();
1500
1501     if (index > closedindex || index == tabbedPane.getTabCount())
1502     {
1503       // modify currently selected tab index if necessary.
1504       index--;
1505     }
1506
1507     this.tabSelectionChanged(index);
1508   }
1509
1510   /**
1511    * DOCUMENT ME!
1512    */
1513   void updateEditMenuBar()
1514   {
1515
1516     if (viewport.getHistoryList().size() > 0)
1517     {
1518       undoMenuItem.setEnabled(true);
1519       CommandI command = viewport.getHistoryList().peek();
1520       undoMenuItem.setText(MessageManager.formatMessage(
1521               "label.undo_command",
1522               new Object[] { command.getDescription() }));
1523     }
1524     else
1525     {
1526       undoMenuItem.setEnabled(false);
1527       undoMenuItem.setText(MessageManager.getString("action.undo"));
1528     }
1529
1530     if (viewport.getRedoList().size() > 0)
1531     {
1532       redoMenuItem.setEnabled(true);
1533
1534       CommandI command = viewport.getRedoList().peek();
1535       redoMenuItem.setText(MessageManager.formatMessage(
1536               "label.redo_command",
1537               new Object[] { command.getDescription() }));
1538     }
1539     else
1540     {
1541       redoMenuItem.setEnabled(false);
1542       redoMenuItem.setText(MessageManager.getString("action.redo"));
1543     }
1544   }
1545
1546   @Override
1547   public void addHistoryItem(CommandI command)
1548   {
1549     if (command.getSize() > 0)
1550     {
1551       viewport.addToHistoryList(command);
1552       viewport.clearRedoList();
1553       updateEditMenuBar();
1554       viewport.updateHiddenColumns();
1555       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1556       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1557       // viewport.getColumnSelection()
1558       // .getHiddenColumns().size() > 0);
1559     }
1560   }
1561
1562   /**
1563    *
1564    * @return alignment objects for all views
1565    */
1566   AlignmentI[] getViewAlignments()
1567   {
1568     if (alignPanels != null)
1569     {
1570       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1571       int i = 0;
1572       for (AlignmentPanel ap : alignPanels)
1573       {
1574         als[i++] = ap.av.getAlignment();
1575       }
1576       return als;
1577     }
1578     if (viewport != null)
1579     {
1580       return new AlignmentI[] { viewport.getAlignment() };
1581     }
1582     return null;
1583   }
1584
1585   /**
1586    * DOCUMENT ME!
1587    *
1588    * @param e
1589    *          DOCUMENT ME!
1590    */
1591   @Override
1592   protected void undoMenuItem_actionPerformed(ActionEvent e)
1593   {
1594     if (viewport.getHistoryList().isEmpty())
1595     {
1596       return;
1597     }
1598     CommandI command = viewport.getHistoryList().pop();
1599     viewport.addToRedoList(command);
1600     command.undoCommand(getViewAlignments());
1601
1602     AlignmentViewport originalSource = getOriginatingSource(command);
1603     updateEditMenuBar();
1604
1605     if (originalSource != null)
1606     {
1607       if (originalSource != viewport)
1608       {
1609         Cache.log
1610                 .warn("Implementation worry: mismatch of viewport origin for undo");
1611       }
1612       originalSource.updateHiddenColumns();
1613       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1614       // null
1615       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1616       // viewport.getColumnSelection()
1617       // .getHiddenColumns().size() > 0);
1618       originalSource.firePropertyChange("alignment", null, originalSource
1619               .getAlignment().getSequences());
1620     }
1621   }
1622
1623   /**
1624    * DOCUMENT ME!
1625    *
1626    * @param e
1627    *          DOCUMENT ME!
1628    */
1629   @Override
1630   protected void redoMenuItem_actionPerformed(ActionEvent e)
1631   {
1632     if (viewport.getRedoList().size() < 1)
1633     {
1634       return;
1635     }
1636
1637     CommandI command = viewport.getRedoList().pop();
1638     viewport.addToHistoryList(command);
1639     command.doCommand(getViewAlignments());
1640
1641     AlignmentViewport originalSource = getOriginatingSource(command);
1642     updateEditMenuBar();
1643
1644     if (originalSource != null)
1645     {
1646
1647       if (originalSource != viewport)
1648       {
1649         Cache.log
1650                 .warn("Implementation worry: mismatch of viewport origin for redo");
1651       }
1652       originalSource.updateHiddenColumns();
1653       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1654       // null
1655       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1656       // viewport.getColumnSelection()
1657       // .getHiddenColumns().size() > 0);
1658       originalSource.firePropertyChange("alignment", null, originalSource
1659               .getAlignment().getSequences());
1660     }
1661   }
1662
1663   AlignmentViewport getOriginatingSource(CommandI command)
1664   {
1665     AlignmentViewport originalSource = null;
1666     // For sequence removal and addition, we need to fire
1667     // the property change event FROM the viewport where the
1668     // original alignment was altered
1669     AlignmentI al = null;
1670     if (command instanceof EditCommand)
1671     {
1672       EditCommand editCommand = (EditCommand) command;
1673       al = editCommand.getAlignment();
1674       List<Component> comps = PaintRefresher.components.get(viewport
1675               .getSequenceSetId());
1676
1677       for (Component comp : comps)
1678       {
1679         if (comp instanceof AlignmentPanel)
1680         {
1681           if (al == ((AlignmentPanel) comp).av.getAlignment())
1682           {
1683             originalSource = ((AlignmentPanel) comp).av;
1684             break;
1685           }
1686         }
1687       }
1688     }
1689
1690     if (originalSource == null)
1691     {
1692       // The original view is closed, we must validate
1693       // the current view against the closed view first
1694       if (al != null)
1695       {
1696         PaintRefresher.validateSequences(al, viewport.getAlignment());
1697       }
1698
1699       originalSource = viewport;
1700     }
1701
1702     return originalSource;
1703   }
1704
1705   /**
1706    * DOCUMENT ME!
1707    *
1708    * @param up
1709    *          DOCUMENT ME!
1710    */
1711   public void moveSelectedSequences(boolean up)
1712   {
1713     SequenceGroup sg = viewport.getSelectionGroup();
1714
1715     if (sg == null)
1716     {
1717       return;
1718     }
1719     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1720             viewport.getHiddenRepSequences(), up);
1721     alignPanel.paintAlignment(true);
1722   }
1723
1724   synchronized void slideSequences(boolean right, int size)
1725   {
1726     List<SequenceI> sg = new ArrayList<SequenceI>();
1727     if (viewport.cursorMode)
1728     {
1729       sg.add(viewport.getAlignment().getSequenceAt(
1730               alignPanel.getSeqPanel().seqCanvas.cursorY));
1731     }
1732     else if (viewport.getSelectionGroup() != null
1733             && viewport.getSelectionGroup().getSize() != viewport
1734                     .getAlignment().getHeight())
1735     {
1736       sg = viewport.getSelectionGroup().getSequences(
1737               viewport.getHiddenRepSequences());
1738     }
1739
1740     if (sg.size() < 1)
1741     {
1742       return;
1743     }
1744
1745     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1746
1747     for (SequenceI seq : viewport.getAlignment().getSequences())
1748     {
1749       if (!sg.contains(seq))
1750       {
1751         invertGroup.add(seq);
1752       }
1753     }
1754
1755     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1756
1757     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1758     for (int i = 0; i < invertGroup.size(); i++)
1759     {
1760       seqs2[i] = invertGroup.get(i);
1761     }
1762
1763     SlideSequencesCommand ssc;
1764     if (right)
1765     {
1766       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1767               size, viewport.getGapCharacter());
1768     }
1769     else
1770     {
1771       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1772               size, viewport.getGapCharacter());
1773     }
1774
1775     int groupAdjustment = 0;
1776     if (ssc.getGapsInsertedBegin() && right)
1777     {
1778       if (viewport.cursorMode)
1779       {
1780         alignPanel.getSeqPanel().moveCursor(size, 0);
1781       }
1782       else
1783       {
1784         groupAdjustment = size;
1785       }
1786     }
1787     else if (!ssc.getGapsInsertedBegin() && !right)
1788     {
1789       if (viewport.cursorMode)
1790       {
1791         alignPanel.getSeqPanel().moveCursor(-size, 0);
1792       }
1793       else
1794       {
1795         groupAdjustment = -size;
1796       }
1797     }
1798
1799     if (groupAdjustment != 0)
1800     {
1801       viewport.getSelectionGroup().setStartRes(
1802               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1803       viewport.getSelectionGroup().setEndRes(
1804               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1805     }
1806
1807     /*
1808      * just extend the last slide command if compatible; but not if in
1809      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1810      */
1811     boolean appendHistoryItem = false;
1812     Deque<CommandI> historyList = viewport.getHistoryList();
1813     boolean inSplitFrame = getSplitViewContainer() != null;
1814     if (!inSplitFrame && historyList != null && historyList.size() > 0
1815             && historyList.peek() instanceof SlideSequencesCommand)
1816     {
1817       appendHistoryItem = ssc
1818               .appendSlideCommand((SlideSequencesCommand) historyList
1819                       .peek());
1820     }
1821
1822     if (!appendHistoryItem)
1823     {
1824       addHistoryItem(ssc);
1825     }
1826
1827     repaint();
1828   }
1829
1830   /**
1831    * DOCUMENT ME!
1832    *
1833    * @param e
1834    *          DOCUMENT ME!
1835    */
1836   @Override
1837   protected void copy_actionPerformed(ActionEvent e)
1838   {
1839     System.gc();
1840     if (viewport.getSelectionGroup() == null)
1841     {
1842       return;
1843     }
1844     // TODO: preserve the ordering of displayed alignment annotation in any
1845     // internal paste (particularly sequence associated annotation)
1846     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1847     String[] omitHidden = null;
1848
1849     if (viewport.hasHiddenColumns())
1850     {
1851       omitHidden = viewport.getViewAsString(true);
1852     }
1853
1854     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1855             seqs, omitHidden, null);
1856
1857     StringSelection ss = new StringSelection(output);
1858
1859     try
1860     {
1861       jalview.gui.Desktop.internalCopy = true;
1862       // Its really worth setting the clipboard contents
1863       // to empty before setting the large StringSelection!!
1864       Toolkit.getDefaultToolkit().getSystemClipboard()
1865               .setContents(new StringSelection(""), null);
1866
1867       Toolkit.getDefaultToolkit().getSystemClipboard()
1868               .setContents(ss, Desktop.instance);
1869     } catch (OutOfMemoryError er)
1870     {
1871       new OOMWarning("copying region", er);
1872       return;
1873     }
1874
1875     ArrayList<int[]> hiddenColumns = null;
1876     if (viewport.hasHiddenColumns())
1877     {
1878       hiddenColumns = new ArrayList<int[]>();
1879       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1880               .getSelectionGroup().getEndRes();
1881       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1882       {
1883         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1884         {
1885           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1886               region[1] - hiddenOffset });
1887         }
1888       }
1889     }
1890
1891     Desktop.jalviewClipboard = new Object[] { seqs,
1892         viewport.getAlignment().getDataset(), hiddenColumns };
1893     statusBar.setText(MessageManager.formatMessage(
1894             "label.copied_sequences_to_clipboard", new Object[] { Integer
1895                     .valueOf(seqs.length).toString() }));
1896   }
1897
1898   /**
1899    * DOCUMENT ME!
1900    *
1901    * @param e
1902    *          DOCUMENT ME!
1903    */
1904   @Override
1905   protected void pasteNew_actionPerformed(ActionEvent e)
1906   {
1907     paste(true);
1908   }
1909
1910   /**
1911    * DOCUMENT ME!
1912    *
1913    * @param e
1914    *          DOCUMENT ME!
1915    */
1916   @Override
1917   protected void pasteThis_actionPerformed(ActionEvent e)
1918   {
1919     paste(false);
1920   }
1921
1922   /**
1923    * Paste contents of Jalview clipboard
1924    *
1925    * @param newAlignment
1926    *          true to paste to a new alignment, otherwise add to this.
1927    */
1928   void paste(boolean newAlignment)
1929   {
1930     boolean externalPaste = true;
1931     try
1932     {
1933       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1934       Transferable contents = c.getContents(this);
1935
1936       if (contents == null)
1937       {
1938         return;
1939       }
1940
1941       String str;
1942       FileFormatI format;
1943       try
1944       {
1945         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1946         if (str.length() < 1)
1947         {
1948           return;
1949         }
1950
1951         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1952
1953       } catch (OutOfMemoryError er)
1954       {
1955         new OOMWarning("Out of memory pasting sequences!!", er);
1956         return;
1957       }
1958
1959       SequenceI[] sequences;
1960       boolean annotationAdded = false;
1961       AlignmentI alignment = null;
1962
1963       if (Desktop.jalviewClipboard != null)
1964       {
1965         // The clipboard was filled from within Jalview, we must use the
1966         // sequences
1967         // And dataset from the copied alignment
1968         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1969         // be doubly sure that we create *new* sequence objects.
1970         sequences = new SequenceI[newseq.length];
1971         for (int i = 0; i < newseq.length; i++)
1972         {
1973           sequences[i] = new Sequence(newseq[i]);
1974         }
1975         alignment = new Alignment(sequences);
1976         externalPaste = false;
1977       }
1978       else
1979       {
1980         // parse the clipboard as an alignment.
1981         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1982                 format);
1983         sequences = alignment.getSequencesArray();
1984       }
1985
1986       int alwidth = 0;
1987       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1988       int fgroup = -1;
1989
1990       if (newAlignment)
1991       {
1992
1993         if (Desktop.jalviewClipboard != null)
1994         {
1995           // dataset is inherited
1996           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1997         }
1998         else
1999         {
2000           // new dataset is constructed
2001           alignment.setDataset(null);
2002         }
2003         alwidth = alignment.getWidth() + 1;
2004       }
2005       else
2006       {
2007         AlignmentI pastedal = alignment; // preserve pasted alignment object
2008         // Add pasted sequences and dataset into existing alignment.
2009         alignment = viewport.getAlignment();
2010         alwidth = alignment.getWidth() + 1;
2011         // decide if we need to import sequences from an existing dataset
2012         boolean importDs = Desktop.jalviewClipboard != null
2013                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2014         // importDs==true instructs us to copy over new dataset sequences from
2015         // an existing alignment
2016         Vector newDs = (importDs) ? new Vector() : null; // used to create
2017         // minimum dataset set
2018
2019         for (int i = 0; i < sequences.length; i++)
2020         {
2021           if (importDs)
2022           {
2023             newDs.addElement(null);
2024           }
2025           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2026           // paste
2027           if (importDs && ds != null)
2028           {
2029             if (!newDs.contains(ds))
2030             {
2031               newDs.setElementAt(ds, i);
2032               ds = new Sequence(ds);
2033               // update with new dataset sequence
2034               sequences[i].setDatasetSequence(ds);
2035             }
2036             else
2037             {
2038               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2039             }
2040           }
2041           else
2042           {
2043             // copy and derive new dataset sequence
2044             sequences[i] = sequences[i].deriveSequence();
2045             alignment.getDataset().addSequence(
2046                     sequences[i].getDatasetSequence());
2047             // TODO: avoid creation of duplicate dataset sequences with a
2048             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2049           }
2050           alignment.addSequence(sequences[i]); // merges dataset
2051         }
2052         if (newDs != null)
2053         {
2054           newDs.clear(); // tidy up
2055         }
2056         if (alignment.getAlignmentAnnotation() != null)
2057         {
2058           for (AlignmentAnnotation alan : alignment
2059                   .getAlignmentAnnotation())
2060           {
2061             if (alan.graphGroup > fgroup)
2062             {
2063               fgroup = alan.graphGroup;
2064             }
2065           }
2066         }
2067         if (pastedal.getAlignmentAnnotation() != null)
2068         {
2069           // Add any annotation attached to alignment.
2070           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2071           for (int i = 0; i < alann.length; i++)
2072           {
2073             annotationAdded = true;
2074             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2075             {
2076               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2077               if (newann.graphGroup > -1)
2078               {
2079                 if (newGraphGroups.size() <= newann.graphGroup
2080                         || newGraphGroups.get(newann.graphGroup) == null)
2081                 {
2082                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2083                   {
2084                     newGraphGroups.add(q, null);
2085                   }
2086                   newGraphGroups.set(newann.graphGroup, new Integer(
2087                           ++fgroup));
2088                 }
2089                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2090                         .intValue();
2091               }
2092
2093               newann.padAnnotation(alwidth);
2094               alignment.addAnnotation(newann);
2095             }
2096           }
2097         }
2098       }
2099       if (!newAlignment)
2100       {
2101         // /////
2102         // ADD HISTORY ITEM
2103         //
2104         addHistoryItem(new EditCommand(
2105                 MessageManager.getString("label.add_sequences"),
2106                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2107       }
2108       // Add any annotations attached to sequences
2109       for (int i = 0; i < sequences.length; i++)
2110       {
2111         if (sequences[i].getAnnotation() != null)
2112         {
2113           AlignmentAnnotation newann;
2114           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2115           {
2116             annotationAdded = true;
2117             newann = sequences[i].getAnnotation()[a];
2118             newann.adjustForAlignment();
2119             newann.padAnnotation(alwidth);
2120             if (newann.graphGroup > -1)
2121             {
2122               if (newann.graphGroup > -1)
2123               {
2124                 if (newGraphGroups.size() <= newann.graphGroup
2125                         || newGraphGroups.get(newann.graphGroup) == null)
2126                 {
2127                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2128                   {
2129                     newGraphGroups.add(q, null);
2130                   }
2131                   newGraphGroups.set(newann.graphGroup, new Integer(
2132                           ++fgroup));
2133                 }
2134                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2135                         .intValue();
2136               }
2137             }
2138             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2139             // was
2140             // duplicated
2141             // earlier
2142             alignment
2143                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2144           }
2145         }
2146       }
2147       if (!newAlignment)
2148       {
2149
2150         // propagate alignment changed.
2151         viewport.setEndSeq(alignment.getHeight());
2152         if (annotationAdded)
2153         {
2154           // Duplicate sequence annotation in all views.
2155           AlignmentI[] alview = this.getViewAlignments();
2156           for (int i = 0; i < sequences.length; i++)
2157           {
2158             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2159             if (sann == null)
2160             {
2161               continue;
2162             }
2163             for (int avnum = 0; avnum < alview.length; avnum++)
2164             {
2165               if (alview[avnum] != alignment)
2166               {
2167                 // duplicate in a view other than the one with input focus
2168                 int avwidth = alview[avnum].getWidth() + 1;
2169                 // this relies on sann being preserved after we
2170                 // modify the sequence's annotation array for each duplication
2171                 for (int a = 0; a < sann.length; a++)
2172                 {
2173                   AlignmentAnnotation newann = new AlignmentAnnotation(
2174                           sann[a]);
2175                   sequences[i].addAlignmentAnnotation(newann);
2176                   newann.padAnnotation(avwidth);
2177                   alview[avnum].addAnnotation(newann); // annotation was
2178                   // duplicated earlier
2179                   // TODO JAL-1145 graphGroups are not updated for sequence
2180                   // annotation added to several views. This may cause
2181                   // strangeness
2182                   alview[avnum].setAnnotationIndex(newann, a);
2183                 }
2184               }
2185             }
2186           }
2187           buildSortByAnnotationScoresMenu();
2188         }
2189         viewport.firePropertyChange("alignment", null,
2190                 alignment.getSequences());
2191         if (alignPanels != null)
2192         {
2193           for (AlignmentPanel ap : alignPanels)
2194           {
2195             ap.validateAnnotationDimensions(false);
2196           }
2197         }
2198         else
2199         {
2200           alignPanel.validateAnnotationDimensions(false);
2201         }
2202
2203       }
2204       else
2205       {
2206         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2207                 DEFAULT_HEIGHT);
2208         String newtitle = new String("Copied sequences");
2209
2210         if (Desktop.jalviewClipboard != null
2211                 && Desktop.jalviewClipboard[2] != null)
2212         {
2213           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2214           for (int[] region : hc)
2215           {
2216             af.viewport.hideColumns(region[0], region[1]);
2217           }
2218         }
2219
2220         // >>>This is a fix for the moment, until a better solution is
2221         // found!!<<<
2222         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2223                 .transferSettings(
2224                         alignPanel.getSeqPanel().seqCanvas
2225                                 .getFeatureRenderer());
2226
2227         // TODO: maintain provenance of an alignment, rather than just make the
2228         // title a concatenation of operations.
2229         if (!externalPaste)
2230         {
2231           if (title.startsWith("Copied sequences"))
2232           {
2233             newtitle = title;
2234           }
2235           else
2236           {
2237             newtitle = newtitle.concat("- from " + title);
2238           }
2239         }
2240         else
2241         {
2242           newtitle = new String("Pasted sequences");
2243         }
2244
2245         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2246                 DEFAULT_HEIGHT);
2247
2248       }
2249
2250     } catch (Exception ex)
2251     {
2252       ex.printStackTrace();
2253       System.out.println("Exception whilst pasting: " + ex);
2254       // could be anything being pasted in here
2255     }
2256
2257   }
2258
2259   @Override
2260   protected void expand_newalign(ActionEvent e)
2261   {
2262     try
2263     {
2264       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2265               .getAlignment(), -1);
2266       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2267               DEFAULT_HEIGHT);
2268       String newtitle = new String("Flanking alignment");
2269
2270       if (Desktop.jalviewClipboard != null
2271               && Desktop.jalviewClipboard[2] != null)
2272       {
2273         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2274         for (int region[] : hc)
2275         {
2276           af.viewport.hideColumns(region[0], region[1]);
2277         }
2278       }
2279
2280       // >>>This is a fix for the moment, until a better solution is
2281       // found!!<<<
2282       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2283               .transferSettings(
2284                       alignPanel.getSeqPanel().seqCanvas
2285                               .getFeatureRenderer());
2286
2287       // TODO: maintain provenance of an alignment, rather than just make the
2288       // title a concatenation of operations.
2289       {
2290         if (title.startsWith("Copied sequences"))
2291         {
2292           newtitle = title;
2293         }
2294         else
2295         {
2296           newtitle = newtitle.concat("- from " + title);
2297         }
2298       }
2299
2300       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2301
2302     } catch (Exception ex)
2303     {
2304       ex.printStackTrace();
2305       System.out.println("Exception whilst pasting: " + ex);
2306       // could be anything being pasted in here
2307     } catch (OutOfMemoryError oom)
2308     {
2309       new OOMWarning("Viewing flanking region of alignment", oom);
2310     }
2311   }
2312
2313   /**
2314    * DOCUMENT ME!
2315    *
2316    * @param e
2317    *          DOCUMENT ME!
2318    */
2319   @Override
2320   protected void cut_actionPerformed(ActionEvent e)
2321   {
2322     copy_actionPerformed(null);
2323     delete_actionPerformed(null);
2324   }
2325
2326   /**
2327    * DOCUMENT ME!
2328    *
2329    * @param e
2330    *          DOCUMENT ME!
2331    */
2332   @Override
2333   protected void delete_actionPerformed(ActionEvent evt)
2334   {
2335
2336     SequenceGroup sg = viewport.getSelectionGroup();
2337     if (sg == null)
2338     {
2339       return;
2340     }
2341
2342     /*
2343      * If the cut affects all sequences, warn, remove highlighted columns
2344      */
2345     if (sg.getSize() == viewport.getAlignment().getHeight())
2346     {
2347       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2348               .getAlignment().getWidth()) ? true : false;
2349       if (isEntireAlignWidth)
2350       {
2351         int confirm = JvOptionPane.showConfirmDialog(this,
2352                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2353                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2354                 JvOptionPane.OK_CANCEL_OPTION);
2355
2356         if (confirm == JvOptionPane.CANCEL_OPTION
2357                 || confirm == JvOptionPane.CLOSED_OPTION)
2358         {
2359           return;
2360         }
2361       }
2362       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2363               sg.getEndRes() + 1);
2364     }
2365     SequenceI[] cut = sg.getSequences()
2366             .toArray(new SequenceI[sg.getSize()]);
2367
2368     addHistoryItem(new EditCommand(
2369             MessageManager.getString("label.cut_sequences"), Action.CUT,
2370             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2371             viewport.getAlignment()));
2372
2373     viewport.setSelectionGroup(null);
2374     viewport.sendSelection();
2375     viewport.getAlignment().deleteGroup(sg);
2376
2377     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2378             .getSequences());
2379     if (viewport.getAlignment().getHeight() < 1)
2380     {
2381       try
2382       {
2383         this.setClosed(true);
2384       } catch (Exception ex)
2385       {
2386       }
2387     }
2388   }
2389
2390   /**
2391    * DOCUMENT ME!
2392    *
2393    * @param e
2394    *          DOCUMENT ME!
2395    */
2396   @Override
2397   protected void deleteGroups_actionPerformed(ActionEvent e)
2398   {
2399     if (avc.deleteGroups())
2400     {
2401       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2402       alignPanel.updateAnnotation();
2403       alignPanel.paintAlignment(true);
2404     }
2405   }
2406
2407   /**
2408    * DOCUMENT ME!
2409    *
2410    * @param e
2411    *          DOCUMENT ME!
2412    */
2413   @Override
2414   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2415   {
2416     SequenceGroup sg = new SequenceGroup();
2417
2418     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2419     {
2420       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2421     }
2422
2423     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2424     viewport.setSelectionGroup(sg);
2425     viewport.sendSelection();
2426     // JAL-2034 - should delegate to
2427     // alignPanel to decide if overview needs
2428     // updating.
2429     alignPanel.paintAlignment(false);
2430     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2431   }
2432
2433   /**
2434    * DOCUMENT ME!
2435    *
2436    * @param e
2437    *          DOCUMENT ME!
2438    */
2439   @Override
2440   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441   {
2442     if (viewport.cursorMode)
2443     {
2444       alignPanel.getSeqPanel().keyboardNo1 = null;
2445       alignPanel.getSeqPanel().keyboardNo2 = null;
2446     }
2447     viewport.setSelectionGroup(null);
2448     viewport.getColumnSelection().clear();
2449     viewport.setSelectionGroup(null);
2450     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2451     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2452     // JAL-2034 - should delegate to
2453     // alignPanel to decide if overview needs
2454     // updating.
2455     alignPanel.paintAlignment(false);
2456     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2457     viewport.sendSelection();
2458   }
2459
2460   /**
2461    * DOCUMENT ME!
2462    *
2463    * @param e
2464    *          DOCUMENT ME!
2465    */
2466   @Override
2467   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2468   {
2469     SequenceGroup sg = viewport.getSelectionGroup();
2470
2471     if (sg == null)
2472     {
2473       selectAllSequenceMenuItem_actionPerformed(null);
2474
2475       return;
2476     }
2477
2478     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2479     {
2480       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2481     }
2482     // JAL-2034 - should delegate to
2483     // alignPanel to decide if overview needs
2484     // updating.
2485
2486     alignPanel.paintAlignment(true);
2487     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2488     viewport.sendSelection();
2489   }
2490
2491   @Override
2492   public void invertColSel_actionPerformed(ActionEvent e)
2493   {
2494     viewport.invertColumnSelection();
2495     alignPanel.paintAlignment(true);
2496     viewport.sendSelection();
2497   }
2498
2499   /**
2500    * DOCUMENT ME!
2501    *
2502    * @param e
2503    *          DOCUMENT ME!
2504    */
2505   @Override
2506   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2507   {
2508     trimAlignment(true);
2509   }
2510
2511   /**
2512    * DOCUMENT ME!
2513    *
2514    * @param e
2515    *          DOCUMENT ME!
2516    */
2517   @Override
2518   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2519   {
2520     trimAlignment(false);
2521   }
2522
2523   void trimAlignment(boolean trimLeft)
2524   {
2525     ColumnSelection colSel = viewport.getColumnSelection();
2526     int column;
2527
2528     if (!colSel.isEmpty())
2529     {
2530       if (trimLeft)
2531       {
2532         column = colSel.getMin();
2533       }
2534       else
2535       {
2536         column = colSel.getMax();
2537       }
2538
2539       SequenceI[] seqs;
2540       if (viewport.getSelectionGroup() != null)
2541       {
2542         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2543                 viewport.getHiddenRepSequences());
2544       }
2545       else
2546       {
2547         seqs = viewport.getAlignment().getSequencesArray();
2548       }
2549
2550       TrimRegionCommand trimRegion;
2551       if (trimLeft)
2552       {
2553         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2554                 column, viewport.getAlignment());
2555         viewport.setStartRes(0);
2556       }
2557       else
2558       {
2559         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2560                 column, viewport.getAlignment());
2561       }
2562
2563       statusBar.setText(MessageManager.formatMessage(
2564               "label.removed_columns",
2565               new String[] { Integer.valueOf(trimRegion.getSize())
2566                       .toString() }));
2567
2568       addHistoryItem(trimRegion);
2569
2570       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2571       {
2572         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2573                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2574         {
2575           viewport.getAlignment().deleteGroup(sg);
2576         }
2577       }
2578
2579       viewport.firePropertyChange("alignment", null, viewport
2580               .getAlignment().getSequences());
2581     }
2582   }
2583
2584   /**
2585    * DOCUMENT ME!
2586    *
2587    * @param e
2588    *          DOCUMENT ME!
2589    */
2590   @Override
2591   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2592   {
2593     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2594
2595     SequenceI[] seqs;
2596     if (viewport.getSelectionGroup() != null)
2597     {
2598       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2599               viewport.getHiddenRepSequences());
2600       start = viewport.getSelectionGroup().getStartRes();
2601       end = viewport.getSelectionGroup().getEndRes();
2602     }
2603     else
2604     {
2605       seqs = viewport.getAlignment().getSequencesArray();
2606     }
2607
2608     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2609             "Remove Gapped Columns", seqs, start, end,
2610             viewport.getAlignment());
2611
2612     addHistoryItem(removeGapCols);
2613
2614     statusBar.setText(MessageManager.formatMessage(
2615             "label.removed_empty_columns",
2616             new Object[] { Integer.valueOf(removeGapCols.getSize())
2617                     .toString() }));
2618
2619     // This is to maintain viewport position on first residue
2620     // of first sequence
2621     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2622     int startRes = seq.findPosition(viewport.startRes);
2623     // ShiftList shifts;
2624     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2625     // edit.alColumnChanges=shifts.getInverse();
2626     // if (viewport.hasHiddenColumns)
2627     // viewport.getColumnSelection().compensateForEdits(shifts);
2628     viewport.setStartRes(seq.findIndex(startRes) - 1);
2629     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2630             .getSequences());
2631
2632   }
2633
2634   /**
2635    * DOCUMENT ME!
2636    *
2637    * @param e
2638    *          DOCUMENT ME!
2639    */
2640   @Override
2641   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2642   {
2643     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2644
2645     SequenceI[] seqs;
2646     if (viewport.getSelectionGroup() != null)
2647     {
2648       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2649               viewport.getHiddenRepSequences());
2650       start = viewport.getSelectionGroup().getStartRes();
2651       end = viewport.getSelectionGroup().getEndRes();
2652     }
2653     else
2654     {
2655       seqs = viewport.getAlignment().getSequencesArray();
2656     }
2657
2658     // This is to maintain viewport position on first residue
2659     // of first sequence
2660     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2661     int startRes = seq.findPosition(viewport.startRes);
2662
2663     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2664             viewport.getAlignment()));
2665
2666     viewport.setStartRes(seq.findIndex(startRes) - 1);
2667
2668     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2669             .getSequences());
2670
2671   }
2672
2673   /**
2674    * DOCUMENT ME!
2675    *
2676    * @param e
2677    *          DOCUMENT ME!
2678    */
2679   @Override
2680   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2681   {
2682     viewport.setPadGaps(padGapsMenuitem.isSelected());
2683     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2684             .getSequences());
2685   }
2686
2687   /**
2688    * DOCUMENT ME!
2689    *
2690    * @param e
2691    *          DOCUMENT ME!
2692    */
2693   @Override
2694   public void findMenuItem_actionPerformed(ActionEvent e)
2695   {
2696     new Finder();
2697   }
2698
2699   /**
2700    * Create a new view of the current alignment.
2701    */
2702   @Override
2703   public void newView_actionPerformed(ActionEvent e)
2704   {
2705     newView(null, true);
2706   }
2707
2708   /**
2709    * Creates and shows a new view of the current alignment.
2710    *
2711    * @param viewTitle
2712    *          title of newly created view; if null, one will be generated
2713    * @param copyAnnotation
2714    *          if true then duplicate all annnotation, groups and settings
2715    * @return new alignment panel, already displayed.
2716    */
2717   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2718   {
2719     /*
2720      * Create a new AlignmentPanel (with its own, new Viewport)
2721      */
2722     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2723             true);
2724     if (!copyAnnotation)
2725     {
2726       /*
2727        * remove all groups and annotation except for the automatic stuff
2728        */
2729       newap.av.getAlignment().deleteAllGroups();
2730       newap.av.getAlignment().deleteAllAnnotations(false);
2731     }
2732
2733     newap.av.setGatherViewsHere(false);
2734
2735     if (viewport.viewName == null)
2736     {
2737       viewport.viewName = MessageManager
2738               .getString("label.view_name_original");
2739     }
2740
2741     /*
2742      * Views share the same edits undo and redo stacks
2743      */
2744     newap.av.setHistoryList(viewport.getHistoryList());
2745     newap.av.setRedoList(viewport.getRedoList());
2746
2747     /*
2748      * Views share the same mappings; need to deregister any new mappings
2749      * created by copyAlignPanel, and register the new reference to the shared
2750      * mappings
2751      */
2752     newap.av.replaceMappings(viewport.getAlignment());
2753
2754     newap.av.viewName = getNewViewName(viewTitle);
2755
2756     addAlignmentPanel(newap, true);
2757     newap.alignmentChanged();
2758
2759     if (alignPanels.size() == 2)
2760     {
2761       viewport.setGatherViewsHere(true);
2762     }
2763     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2764     return newap;
2765   }
2766
2767   /**
2768    * Make a new name for the view, ensuring it is unique within the current
2769    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2770    * these now use viewId. Unique view names are still desirable for usability.)
2771    *
2772    * @param viewTitle
2773    * @return
2774    */
2775   protected String getNewViewName(String viewTitle)
2776   {
2777     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2778     boolean addFirstIndex = false;
2779     if (viewTitle == null || viewTitle.trim().length() == 0)
2780     {
2781       viewTitle = MessageManager.getString("action.view");
2782       addFirstIndex = true;
2783     }
2784     else
2785     {
2786       index = 1;// we count from 1 if given a specific name
2787     }
2788     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2789
2790     List<Component> comps = PaintRefresher.components.get(viewport
2791             .getSequenceSetId());
2792
2793     List<String> existingNames = getExistingViewNames(comps);
2794
2795     while (existingNames.contains(newViewName))
2796     {
2797       newViewName = viewTitle + " " + (++index);
2798     }
2799     return newViewName;
2800   }
2801
2802   /**
2803    * Returns a list of distinct view names found in the given list of
2804    * components. View names are held on the viewport of an AlignmentPanel.
2805    *
2806    * @param comps
2807    * @return
2808    */
2809   protected List<String> getExistingViewNames(List<Component> comps)
2810   {
2811     List<String> existingNames = new ArrayList<String>();
2812     for (Component comp : comps)
2813     {
2814       if (comp instanceof AlignmentPanel)
2815       {
2816         AlignmentPanel ap = (AlignmentPanel) comp;
2817         if (!existingNames.contains(ap.av.viewName))
2818         {
2819           existingNames.add(ap.av.viewName);
2820         }
2821       }
2822     }
2823     return existingNames;
2824   }
2825
2826   /**
2827    * Explode tabbed views into separate windows.
2828    */
2829   @Override
2830   public void expandViews_actionPerformed(ActionEvent e)
2831   {
2832     Desktop.explodeViews(this);
2833   }
2834
2835   /**
2836    * Gather views in separate windows back into a tabbed presentation.
2837    */
2838   @Override
2839   public void gatherViews_actionPerformed(ActionEvent e)
2840   {
2841     Desktop.instance.gatherViews(this);
2842   }
2843
2844   /**
2845    * DOCUMENT ME!
2846    *
2847    * @param e
2848    *          DOCUMENT ME!
2849    */
2850   @Override
2851   public void font_actionPerformed(ActionEvent e)
2852   {
2853     new FontChooser(alignPanel);
2854   }
2855
2856   /**
2857    * DOCUMENT ME!
2858    *
2859    * @param e
2860    *          DOCUMENT ME!
2861    */
2862   @Override
2863   protected void seqLimit_actionPerformed(ActionEvent e)
2864   {
2865     viewport.setShowJVSuffix(seqLimits.isSelected());
2866
2867     alignPanel.getIdPanel().getIdCanvas()
2868             .setPreferredSize(alignPanel.calculateIdWidth());
2869     alignPanel.paintAlignment(true);
2870   }
2871
2872   @Override
2873   public void idRightAlign_actionPerformed(ActionEvent e)
2874   {
2875     viewport.setRightAlignIds(idRightAlign.isSelected());
2876     alignPanel.paintAlignment(true);
2877   }
2878
2879   @Override
2880   public void centreColumnLabels_actionPerformed(ActionEvent e)
2881   {
2882     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2883     alignPanel.paintAlignment(true);
2884   }
2885
2886   /*
2887    * (non-Javadoc)
2888    *
2889    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2890    */
2891   @Override
2892   protected void followHighlight_actionPerformed()
2893   {
2894     /*
2895      * Set the 'follow' flag on the Viewport (and scroll to position if now
2896      * true).
2897      */
2898     final boolean state = this.followHighlightMenuItem.getState();
2899     viewport.setFollowHighlight(state);
2900     if (state)
2901     {
2902       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2903     }
2904   }
2905
2906   /**
2907    * DOCUMENT ME!
2908    *
2909    * @param e
2910    *          DOCUMENT ME!
2911    */
2912   @Override
2913   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2914   {
2915     viewport.setColourText(colourTextMenuItem.isSelected());
2916     alignPanel.paintAlignment(true);
2917   }
2918
2919   /**
2920    * DOCUMENT ME!
2921    *
2922    * @param e
2923    *          DOCUMENT ME!
2924    */
2925   @Override
2926   public void wrapMenuItem_actionPerformed(ActionEvent e)
2927   {
2928     scaleAbove.setVisible(wrapMenuItem.isSelected());
2929     scaleLeft.setVisible(wrapMenuItem.isSelected());
2930     scaleRight.setVisible(wrapMenuItem.isSelected());
2931     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2932     alignPanel.updateLayout();
2933   }
2934
2935   @Override
2936   public void showAllSeqs_actionPerformed(ActionEvent e)
2937   {
2938     viewport.showAllHiddenSeqs();
2939   }
2940
2941   @Override
2942   public void showAllColumns_actionPerformed(ActionEvent e)
2943   {
2944     viewport.showAllHiddenColumns();
2945     repaint();
2946     viewport.sendSelection();
2947   }
2948
2949   @Override
2950   public void hideSelSequences_actionPerformed(ActionEvent e)
2951   {
2952     viewport.hideAllSelectedSeqs();
2953     // alignPanel.paintAlignment(true);
2954   }
2955
2956   /**
2957    * called by key handler and the hide all/show all menu items
2958    *
2959    * @param toggleSeqs
2960    * @param toggleCols
2961    */
2962   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2963   {
2964
2965     boolean hide = false;
2966     SequenceGroup sg = viewport.getSelectionGroup();
2967     if (!toggleSeqs && !toggleCols)
2968     {
2969       // Hide everything by the current selection - this is a hack - we do the
2970       // invert and then hide
2971       // first check that there will be visible columns after the invert.
2972       if (viewport.hasSelectedColumns()
2973               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2974                       .getEndRes()))
2975       {
2976         // now invert the sequence set, if required - empty selection implies
2977         // that no hiding is required.
2978         if (sg != null)
2979         {
2980           invertSequenceMenuItem_actionPerformed(null);
2981           sg = viewport.getSelectionGroup();
2982           toggleSeqs = true;
2983
2984         }
2985         viewport.expandColSelection(sg, true);
2986         // finally invert the column selection and get the new sequence
2987         // selection.
2988         invertColSel_actionPerformed(null);
2989         toggleCols = true;
2990       }
2991     }
2992
2993     if (toggleSeqs)
2994     {
2995       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2996       {
2997         hideSelSequences_actionPerformed(null);
2998         hide = true;
2999       }
3000       else if (!(toggleCols && viewport.hasSelectedColumns()))
3001       {
3002         showAllSeqs_actionPerformed(null);
3003       }
3004     }
3005
3006     if (toggleCols)
3007     {
3008       if (viewport.hasSelectedColumns())
3009       {
3010         hideSelColumns_actionPerformed(null);
3011         if (!toggleSeqs)
3012         {
3013           viewport.setSelectionGroup(sg);
3014         }
3015       }
3016       else if (!hide)
3017       {
3018         showAllColumns_actionPerformed(null);
3019       }
3020     }
3021   }
3022
3023   /*
3024    * (non-Javadoc)
3025    *
3026    * @see
3027    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3028    * event.ActionEvent)
3029    */
3030   @Override
3031   public void hideAllButSelection_actionPerformed(ActionEvent e)
3032   {
3033     toggleHiddenRegions(false, false);
3034     viewport.sendSelection();
3035   }
3036
3037   /*
3038    * (non-Javadoc)
3039    *
3040    * @see
3041    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3042    * .ActionEvent)
3043    */
3044   @Override
3045   public void hideAllSelection_actionPerformed(ActionEvent e)
3046   {
3047     SequenceGroup sg = viewport.getSelectionGroup();
3048     viewport.expandColSelection(sg, false);
3049     viewport.hideAllSelectedSeqs();
3050     viewport.hideSelectedColumns();
3051     alignPanel.paintAlignment(true);
3052     viewport.sendSelection();
3053   }
3054
3055   /*
3056    * (non-Javadoc)
3057    *
3058    * @see
3059    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3060    * ActionEvent)
3061    */
3062   @Override
3063   public void showAllhidden_actionPerformed(ActionEvent e)
3064   {
3065     viewport.showAllHiddenColumns();
3066     viewport.showAllHiddenSeqs();
3067     alignPanel.paintAlignment(true);
3068     viewport.sendSelection();
3069   }
3070
3071   @Override
3072   public void hideSelColumns_actionPerformed(ActionEvent e)
3073   {
3074     viewport.hideSelectedColumns();
3075     alignPanel.paintAlignment(true);
3076     viewport.sendSelection();
3077   }
3078
3079   @Override
3080   public void hiddenMarkers_actionPerformed(ActionEvent e)
3081   {
3082     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3083     repaint();
3084   }
3085
3086   /**
3087    * DOCUMENT ME!
3088    *
3089    * @param e
3090    *          DOCUMENT ME!
3091    */
3092   @Override
3093   protected void scaleAbove_actionPerformed(ActionEvent e)
3094   {
3095     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3096     alignPanel.paintAlignment(true);
3097   }
3098
3099   /**
3100    * DOCUMENT ME!
3101    *
3102    * @param e
3103    *          DOCUMENT ME!
3104    */
3105   @Override
3106   protected void scaleLeft_actionPerformed(ActionEvent e)
3107   {
3108     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3109     alignPanel.paintAlignment(true);
3110   }
3111
3112   /**
3113    * DOCUMENT ME!
3114    *
3115    * @param e
3116    *          DOCUMENT ME!
3117    */
3118   @Override
3119   protected void scaleRight_actionPerformed(ActionEvent e)
3120   {
3121     viewport.setScaleRightWrapped(scaleRight.isSelected());
3122     alignPanel.paintAlignment(true);
3123   }
3124
3125   /**
3126    * DOCUMENT ME!
3127    *
3128    * @param e
3129    *          DOCUMENT ME!
3130    */
3131   @Override
3132   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3133   {
3134     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3135     alignPanel.paintAlignment(true);
3136   }
3137
3138   /**
3139    * DOCUMENT ME!
3140    *
3141    * @param e
3142    *          DOCUMENT ME!
3143    */
3144   @Override
3145   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3146   {
3147     viewport.setShowText(viewTextMenuItem.isSelected());
3148     alignPanel.paintAlignment(true);
3149   }
3150
3151   /**
3152    * DOCUMENT ME!
3153    *
3154    * @param e
3155    *          DOCUMENT ME!
3156    */
3157   @Override
3158   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3159   {
3160     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3161     alignPanel.paintAlignment(true);
3162   }
3163
3164   public FeatureSettings featureSettings;
3165
3166   @Override
3167   public FeatureSettingsControllerI getFeatureSettingsUI()
3168   {
3169     return featureSettings;
3170   }
3171
3172   @Override
3173   public void featureSettings_actionPerformed(ActionEvent e)
3174   {
3175     if (featureSettings != null)
3176     {
3177       featureSettings.close();
3178       featureSettings = null;
3179     }
3180     if (!showSeqFeatures.isSelected())
3181     {
3182       // make sure features are actually displayed
3183       showSeqFeatures.setSelected(true);
3184       showSeqFeatures_actionPerformed(null);
3185     }
3186     featureSettings = new FeatureSettings(this);
3187   }
3188
3189   /**
3190    * Set or clear 'Show Sequence Features'
3191    *
3192    * @param evt
3193    *          DOCUMENT ME!
3194    */
3195   @Override
3196   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3197   {
3198     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3199     alignPanel.paintAlignment(true);
3200     if (alignPanel.getOverviewPanel() != null)
3201     {
3202       alignPanel.getOverviewPanel().updateOverviewImage();
3203     }
3204   }
3205
3206   /**
3207    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3208    * the annotations panel as a whole.
3209    *
3210    * The options to show/hide all annotations should be enabled when the panel
3211    * is shown, and disabled when the panel is hidden.
3212    *
3213    * @param e
3214    */
3215   @Override
3216   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3217   {
3218     final boolean setVisible = annotationPanelMenuItem.isSelected();
3219     viewport.setShowAnnotation(setVisible);
3220     this.showAllSeqAnnotations.setEnabled(setVisible);
3221     this.hideAllSeqAnnotations.setEnabled(setVisible);
3222     this.showAllAlAnnotations.setEnabled(setVisible);
3223     this.hideAllAlAnnotations.setEnabled(setVisible);
3224     alignPanel.updateLayout();
3225   }
3226
3227   @Override
3228   public void alignmentProperties()
3229   {
3230     JEditorPane editPane = new JEditorPane("text/html", "");
3231     editPane.setEditable(false);
3232     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3233             .formatAsHtml();
3234     editPane.setText(MessageManager.formatMessage("label.html_content",
3235             new Object[] { contents.toString() }));
3236     JInternalFrame frame = new JInternalFrame();
3237     frame.getContentPane().add(new JScrollPane(editPane));
3238
3239     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3240             "label.alignment_properties", new Object[] { getTitle() }),
3241             500, 400);
3242   }
3243
3244   /**
3245    * DOCUMENT ME!
3246    *
3247    * @param e
3248    *          DOCUMENT ME!
3249    */
3250   @Override
3251   public void overviewMenuItem_actionPerformed(ActionEvent e)
3252   {
3253     if (alignPanel.overviewPanel != null)
3254     {
3255       return;
3256     }
3257
3258     JInternalFrame frame = new JInternalFrame();
3259     OverviewPanel overview = new OverviewPanel(alignPanel);
3260     frame.setContentPane(overview);
3261     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3262             "label.overview_params", new Object[] { this.getTitle() }),
3263             frame.getWidth(), frame.getHeight());
3264     frame.pack();
3265     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3266     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3267     {
3268       @Override
3269       public void internalFrameClosed(
3270               javax.swing.event.InternalFrameEvent evt)
3271       {
3272         alignPanel.setOverviewPanel(null);
3273       };
3274     });
3275
3276     alignPanel.setOverviewPanel(overview);
3277   }
3278
3279   @Override
3280   public void textColour_actionPerformed()
3281   {
3282     new TextColourChooser().chooseColour(alignPanel, null);
3283   }
3284
3285   /*
3286    * public void covariationColour_actionPerformed() {
3287    * changeColour(new
3288    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3289    * ()[0])); }
3290    */
3291   @Override
3292   public void annotationColour_actionPerformed()
3293   {
3294     new AnnotationColourChooser(viewport, alignPanel);
3295   }
3296
3297   @Override
3298   public void annotationColumn_actionPerformed(ActionEvent e)
3299   {
3300     new AnnotationColumnChooser(viewport, alignPanel);
3301   }
3302
3303   /**
3304    * Action on the user checking or unchecking the option to apply the selected
3305    * colour scheme to all groups. If unchecked, groups may have their own
3306    * independent colour schemes.
3307    *
3308    * @param selected
3309    */
3310   @Override
3311   public void applyToAllGroups_actionPerformed(boolean selected)
3312   {
3313     viewport.setColourAppliesToAllGroups(selected);
3314   }
3315
3316   /**
3317    * Action on user selecting a colour from the colour menu
3318    *
3319    * @param name
3320    *          the name (not the menu item label!) of the colour scheme
3321    */
3322   @Override
3323   public void changeColour_actionPerformed(String name)
3324   {
3325     /*
3326      * 'User Defined' opens a panel to configure or load a
3327      * user-defined colour scheme
3328      */
3329     if (ResidueColourScheme.USER_DEFINED.equals(name))
3330     {
3331       new UserDefinedColours(alignPanel, null);
3332       return;
3333     }
3334
3335     /*
3336      * otherwise set the chosen colour scheme (or null for 'None')
3337      */
3338     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3339             viewport.getAlignment(), viewport.getHiddenRepSequences());
3340     changeColour(cs);
3341   }
3342
3343   /**
3344    * Actions on setting or changing the alignment colour scheme
3345    *
3346    * @param cs
3347    */
3348   @Override
3349   public void changeColour(ColourSchemeI cs)
3350   {
3351     // TODO: pull up to controller method
3352     if (cs != null)
3353     {
3354       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3355     }
3356
3357     viewport.setGlobalColourScheme(cs);
3358
3359     alignPanel.paintAlignment(true);
3360   }
3361
3362   /**
3363    * Show the PID threshold slider panel
3364    */
3365   @Override
3366   protected void modifyPID_actionPerformed()
3367   {
3368     SliderPanel.setPIDSliderSource(alignPanel,
3369             viewport.getResidueShading(), alignPanel.getViewName());
3370     SliderPanel.showPIDSlider();
3371   }
3372
3373   /**
3374    * Show the Conservation slider panel
3375    */
3376   @Override
3377   protected void modifyConservation_actionPerformed()
3378   {
3379     SliderPanel.setConservationSlider(alignPanel,
3380             viewport.getResidueShading(), alignPanel.getViewName());
3381     SliderPanel.showConservationSlider();
3382   }
3383
3384   /**
3385    * Action on selecting or deselecting (Colour) By Conservation
3386    */
3387   @Override
3388   public void conservationMenuItem_actionPerformed(boolean selected)
3389   {
3390     modifyConservation.setEnabled(selected);
3391     viewport.setConservationSelected(selected);
3392     viewport.getResidueShading().setConservationApplied(selected);
3393
3394     changeColour(viewport.getGlobalColourScheme());
3395     if (selected)
3396     {
3397       modifyConservation_actionPerformed();
3398     }
3399     else
3400     {
3401       SliderPanel.hideConservationSlider();
3402     }
3403   }
3404
3405   /**
3406    * Action on selecting or deselecting (Colour) Above PID Threshold
3407    */
3408   @Override
3409   public void abovePIDThreshold_actionPerformed(boolean selected)
3410   {
3411     modifyPID.setEnabled(selected);
3412     viewport.setAbovePIDThreshold(selected);
3413     if (!selected)
3414     {
3415       viewport.getResidueShading().setThreshold(0,
3416               viewport.isIgnoreGapsConsensus());
3417     }
3418
3419     changeColour(viewport.getGlobalColourScheme());
3420     if (selected)
3421     {
3422       modifyPID_actionPerformed();
3423     }
3424     else
3425     {
3426       SliderPanel.hidePIDSlider();
3427     }
3428   }
3429
3430   /**
3431    * DOCUMENT ME!
3432    *
3433    * @param e
3434    *          DOCUMENT ME!
3435    */
3436   @Override
3437   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3438   {
3439     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3440     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3441             .getAlignment().getSequenceAt(0), null);
3442     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3443             viewport.getAlignment()));
3444     alignPanel.paintAlignment(true);
3445   }
3446
3447   /**
3448    * DOCUMENT ME!
3449    *
3450    * @param e
3451    *          DOCUMENT ME!
3452    */
3453   @Override
3454   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3455   {
3456     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3457     AlignmentSorter.sortByID(viewport.getAlignment());
3458     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3459             viewport.getAlignment()));
3460     alignPanel.paintAlignment(true);
3461   }
3462
3463   /**
3464    * DOCUMENT ME!
3465    *
3466    * @param e
3467    *          DOCUMENT ME!
3468    */
3469   @Override
3470   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3471   {
3472     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473     AlignmentSorter.sortByLength(viewport.getAlignment());
3474     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3475             viewport.getAlignment()));
3476     alignPanel.paintAlignment(true);
3477   }
3478
3479   /**
3480    * DOCUMENT ME!
3481    *
3482    * @param e
3483    *          DOCUMENT ME!
3484    */
3485   @Override
3486   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3487   {
3488     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489     AlignmentSorter.sortByGroup(viewport.getAlignment());
3490     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3491             viewport.getAlignment()));
3492
3493     alignPanel.paintAlignment(true);
3494   }
3495
3496   /**
3497    * DOCUMENT ME!
3498    *
3499    * @param e
3500    *          DOCUMENT ME!
3501    */
3502   @Override
3503   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3504   {
3505     new RedundancyPanel(alignPanel, this);
3506   }
3507
3508   /**
3509    * DOCUMENT ME!
3510    *
3511    * @param e
3512    *          DOCUMENT ME!
3513    */
3514   @Override
3515   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3516   {
3517     if ((viewport.getSelectionGroup() == null)
3518             || (viewport.getSelectionGroup().getSize() < 2))
3519     {
3520       JvOptionPane.showInternalMessageDialog(this, MessageManager
3521               .getString("label.you_must_select_least_two_sequences"),
3522               MessageManager.getString("label.invalid_selection"),
3523               JvOptionPane.WARNING_MESSAGE);
3524     }
3525     else
3526     {
3527       JInternalFrame frame = new JInternalFrame();
3528       frame.setContentPane(new PairwiseAlignPanel(viewport));
3529       Desktop.addInternalFrame(frame,
3530               MessageManager.getString("action.pairwise_alignment"), 600,
3531               500);
3532     }
3533   }
3534
3535   /**
3536    * DOCUMENT ME!
3537    *
3538    * @param e
3539    *          DOCUMENT ME!
3540    */
3541   @Override
3542   public void PCAMenuItem_actionPerformed(ActionEvent e)
3543   {
3544     if (((viewport.getSelectionGroup() != null)
3545             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3546             .getSelectionGroup().getSize() > 0))
3547             || (viewport.getAlignment().getHeight() < 4))
3548     {
3549       JvOptionPane
3550               .showInternalMessageDialog(
3551                       this,
3552                       MessageManager
3553                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3554                       MessageManager
3555                               .getString("label.sequence_selection_insufficient"),
3556                       JvOptionPane.WARNING_MESSAGE);
3557
3558       return;
3559     }
3560
3561     new PCAPanel(alignPanel);
3562   }
3563
3564   @Override
3565   public void autoCalculate_actionPerformed(ActionEvent e)
3566   {
3567     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3568     if (viewport.autoCalculateConsensus)
3569     {
3570       viewport.firePropertyChange("alignment", null, viewport
3571               .getAlignment().getSequences());
3572     }
3573   }
3574
3575   @Override
3576   public void sortByTreeOption_actionPerformed(ActionEvent e)
3577   {
3578     viewport.sortByTree = sortByTree.isSelected();
3579   }
3580
3581   @Override
3582   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3583   {
3584     viewport.followSelection = listenToViewSelections.isSelected();
3585   }
3586
3587   /**
3588    * DOCUMENT ME!
3589    *
3590    * @param type
3591    *          DOCUMENT ME!
3592    * @param pwType
3593    *          DOCUMENT ME!
3594    * @param title
3595    *          DOCUMENT ME!
3596    */
3597   void newTreePanel(String type, String pwType, String title)
3598   {
3599     TreePanel tp;
3600
3601     if (viewport.getSelectionGroup() != null
3602             && viewport.getSelectionGroup().getSize() > 0)
3603     {
3604       if (viewport.getSelectionGroup().getSize() < 3)
3605       {
3606         JvOptionPane
3607                 .showMessageDialog(
3608                         Desktop.desktop,
3609                         MessageManager
3610                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3611                         MessageManager
3612                                 .getString("label.not_enough_sequences"),
3613                         JvOptionPane.WARNING_MESSAGE);
3614         return;
3615       }
3616
3617       SequenceGroup sg = viewport.getSelectionGroup();
3618
3619       /* Decide if the selection is a column region */
3620       for (SequenceI _s : sg.getSequences())
3621       {
3622         if (_s.getLength() < sg.getEndRes())
3623         {
3624           JvOptionPane
3625                   .showMessageDialog(
3626                           Desktop.desktop,
3627                           MessageManager
3628                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3629                           MessageManager
3630                                   .getString("label.sequences_selection_not_aligned"),
3631                           JvOptionPane.WARNING_MESSAGE);
3632
3633           return;
3634         }
3635       }
3636
3637       title = title + " on region";
3638       tp = new TreePanel(alignPanel, type, pwType);
3639     }
3640     else
3641     {
3642       // are the visible sequences aligned?
3643       if (!viewport.getAlignment().isAligned(false))
3644       {
3645         JvOptionPane
3646                 .showMessageDialog(
3647                         Desktop.desktop,
3648                         MessageManager
3649                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3650                         MessageManager
3651                                 .getString("label.sequences_not_aligned"),
3652                         JvOptionPane.WARNING_MESSAGE);
3653
3654         return;
3655       }
3656
3657       if (viewport.getAlignment().getHeight() < 2)
3658       {
3659         return;
3660       }
3661
3662       tp = new TreePanel(alignPanel, type, pwType);
3663     }
3664
3665     title += " from ";
3666
3667     if (viewport.viewName != null)
3668     {
3669       title += viewport.viewName + " of ";
3670     }
3671
3672     title += this.title;
3673
3674     Desktop.addInternalFrame(tp, title, 600, 500);
3675   }
3676
3677   /**
3678    * DOCUMENT ME!
3679    *
3680    * @param title
3681    *          DOCUMENT ME!
3682    * @param order
3683    *          DOCUMENT ME!
3684    */
3685   public void addSortByOrderMenuItem(String title,
3686           final AlignmentOrder order)
3687   {
3688     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3689             "action.by_title_param", new Object[] { title }));
3690     sort.add(item);
3691     item.addActionListener(new java.awt.event.ActionListener()
3692     {
3693       @Override
3694       public void actionPerformed(ActionEvent e)
3695       {
3696         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3697
3698         // TODO: JBPNote - have to map order entries to curent SequenceI
3699         // pointers
3700         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3701
3702         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3703                 .getAlignment()));
3704
3705         alignPanel.paintAlignment(true);
3706       }
3707     });
3708   }
3709
3710   /**
3711    * Add a new sort by annotation score menu item
3712    *
3713    * @param sort
3714    *          the menu to add the option to
3715    * @param scoreLabel
3716    *          the label used to retrieve scores for each sequence on the
3717    *          alignment
3718    */
3719   public void addSortByAnnotScoreMenuItem(JMenu sort,
3720           final String scoreLabel)
3721   {
3722     final JMenuItem item = new JMenuItem(scoreLabel);
3723     sort.add(item);
3724     item.addActionListener(new java.awt.event.ActionListener()
3725     {
3726       @Override
3727       public void actionPerformed(ActionEvent e)
3728       {
3729         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3730         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3731                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3732         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3733                 viewport.getAlignment()));
3734         alignPanel.paintAlignment(true);
3735       }
3736     });
3737   }
3738
3739   /**
3740    * last hash for alignment's annotation array - used to minimise cost of
3741    * rebuild.
3742    */
3743   protected int _annotationScoreVectorHash;
3744
3745   /**
3746    * search the alignment and rebuild the sort by annotation score submenu the
3747    * last alignment annotation vector hash is stored to minimize cost of
3748    * rebuilding in subsequence calls.
3749    *
3750    */
3751   @Override
3752   public void buildSortByAnnotationScoresMenu()
3753   {
3754     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3755     {
3756       return;
3757     }
3758
3759     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3760     {
3761       sortByAnnotScore.removeAll();
3762       // almost certainly a quicker way to do this - but we keep it simple
3763       Hashtable scoreSorts = new Hashtable();
3764       AlignmentAnnotation aann[];
3765       for (SequenceI sqa : viewport.getAlignment().getSequences())
3766       {
3767         aann = sqa.getAnnotation();
3768         for (int i = 0; aann != null && i < aann.length; i++)
3769         {
3770           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3771           {
3772             scoreSorts.put(aann[i].label, aann[i].label);
3773           }
3774         }
3775       }
3776       Enumeration labels = scoreSorts.keys();
3777       while (labels.hasMoreElements())
3778       {
3779         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3780                 (String) labels.nextElement());
3781       }
3782       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3783       scoreSorts.clear();
3784
3785       _annotationScoreVectorHash = viewport.getAlignment()
3786               .getAlignmentAnnotation().hashCode();
3787     }
3788   }
3789
3790   /**
3791    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3792    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3793    * call. Listeners are added to remove the menu item when the treePanel is
3794    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3795    * modified.
3796    */
3797   @Override
3798   public void buildTreeSortMenu()
3799   {
3800     sortByTreeMenu.removeAll();
3801
3802     List<Component> comps = PaintRefresher.components.get(viewport
3803             .getSequenceSetId());
3804     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3805     for (Component comp : comps)
3806     {
3807       if (comp instanceof TreePanel)
3808       {
3809         treePanels.add((TreePanel) comp);
3810       }
3811     }
3812
3813     if (treePanels.size() < 1)
3814     {
3815       sortByTreeMenu.setVisible(false);
3816       return;
3817     }
3818
3819     sortByTreeMenu.setVisible(true);
3820
3821     for (final TreePanel tp : treePanels)
3822     {
3823       final JMenuItem item = new JMenuItem(tp.getTitle());
3824       item.addActionListener(new java.awt.event.ActionListener()
3825       {
3826         @Override
3827         public void actionPerformed(ActionEvent e)
3828         {
3829           tp.sortByTree_actionPerformed();
3830           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3831
3832         }
3833       });
3834
3835       sortByTreeMenu.add(item);
3836     }
3837   }
3838
3839   public boolean sortBy(AlignmentOrder alorder, String undoname)
3840   {
3841     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3842     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3843     if (undoname != null)
3844     {
3845       addHistoryItem(new OrderCommand(undoname, oldOrder,
3846               viewport.getAlignment()));
3847     }
3848     alignPanel.paintAlignment(true);
3849     return true;
3850   }
3851
3852   /**
3853    * Work out whether the whole set of sequences or just the selected set will
3854    * be submitted for multiple alignment.
3855    *
3856    */
3857   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3858   {
3859     // Now, check we have enough sequences
3860     AlignmentView msa = null;
3861
3862     if ((viewport.getSelectionGroup() != null)
3863             && (viewport.getSelectionGroup().getSize() > 1))
3864     {
3865       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3866       // some common interface!
3867       /*
3868        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3869        * SequenceI[sz = seqs.getSize(false)];
3870        *
3871        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3872        * seqs.getSequenceAt(i); }
3873        */
3874       msa = viewport.getAlignmentView(true);
3875     }
3876     else if (viewport.getSelectionGroup() != null
3877             && viewport.getSelectionGroup().getSize() == 1)
3878     {
3879       int option = JvOptionPane.showConfirmDialog(this,
3880               MessageManager.getString("warn.oneseq_msainput_selection"),
3881               MessageManager.getString("label.invalid_selection"),
3882               JvOptionPane.OK_CANCEL_OPTION);
3883       if (option == JvOptionPane.OK_OPTION)
3884       {
3885         msa = viewport.getAlignmentView(false);
3886       }
3887     }
3888     else
3889     {
3890       msa = viewport.getAlignmentView(false);
3891     }
3892     return msa;
3893   }
3894
3895   /**
3896    * Decides what is submitted to a secondary structure prediction service: the
3897    * first sequence in the alignment, or in the current selection, or, if the
3898    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3899    * region or the whole alignment. (where the first sequence in the set is the
3900    * one that the prediction will be for).
3901    */
3902   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3903   {
3904     AlignmentView seqs = null;
3905
3906     if ((viewport.getSelectionGroup() != null)
3907             && (viewport.getSelectionGroup().getSize() > 0))
3908     {
3909       seqs = viewport.getAlignmentView(true);
3910     }
3911     else
3912     {
3913       seqs = viewport.getAlignmentView(false);
3914     }
3915     // limit sequences - JBPNote in future - could spawn multiple prediction
3916     // jobs
3917     // TODO: viewport.getAlignment().isAligned is a global state - the local
3918     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3919     if (!viewport.getAlignment().isAligned(false))
3920     {
3921       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3922       // TODO: if seqs.getSequences().length>1 then should really have warned
3923       // user!
3924
3925     }
3926     return seqs;
3927   }
3928
3929   /**
3930    * DOCUMENT ME!
3931    *
3932    * @param e
3933    *          DOCUMENT ME!
3934    */
3935   @Override
3936   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3937   {
3938     // Pick the tree file
3939     JalviewFileChooser chooser = new JalviewFileChooser(
3940             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3941     chooser.setFileView(new JalviewFileView());
3942     chooser.setDialogTitle(MessageManager
3943             .getString("label.select_newick_like_tree_file"));
3944     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3945
3946     int value = chooser.showOpenDialog(null);
3947
3948     if (value == JalviewFileChooser.APPROVE_OPTION)
3949     {
3950       String choice = chooser.getSelectedFile().getPath();
3951       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3952       jalview.io.NewickFile fin = null;
3953       try
3954       {
3955         fin = new NewickFile(choice, DataSourceType.FILE);
3956         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3957       } catch (Exception ex)
3958       {
3959         JvOptionPane
3960                 .showMessageDialog(
3961                         Desktop.desktop,
3962                         ex.getMessage(),
3963                         MessageManager
3964                                 .getString("label.problem_reading_tree_file"),
3965                         JvOptionPane.WARNING_MESSAGE);
3966         ex.printStackTrace();
3967       }
3968       if (fin != null && fin.hasWarningMessage())
3969       {
3970         JvOptionPane.showMessageDialog(Desktop.desktop, fin
3971                 .getWarningMessage(), MessageManager
3972                 .getString("label.possible_problem_with_tree_file"),
3973                 JvOptionPane.WARNING_MESSAGE);
3974       }
3975     }
3976   }
3977
3978   public TreePanel ShowNewickTree(NewickFile nf, String title)
3979   {
3980     return ShowNewickTree(nf, title, 600, 500, 4, 5);
3981   }
3982
3983   public TreePanel ShowNewickTree(NewickFile nf, String title,
3984           AlignmentView input)
3985   {
3986     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3987   }
3988
3989   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3990           int h, int x, int y)
3991   {
3992     return ShowNewickTree(nf, title, null, w, h, x, y);
3993   }
3994
3995   /**
3996    * Add a treeviewer for the tree extracted from a newick file object to the
3997    * current alignment view
3998    *
3999    * @param nf
4000    *          the tree
4001    * @param title
4002    *          tree viewer title
4003    * @param input
4004    *          Associated alignment input data (or null)
4005    * @param w
4006    *          width
4007    * @param h
4008    *          height
4009    * @param x
4010    *          position
4011    * @param y
4012    *          position
4013    * @return TreePanel handle
4014    */
4015   public TreePanel ShowNewickTree(NewickFile nf, String title,
4016           AlignmentView input, int w, int h, int x, int y)
4017   {
4018     TreePanel tp = null;
4019
4020     try
4021     {
4022       nf.parse();
4023
4024       if (nf.getTree() != null)
4025       {
4026         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4027
4028         tp.setSize(w, h);
4029
4030         if (x > 0 && y > 0)
4031         {
4032           tp.setLocation(x, y);
4033         }
4034
4035         Desktop.addInternalFrame(tp, title, w, h);
4036       }
4037     } catch (Exception ex)
4038     {
4039       ex.printStackTrace();
4040     }
4041
4042     return tp;
4043   }
4044
4045   private boolean buildingMenu = false;
4046
4047   /**
4048    * Generates menu items and listener event actions for web service clients
4049    *
4050    */
4051   public void BuildWebServiceMenu()
4052   {
4053     while (buildingMenu)
4054     {
4055       try
4056       {
4057         System.err.println("Waiting for building menu to finish.");
4058         Thread.sleep(10);
4059       } catch (Exception e)
4060       {
4061       }
4062     }
4063     final AlignFrame me = this;
4064     buildingMenu = true;
4065     new Thread(new Runnable()
4066     {
4067       @Override
4068       public void run()
4069       {
4070         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4071         try
4072         {
4073           // System.err.println("Building ws menu again "
4074           // + Thread.currentThread());
4075           // TODO: add support for context dependent disabling of services based
4076           // on
4077           // alignment and current selection
4078           // TODO: add additional serviceHandle parameter to specify abstract
4079           // handler
4080           // class independently of AbstractName
4081           // TODO: add in rediscovery GUI function to restart discoverer
4082           // TODO: group services by location as well as function and/or
4083           // introduce
4084           // object broker mechanism.
4085           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4086           final IProgressIndicator af = me;
4087
4088           /*
4089            * do not i18n these strings - they are hard-coded in class
4090            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4091            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4092            */
4093           final JMenu msawsmenu = new JMenu("Alignment");
4094           final JMenu secstrmenu = new JMenu(
4095                   "Secondary Structure Prediction");
4096           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4097           final JMenu analymenu = new JMenu("Analysis");
4098           final JMenu dismenu = new JMenu("Protein Disorder");
4099           // JAL-940 - only show secondary structure prediction services from
4100           // the legacy server
4101           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4102               // &&
4103           Discoverer.services != null && (Discoverer.services.size() > 0))
4104           {
4105             // TODO: refactor to allow list of AbstractName/Handler bindings to
4106             // be
4107             // stored or retrieved from elsewhere
4108             // No MSAWS used any more:
4109             // Vector msaws = null; // (Vector)
4110             // Discoverer.services.get("MsaWS");
4111             Vector secstrpr = (Vector) Discoverer.services
4112                     .get("SecStrPred");
4113             if (secstrpr != null)
4114             {
4115               // Add any secondary structure prediction services
4116               for (int i = 0, j = secstrpr.size(); i < j; i++)
4117               {
4118                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4119                         .get(i);
4120                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4121                         .getServiceClient(sh);
4122                 int p = secstrmenu.getItemCount();
4123                 impl.attachWSMenuEntry(secstrmenu, me);
4124                 int q = secstrmenu.getItemCount();
4125                 for (int litm = p; litm < q; litm++)
4126                 {
4127                   legacyItems.add(secstrmenu.getItem(litm));
4128                 }
4129               }
4130             }
4131           }
4132
4133           // Add all submenus in the order they should appear on the web
4134           // services menu
4135           wsmenu.add(msawsmenu);
4136           wsmenu.add(secstrmenu);
4137           wsmenu.add(dismenu);
4138           wsmenu.add(analymenu);
4139           // No search services yet
4140           // wsmenu.add(seqsrchmenu);
4141
4142           javax.swing.SwingUtilities.invokeLater(new Runnable()
4143           {
4144             @Override
4145             public void run()
4146             {
4147               try
4148               {
4149                 webService.removeAll();
4150                 // first, add discovered services onto the webservices menu
4151                 if (wsmenu.size() > 0)
4152                 {
4153                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4154                   {
4155                     webService.add(wsmenu.get(i));
4156                   }
4157                 }
4158                 else
4159                 {
4160                   webService.add(me.webServiceNoServices);
4161                 }
4162                 // TODO: move into separate menu builder class.
4163                 boolean new_sspred = false;
4164                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4165                 {
4166                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4167                   if (jws2servs != null)
4168                   {
4169                     if (jws2servs.hasServices())
4170                     {
4171                       jws2servs.attachWSMenuEntry(webService, me);
4172                       for (Jws2Instance sv : jws2servs.getServices())
4173                       {
4174                         if (sv.description.toLowerCase().contains("jpred"))
4175                         {
4176                           for (JMenuItem jmi : legacyItems)
4177                           {
4178                             jmi.setVisible(false);
4179                           }
4180                         }
4181                       }
4182
4183                     }
4184                     if (jws2servs.isRunning())
4185                     {
4186                       JMenuItem tm = new JMenuItem(
4187                               "Still discovering JABA Services");
4188                       tm.setEnabled(false);
4189                       webService.add(tm);
4190                     }
4191                   }
4192                 }
4193                 build_urlServiceMenu(me.webService);
4194                 build_fetchdbmenu(webService);
4195                 for (JMenu item : wsmenu)
4196                 {
4197                   if (item.getItemCount() == 0)
4198                   {
4199                     item.setEnabled(false);
4200                   }
4201                   else
4202                   {
4203                     item.setEnabled(true);
4204                   }
4205                 }
4206               } catch (Exception e)
4207               {
4208                 Cache.log
4209                         .debug("Exception during web service menu building process.",
4210                                 e);
4211               }
4212             }
4213           });
4214         } catch (Exception e)
4215         {
4216         }
4217         buildingMenu = false;
4218       }
4219     }).start();
4220
4221   }
4222
4223   /**
4224    * construct any groupURL type service menu entries.
4225    *
4226    * @param webService
4227    */
4228   private void build_urlServiceMenu(JMenu webService)
4229   {
4230     // TODO: remove this code when 2.7 is released
4231     // DEBUG - alignmentView
4232     /*
4233      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4234      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4235      *
4236      * @Override public void actionPerformed(ActionEvent e) {
4237      * jalview.datamodel.AlignmentView
4238      * .testSelectionViews(af.viewport.getAlignment(),
4239      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4240      *
4241      * }); webService.add(testAlView);
4242      */
4243     // TODO: refactor to RestClient discoverer and merge menu entries for
4244     // rest-style services with other types of analysis/calculation service
4245     // SHmmr test client - still being implemented.
4246     // DEBUG - alignmentView
4247
4248     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4249             .getRestClients())
4250     {
4251       client.attachWSMenuEntry(
4252               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4253               this);
4254     }
4255   }
4256
4257   /**
4258    * Searches the alignment sequences for xRefs and builds the Show
4259    * Cross-References menu (formerly called Show Products), with database
4260    * sources for which cross-references are found (protein sources for a
4261    * nucleotide alignment and vice versa)
4262    *
4263    * @return true if Show Cross-references menu should be enabled
4264    */
4265   public boolean canShowProducts()
4266   {
4267     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4268     AlignmentI dataset = viewport.getAlignment().getDataset();
4269
4270     showProducts.removeAll();
4271     final boolean dna = viewport.getAlignment().isNucleotide();
4272
4273     if (seqs == null || seqs.length == 0)
4274     {
4275       // nothing to see here.
4276       return false;
4277     }
4278
4279     boolean showp = false;
4280     try
4281     {
4282       List<String> ptypes = new CrossRef(seqs, dataset)
4283               .findXrefSourcesForSequences(dna);
4284
4285       for (final String source : ptypes)
4286       {
4287         showp = true;
4288         final AlignFrame af = this;
4289         JMenuItem xtype = new JMenuItem(source);
4290         xtype.addActionListener(new ActionListener()
4291         {
4292           @Override
4293           public void actionPerformed(ActionEvent e)
4294           {
4295             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4296           }
4297         });
4298         showProducts.add(xtype);
4299       }
4300       showProducts.setVisible(showp);
4301       showProducts.setEnabled(showp);
4302     } catch (Exception e)
4303     {
4304       Cache.log
4305               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4306                       e);
4307       return false;
4308     }
4309     return showp;
4310   }
4311
4312   /**
4313    * Finds and displays cross-references for the selected sequences (protein
4314    * products for nucleotide sequences, dna coding sequences for peptides).
4315    *
4316    * @param sel
4317    *          the sequences to show cross-references for
4318    * @param dna
4319    *          true if from a nucleotide alignment (so showing proteins)
4320    * @param source
4321    *          the database to show cross-references for
4322    */
4323   protected void showProductsFor(final SequenceI[] sel,
4324           final boolean _odna, final String source)
4325   {
4326     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4327             .start();
4328   }
4329
4330   /**
4331    * Construct and display a new frame containing the translation of this
4332    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4333    */
4334   @Override
4335   public void showTranslation_actionPerformed(ActionEvent e)
4336   {
4337     AlignmentI al = null;
4338     try
4339     {
4340       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4341
4342       al = dna.translateCdna();
4343     } catch (Exception ex)
4344     {
4345       jalview.bin.Cache.log.error(
4346               "Exception during translation. Please report this !", ex);
4347       final String msg = MessageManager
4348               .getString("label.error_when_translating_sequences_submit_bug_report");
4349       final String errorTitle = MessageManager
4350               .getString("label.implementation_error")
4351               + MessageManager.getString("label.translation_failed");
4352       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4353               JvOptionPane.ERROR_MESSAGE);
4354       return;
4355     }
4356     if (al == null || al.getHeight() == 0)
4357     {
4358       final String msg = MessageManager
4359               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4360       final String errorTitle = MessageManager
4361               .getString("label.translation_failed");
4362       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4363               JvOptionPane.WARNING_MESSAGE);
4364     }
4365     else
4366     {
4367       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4368       af.setFileFormat(this.currentFileFormat);
4369       final String newTitle = MessageManager.formatMessage(
4370               "label.translation_of_params",
4371               new Object[] { this.getTitle() });
4372       af.setTitle(newTitle);
4373       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4374       {
4375         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4376         viewport.openSplitFrame(af, new Alignment(seqs));
4377       }
4378       else
4379       {
4380         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4381                 DEFAULT_HEIGHT);
4382       }
4383     }
4384   }
4385
4386   /**
4387    * Set the file format
4388    *
4389    * @param format
4390    */
4391   public void setFileFormat(FileFormatI format)
4392   {
4393     this.currentFileFormat = format;
4394   }
4395
4396   /**
4397    * Try to load a features file onto the alignment.
4398    *
4399    * @param file
4400    *          contents or path to retrieve file
4401    * @param sourceType
4402    *          access mode of file (see jalview.io.AlignFile)
4403    * @return true if features file was parsed correctly.
4404    */
4405   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4406   {
4407     return avc.parseFeaturesFile(file, sourceType,
4408             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4409
4410   }
4411
4412   @Override
4413   public void refreshFeatureUI(boolean enableIfNecessary)
4414   {
4415     // note - currently this is only still here rather than in the controller
4416     // because of the featureSettings hard reference that is yet to be
4417     // abstracted
4418     if (enableIfNecessary)
4419     {
4420       viewport.setShowSequenceFeatures(true);
4421       showSeqFeatures.setSelected(true);
4422     }
4423
4424   }
4425
4426   @Override
4427   public void dragEnter(DropTargetDragEvent evt)
4428   {
4429   }
4430
4431   @Override
4432   public void dragExit(DropTargetEvent evt)
4433   {
4434   }
4435
4436   @Override
4437   public void dragOver(DropTargetDragEvent evt)
4438   {
4439   }
4440
4441   @Override
4442   public void dropActionChanged(DropTargetDragEvent evt)
4443   {
4444   }
4445
4446   @Override
4447   public void drop(DropTargetDropEvent evt)
4448   {
4449     // JAL-1552 - acceptDrop required before getTransferable call for
4450     // Java's Transferable for native dnd
4451     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4452     Transferable t = evt.getTransferable();
4453     List<String> files = new ArrayList<String>();
4454     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4455
4456     try
4457     {
4458       Desktop.transferFromDropTarget(files, protocols, evt, t);
4459     } catch (Exception e)
4460     {
4461       e.printStackTrace();
4462     }
4463     if (files != null)
4464     {
4465       try
4466       {
4467         // check to see if any of these files have names matching sequences in
4468         // the alignment
4469         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4470                 .getAlignment().getSequencesArray());
4471         /**
4472          * Object[] { String,SequenceI}
4473          */
4474         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4475         ArrayList<String> filesnotmatched = new ArrayList<String>();
4476         for (int i = 0; i < files.size(); i++)
4477         {
4478           String file = files.get(i).toString();
4479           String pdbfn = "";
4480           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4481           if (protocol == DataSourceType.FILE)
4482           {
4483             File fl = new File(file);
4484             pdbfn = fl.getName();
4485           }
4486           else if (protocol == DataSourceType.URL)
4487           {
4488             URL url = new URL(file);
4489             pdbfn = url.getFile();
4490           }
4491           if (pdbfn.length() > 0)
4492           {
4493             // attempt to find a match in the alignment
4494             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4495             int l = 0, c = pdbfn.indexOf(".");
4496             while (mtch == null && c != -1)
4497             {
4498               do
4499               {
4500                 l = c;
4501               } while ((c = pdbfn.indexOf(".", l)) > l);
4502               if (l > -1)
4503               {
4504                 pdbfn = pdbfn.substring(0, l);
4505               }
4506               mtch = idm.findAllIdMatches(pdbfn);
4507             }
4508             if (mtch != null)
4509             {
4510               FileFormatI type = null;
4511               try
4512               {
4513                 type = new IdentifyFile().identify(file, protocol);
4514               } catch (Exception ex)
4515               {
4516                 type = null;
4517               }
4518               if (type != null && type.isStructureFile())
4519               {
4520                 filesmatched.add(new Object[] { file, protocol, mtch });
4521                 continue;
4522               }
4523             }
4524             // File wasn't named like one of the sequences or wasn't a PDB file.
4525             filesnotmatched.add(file);
4526           }
4527         }
4528         int assocfiles = 0;
4529         if (filesmatched.size() > 0)
4530         {
4531           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4532                   || JvOptionPane
4533                           .showConfirmDialog(
4534                                   this,
4535                                   MessageManager
4536                                           .formatMessage(
4537                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4538                                                   new Object[] { Integer
4539                                                           .valueOf(
4540                                                                   filesmatched
4541                                                                           .size())
4542                                                           .toString() }),
4543                                   MessageManager
4544                                           .getString("label.automatically_associate_structure_files_by_name"),
4545                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4546
4547           {
4548             for (Object[] fm : filesmatched)
4549             {
4550               // try and associate
4551               // TODO: may want to set a standard ID naming formalism for
4552               // associating PDB files which have no IDs.
4553               for (SequenceI toassoc : (SequenceI[]) fm[2])
4554               {
4555                 PDBEntry pe = new AssociatePdbFileWithSeq()
4556                         .associatePdbWithSeq((String) fm[0],
4557                                 (DataSourceType) fm[1], toassoc, false,
4558                                 Desktop.instance);
4559                 if (pe != null)
4560                 {
4561                   System.err.println("Associated file : "
4562                           + ((String) fm[0]) + " with "
4563                           + toassoc.getDisplayId(true));
4564                   assocfiles++;
4565                 }
4566               }
4567               alignPanel.paintAlignment(true);
4568             }
4569           }
4570         }
4571         if (filesnotmatched.size() > 0)
4572         {
4573           if (assocfiles > 0
4574                   && (Cache.getDefault(
4575                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4576                           .showConfirmDialog(
4577                                   this,
4578                                   "<html>"
4579                                           + MessageManager
4580                                                   .formatMessage(
4581                                                           "label.ignore_unmatched_dropped_files_info",
4582                                                           new Object[] { Integer
4583                                                                   .valueOf(
4584                                                                           filesnotmatched
4585                                                                                   .size())
4586                                                                   .toString() })
4587                                           + "</html>",
4588                                   MessageManager
4589                                           .getString("label.ignore_unmatched_dropped_files"),
4590                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4591           {
4592             return;
4593           }
4594           for (String fn : filesnotmatched)
4595           {
4596             loadJalviewDataFile(fn, null, null, null);
4597           }
4598
4599         }
4600       } catch (Exception ex)
4601       {
4602         ex.printStackTrace();
4603       }
4604     }
4605   }
4606
4607   /**
4608    * Attempt to load a "dropped" file or URL string: First by testing whether
4609    * it's an Annotation file, then a JNet file, and finally a features file. If
4610    * all are false then the user may have dropped an alignment file onto this
4611    * AlignFrame.
4612    *
4613    * @param file
4614    *          either a filename or a URL string.
4615    */
4616   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4617           FileFormatI format, SequenceI assocSeq)
4618   {
4619     try
4620     {
4621       if (sourceType == null)
4622       {
4623         sourceType = FormatAdapter.checkProtocol(file);
4624       }
4625       // if the file isn't identified, or not positively identified as some
4626       // other filetype (PFAM is default unidentified alignment file type) then
4627       // try to parse as annotation.
4628       boolean isAnnotation = (format == null || FileFormat.Pfam
4629               .equals(format)) ? new AnnotationFile()
4630               .annotateAlignmentView(viewport, file, sourceType) : false;
4631
4632       if (!isAnnotation)
4633       {
4634         // first see if its a T-COFFEE score file
4635         TCoffeeScoreFile tcf = null;
4636         try
4637         {
4638           tcf = new TCoffeeScoreFile(file, sourceType);
4639           if (tcf.isValid())
4640           {
4641             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4642             {
4643               buildColourMenu();
4644               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4645               isAnnotation = true;
4646               statusBar
4647                       .setText(MessageManager
4648                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4649             }
4650             else
4651             {
4652               // some problem - if no warning its probable that the ID matching
4653               // process didn't work
4654               JvOptionPane
4655                       .showMessageDialog(
4656                               Desktop.desktop,
4657                               tcf.getWarningMessage() == null ? MessageManager
4658                                       .getString("label.check_file_matches_sequence_ids_alignment")
4659                                       : tcf.getWarningMessage(),
4660                               MessageManager
4661                                       .getString("label.problem_reading_tcoffee_score_file"),
4662                               JvOptionPane.WARNING_MESSAGE);
4663             }
4664           }
4665           else
4666           {
4667             tcf = null;
4668           }
4669         } catch (Exception x)
4670         {
4671           Cache.log
4672                   .debug("Exception when processing data source as T-COFFEE score file",
4673                           x);
4674           tcf = null;
4675         }
4676         if (tcf == null)
4677         {
4678           // try to see if its a JNet 'concise' style annotation file *before*
4679           // we
4680           // try to parse it as a features file
4681           if (format == null)
4682           {
4683             format = new IdentifyFile().identify(file, sourceType);
4684           }
4685           if (FileFormat.Jnet.equals(format))
4686           {
4687             JPredFile predictions = new JPredFile(file, sourceType);
4688             new JnetAnnotationMaker();
4689             JnetAnnotationMaker.add_annotation(predictions,
4690                     viewport.getAlignment(), 0, false);
4691             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4692             viewport.getAlignment().setSeqrep(repseq);
4693             ColumnSelection cs = new ColumnSelection();
4694             cs.hideInsertionsFor(repseq);
4695             viewport.setColumnSelection(cs);
4696             isAnnotation = true;
4697           }
4698           // else if (IdentifyFile.FeaturesFile.equals(format))
4699           else if (FileFormat.Features.equals(format))
4700           {
4701             if (parseFeaturesFile(file, sourceType))
4702             {
4703               alignPanel.paintAlignment(true);
4704             }
4705           }
4706           else
4707           {
4708             new FileLoader().LoadFile(viewport, file, sourceType, format);
4709           }
4710         }
4711       }
4712       if (isAnnotation)
4713       {
4714
4715         alignPanel.adjustAnnotationHeight();
4716         viewport.updateSequenceIdColours();
4717         buildSortByAnnotationScoresMenu();
4718         alignPanel.paintAlignment(true);
4719       }
4720     } catch (Exception ex)
4721     {
4722       ex.printStackTrace();
4723     } catch (OutOfMemoryError oom)
4724     {
4725       try
4726       {
4727         System.gc();
4728       } catch (Exception x)
4729       {
4730       }
4731       new OOMWarning(
4732               "loading data "
4733                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4734                               : "using " + sourceType + " from " + file)
4735                               : ".")
4736                       + (format != null ? "(parsing as '" + format
4737                               + "' file)" : ""), oom, Desktop.desktop);
4738     }
4739   }
4740
4741   /**
4742    * Method invoked by the ChangeListener on the tabbed pane, in other words
4743    * when a different tabbed pane is selected by the user or programmatically.
4744    */
4745   @Override
4746   public void tabSelectionChanged(int index)
4747   {
4748     if (index > -1)
4749     {
4750       alignPanel = alignPanels.get(index);
4751       viewport = alignPanel.av;
4752       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4753       setMenusFromViewport(viewport);
4754     }
4755
4756     /*
4757      * 'focus' any colour slider that is open to the selected viewport
4758      */
4759     if (viewport.getConservationSelected())
4760     {
4761       SliderPanel.setConservationSlider(alignPanel,
4762               viewport.getResidueShading(), alignPanel.getViewName());
4763     }
4764     else
4765     {
4766       SliderPanel.hideConservationSlider();
4767     }
4768     if (viewport.getAbovePIDThreshold())
4769     {
4770       SliderPanel.setPIDSliderSource(alignPanel,
4771               viewport.getResidueShading(), alignPanel.getViewName());
4772     }
4773     else
4774     {
4775       SliderPanel.hidePIDSlider();
4776     }
4777
4778     /*
4779      * If there is a frame linked to this one in a SplitPane, switch it to the
4780      * same view tab index. No infinite recursion of calls should happen, since
4781      * tabSelectionChanged() should not get invoked on setting the selected
4782      * index to an unchanged value. Guard against setting an invalid index
4783      * before the new view peer tab has been created.
4784      */
4785     final AlignViewportI peer = viewport.getCodingComplement();
4786     if (peer != null)
4787     {
4788       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4789       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4790       {
4791         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4792       }
4793     }
4794   }
4795
4796   /**
4797    * On right mouse click on view tab, prompt for and set new view name.
4798    */
4799   @Override
4800   public void tabbedPane_mousePressed(MouseEvent e)
4801   {
4802     if (e.isPopupTrigger())
4803     {
4804       String msg = MessageManager.getString("label.enter_view_name");
4805       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4806               JvOptionPane.QUESTION_MESSAGE);
4807
4808       if (reply != null)
4809       {
4810         viewport.viewName = reply;
4811         // TODO warn if reply is in getExistingViewNames()?
4812         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4813       }
4814     }
4815   }
4816
4817   public AlignViewport getCurrentView()
4818   {
4819     return viewport;
4820   }
4821
4822   /**
4823    * Open the dialog for regex description parsing.
4824    */
4825   @Override
4826   protected void extractScores_actionPerformed(ActionEvent e)
4827   {
4828     ParseProperties pp = new jalview.analysis.ParseProperties(
4829             viewport.getAlignment());
4830     // TODO: verify regex and introduce GUI dialog for version 2.5
4831     // if (pp.getScoresFromDescription("col", "score column ",
4832     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4833     // true)>0)
4834     if (pp.getScoresFromDescription("description column",
4835             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4836     {
4837       buildSortByAnnotationScoresMenu();
4838     }
4839   }
4840
4841   /*
4842    * (non-Javadoc)
4843    *
4844    * @see
4845    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4846    * )
4847    */
4848   @Override
4849   protected void showDbRefs_actionPerformed(ActionEvent e)
4850   {
4851     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4852   }
4853
4854   /*
4855    * (non-Javadoc)
4856    *
4857    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4858    * ActionEvent)
4859    */
4860   @Override
4861   protected void showNpFeats_actionPerformed(ActionEvent e)
4862   {
4863     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4864   }
4865
4866   /**
4867    * find the viewport amongst the tabs in this alignment frame and close that
4868    * tab
4869    *
4870    * @param av
4871    */
4872   public boolean closeView(AlignViewportI av)
4873   {
4874     if (viewport == av)
4875     {
4876       this.closeMenuItem_actionPerformed(false);
4877       return true;
4878     }
4879     Component[] comp = tabbedPane.getComponents();
4880     for (int i = 0; comp != null && i < comp.length; i++)
4881     {
4882       if (comp[i] instanceof AlignmentPanel)
4883       {
4884         if (((AlignmentPanel) comp[i]).av == av)
4885         {
4886           // close the view.
4887           closeView((AlignmentPanel) comp[i]);
4888           return true;
4889         }
4890       }
4891     }
4892     return false;
4893   }
4894
4895   protected void build_fetchdbmenu(JMenu webService)
4896   {
4897     // Temporary hack - DBRef Fetcher always top level ws entry.
4898     // TODO We probably want to store a sequence database checklist in
4899     // preferences and have checkboxes.. rather than individual sources selected
4900     // here
4901     final JMenu rfetch = new JMenu(
4902             MessageManager.getString("action.fetch_db_references"));
4903     rfetch.setToolTipText(MessageManager
4904             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4905     webService.add(rfetch);
4906
4907     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4908             MessageManager.getString("option.trim_retrieved_seqs"));
4909     trimrs.setToolTipText(MessageManager
4910             .getString("label.trim_retrieved_sequences"));
4911     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4912     trimrs.addActionListener(new ActionListener()
4913     {
4914       @Override
4915       public void actionPerformed(ActionEvent e)
4916       {
4917         trimrs.setSelected(trimrs.isSelected());
4918         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4919                 Boolean.valueOf(trimrs.isSelected()).toString());
4920       };
4921     });
4922     rfetch.add(trimrs);
4923     JMenuItem fetchr = new JMenuItem(
4924             MessageManager.getString("label.standard_databases"));
4925     fetchr.setToolTipText(MessageManager
4926             .getString("label.fetch_embl_uniprot"));
4927     fetchr.addActionListener(new ActionListener()
4928     {
4929
4930       @Override
4931       public void actionPerformed(ActionEvent e)
4932       {
4933         new Thread(new Runnable()
4934         {
4935           @Override
4936           public void run()
4937           {
4938             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4939                     .getAlignment().isNucleotide();
4940             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4941                     .getSequenceSelection(), alignPanel.alignFrame, null,
4942                     alignPanel.alignFrame.featureSettings, isNucleotide);
4943             dbRefFetcher.addListener(new FetchFinishedListenerI()
4944             {
4945               @Override
4946               public void finished()
4947               {
4948                 AlignFrame.this.setMenusForViewport();
4949               }
4950             });
4951             dbRefFetcher.fetchDBRefs(false);
4952           }
4953         }).start();
4954
4955       }
4956
4957     });
4958     rfetch.add(fetchr);
4959     final AlignFrame me = this;
4960     new Thread(new Runnable()
4961     {
4962       @Override
4963       public void run()
4964       {
4965         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4966                 .getSequenceFetcherSingleton(me);
4967         javax.swing.SwingUtilities.invokeLater(new Runnable()
4968         {
4969           @Override
4970           public void run()
4971           {
4972             String[] dbclasses = sf.getOrderedSupportedSources();
4973             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4974             // jalview.util.QuickSort.sort(otherdb, otherdb);
4975             List<DbSourceProxy> otherdb;
4976             JMenu dfetch = new JMenu();
4977             JMenu ifetch = new JMenu();
4978             JMenuItem fetchr = null;
4979             int comp = 0, icomp = 0, mcomp = 15;
4980             String mname = null;
4981             int dbi = 0;
4982             for (String dbclass : dbclasses)
4983             {
4984               otherdb = sf.getSourceProxy(dbclass);
4985               // add a single entry for this class, or submenu allowing 'fetch
4986               // all' or pick one
4987               if (otherdb == null || otherdb.size() < 1)
4988               {
4989                 continue;
4990               }
4991               // List<DbSourceProxy> dbs=otherdb;
4992               // otherdb=new ArrayList<DbSourceProxy>();
4993               // for (DbSourceProxy db:dbs)
4994               // {
4995               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4996               // }
4997               if (mname == null)
4998               {
4999                 mname = "From " + dbclass;
5000               }
5001               if (otherdb.size() == 1)
5002               {
5003                 final DbSourceProxy[] dassource = otherdb
5004                         .toArray(new DbSourceProxy[0]);
5005                 DbSourceProxy src = otherdb.get(0);
5006                 fetchr = new JMenuItem(src.getDbSource());
5007                 fetchr.addActionListener(new ActionListener()
5008                 {
5009
5010                   @Override
5011                   public void actionPerformed(ActionEvent e)
5012                   {
5013                     new Thread(new Runnable()
5014                     {
5015
5016                       @Override
5017                       public void run()
5018                       {
5019                         boolean isNucleotide = alignPanel.alignFrame
5020                                 .getViewport().getAlignment()
5021                                 .isNucleotide();
5022                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5023                                 alignPanel.av.getSequenceSelection(),
5024                                 alignPanel.alignFrame, dassource,
5025                                 alignPanel.alignFrame.featureSettings,
5026                                 isNucleotide);
5027                         dbRefFetcher
5028                                 .addListener(new FetchFinishedListenerI()
5029                                 {
5030                                   @Override
5031                                   public void finished()
5032                                   {
5033                                     AlignFrame.this.setMenusForViewport();
5034                                   }
5035                                 });
5036                         dbRefFetcher.fetchDBRefs(false);
5037                       }
5038                     }).start();
5039                   }
5040
5041                 });
5042                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5043                         MessageManager.formatMessage(
5044                                 "label.fetch_retrieve_from",
5045                                 new Object[] { src.getDbName() })));
5046                 dfetch.add(fetchr);
5047                 comp++;
5048               }
5049               else
5050               {
5051                 final DbSourceProxy[] dassource = otherdb
5052                         .toArray(new DbSourceProxy[0]);
5053                 // fetch all entry
5054                 DbSourceProxy src = otherdb.get(0);
5055                 fetchr = new JMenuItem(MessageManager.formatMessage(
5056                         "label.fetch_all_param",
5057                         new Object[] { src.getDbSource() }));
5058                 fetchr.addActionListener(new ActionListener()
5059                 {
5060                   @Override
5061                   public void actionPerformed(ActionEvent e)
5062                   {
5063                     new Thread(new Runnable()
5064                     {
5065
5066                       @Override
5067                       public void run()
5068                       {
5069                         boolean isNucleotide = alignPanel.alignFrame
5070                                 .getViewport().getAlignment()
5071                                 .isNucleotide();
5072                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5073                                 alignPanel.av.getSequenceSelection(),
5074                                 alignPanel.alignFrame, dassource,
5075                                 alignPanel.alignFrame.featureSettings,
5076                                 isNucleotide);
5077                         dbRefFetcher
5078                                 .addListener(new FetchFinishedListenerI()
5079                                 {
5080                                   @Override
5081                                   public void finished()
5082                                   {
5083                                     AlignFrame.this.setMenusForViewport();
5084                                   }
5085                                 });
5086                         dbRefFetcher.fetchDBRefs(false);
5087                       }
5088                     }).start();
5089                   }
5090                 });
5091
5092                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5093                         MessageManager.formatMessage(
5094                                 "label.fetch_retrieve_from_all_sources",
5095                                 new Object[] {
5096                                     Integer.valueOf(otherdb.size())
5097                                             .toString(), src.getDbSource(),
5098                                     src.getDbName() })));
5099                 dfetch.add(fetchr);
5100                 comp++;
5101                 // and then build the rest of the individual menus
5102                 ifetch = new JMenu(MessageManager.formatMessage(
5103                         "label.source_from_db_source",
5104                         new Object[] { src.getDbSource() }));
5105                 icomp = 0;
5106                 String imname = null;
5107                 int i = 0;
5108                 for (DbSourceProxy sproxy : otherdb)
5109                 {
5110                   String dbname = sproxy.getDbName();
5111                   String sname = dbname.length() > 5 ? dbname.substring(0,
5112                           5) + "..." : dbname;
5113                   String msname = dbname.length() > 10 ? dbname.substring(
5114                           0, 10) + "..." : dbname;
5115                   if (imname == null)
5116                   {
5117                     imname = MessageManager.formatMessage(
5118                             "label.from_msname", new Object[] { sname });
5119                   }
5120                   fetchr = new JMenuItem(msname);
5121                   final DbSourceProxy[] dassrc = { sproxy };
5122                   fetchr.addActionListener(new ActionListener()
5123                   {
5124
5125                     @Override
5126                     public void actionPerformed(ActionEvent e)
5127                     {
5128                       new Thread(new Runnable()
5129                       {
5130
5131                         @Override
5132                         public void run()
5133                         {
5134                           boolean isNucleotide = alignPanel.alignFrame
5135                                   .getViewport().getAlignment()
5136                                   .isNucleotide();
5137                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5138                                   alignPanel.av.getSequenceSelection(),
5139                                   alignPanel.alignFrame, dassrc,
5140                                   alignPanel.alignFrame.featureSettings,
5141                                   isNucleotide);
5142                           dbRefFetcher
5143                                   .addListener(new FetchFinishedListenerI()
5144                                   {
5145                                     @Override
5146                                     public void finished()
5147                                     {
5148                                       AlignFrame.this.setMenusForViewport();
5149                                     }
5150                                   });
5151                           dbRefFetcher.fetchDBRefs(false);
5152                         }
5153                       }).start();
5154                     }
5155
5156                   });
5157                   fetchr.setToolTipText("<html>"
5158                           + MessageManager.formatMessage(
5159                                   "label.fetch_retrieve_from", new Object[]
5160                                   { dbname }));
5161                   ifetch.add(fetchr);
5162                   ++i;
5163                   if (++icomp >= mcomp || i == (otherdb.size()))
5164                   {
5165                     ifetch.setText(MessageManager.formatMessage(
5166                             "label.source_to_target", imname, sname));
5167                     dfetch.add(ifetch);
5168                     ifetch = new JMenu();
5169                     imname = null;
5170                     icomp = 0;
5171                     comp++;
5172                   }
5173                 }
5174               }
5175               ++dbi;
5176               if (comp >= mcomp || dbi >= (dbclasses.length))
5177               {
5178                 dfetch.setText(MessageManager.formatMessage(
5179                         "label.source_to_target", mname, dbclass));
5180                 rfetch.add(dfetch);
5181                 dfetch = new JMenu();
5182                 mname = null;
5183                 comp = 0;
5184               }
5185             }
5186           }
5187         });
5188       }
5189     }).start();
5190
5191   }
5192
5193   /**
5194    * Left justify the whole alignment.
5195    */
5196   @Override
5197   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5198   {
5199     AlignmentI al = viewport.getAlignment();
5200     al.justify(false);
5201     viewport.firePropertyChange("alignment", null, al);
5202   }
5203
5204   /**
5205    * Right justify the whole alignment.
5206    */
5207   @Override
5208   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5209   {
5210     AlignmentI al = viewport.getAlignment();
5211     al.justify(true);
5212     viewport.firePropertyChange("alignment", null, al);
5213   }
5214
5215   @Override
5216   public void setShowSeqFeatures(boolean b)
5217   {
5218     showSeqFeatures.setSelected(b);
5219     viewport.setShowSequenceFeatures(b);
5220   }
5221
5222   /*
5223    * (non-Javadoc)
5224    *
5225    * @see
5226    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5227    * awt.event.ActionEvent)
5228    */
5229   @Override
5230   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5231   {
5232     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5233     alignPanel.paintAlignment(true);
5234   }
5235
5236   /*
5237    * (non-Javadoc)
5238    *
5239    * @see
5240    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5241    * .ActionEvent)
5242    */
5243   @Override
5244   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5245   {
5246     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5247     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5248
5249   }
5250
5251   /*
5252    * (non-Javadoc)
5253    *
5254    * @see
5255    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5256    * .event.ActionEvent)
5257    */
5258   @Override
5259   protected void showGroupConservation_actionPerformed(ActionEvent e)
5260   {
5261     viewport.setShowGroupConservation(showGroupConservation.getState());
5262     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5263   }
5264
5265   /*
5266    * (non-Javadoc)
5267    *
5268    * @see
5269    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5270    * .event.ActionEvent)
5271    */
5272   @Override
5273   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5274   {
5275     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5276     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5277   }
5278
5279   /*
5280    * (non-Javadoc)
5281    *
5282    * @see
5283    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5284    * .event.ActionEvent)
5285    */
5286   @Override
5287   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5288   {
5289     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5290     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5291   }
5292
5293   @Override
5294   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5295   {
5296     showSequenceLogo.setState(true);
5297     viewport.setShowSequenceLogo(true);
5298     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5299     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5300   }
5301
5302   @Override
5303   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5304   {
5305     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5306   }
5307
5308   /*
5309    * (non-Javadoc)
5310    *
5311    * @see
5312    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5313    * .event.ActionEvent)
5314    */
5315   @Override
5316   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5317   {
5318     if (avc.makeGroupsFromSelection())
5319     {
5320       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5321       alignPanel.updateAnnotation();
5322       alignPanel.paintAlignment(true);
5323     }
5324   }
5325
5326   public void clearAlignmentSeqRep()
5327   {
5328     // TODO refactor alignmentseqrep to controller
5329     if (viewport.getAlignment().hasSeqrep())
5330     {
5331       viewport.getAlignment().setSeqrep(null);
5332       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5333       alignPanel.updateAnnotation();
5334       alignPanel.paintAlignment(true);
5335     }
5336   }
5337
5338   @Override
5339   protected void createGroup_actionPerformed(ActionEvent e)
5340   {
5341     if (avc.createGroup())
5342     {
5343       alignPanel.alignmentChanged();
5344     }
5345   }
5346
5347   @Override
5348   protected void unGroup_actionPerformed(ActionEvent e)
5349   {
5350     if (avc.unGroup())
5351     {
5352       alignPanel.alignmentChanged();
5353     }
5354   }
5355
5356   /**
5357    * make the given alignmentPanel the currently selected tab
5358    *
5359    * @param alignmentPanel
5360    */
5361   public void setDisplayedView(AlignmentPanel alignmentPanel)
5362   {
5363     if (!viewport.getSequenceSetId().equals(
5364             alignmentPanel.av.getSequenceSetId()))
5365     {
5366       throw new Error(
5367               MessageManager
5368                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5369     }
5370     if (tabbedPane != null
5371             && tabbedPane.getTabCount() > 0
5372             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5373                     .getSelectedIndex())
5374     {
5375       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5376     }
5377   }
5378
5379   /**
5380    * Action on selection of menu options to Show or Hide annotations.
5381    *
5382    * @param visible
5383    * @param forSequences
5384    *          update sequence-related annotations
5385    * @param forAlignment
5386    *          update non-sequence-related annotations
5387    */
5388   @Override
5389   protected void setAnnotationsVisibility(boolean visible,
5390           boolean forSequences, boolean forAlignment)
5391   {
5392     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5393             .getAlignmentAnnotation();
5394     if (anns == null)
5395     {
5396       return;
5397     }
5398     for (AlignmentAnnotation aa : anns)
5399     {
5400       /*
5401        * don't display non-positional annotations on an alignment
5402        */
5403       if (aa.annotations == null)
5404       {
5405         continue;
5406       }
5407       boolean apply = (aa.sequenceRef == null && forAlignment)
5408               || (aa.sequenceRef != null && forSequences);
5409       if (apply)
5410       {
5411         aa.visible = visible;
5412       }
5413     }
5414     alignPanel.validateAnnotationDimensions(true);
5415     alignPanel.alignmentChanged();
5416   }
5417
5418   /**
5419    * Store selected annotation sort order for the view and repaint.
5420    */
5421   @Override
5422   protected void sortAnnotations_actionPerformed()
5423   {
5424     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5425     this.alignPanel.av
5426             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5427     alignPanel.paintAlignment(true);
5428   }
5429
5430   /**
5431    *
5432    * @return alignment panels in this alignment frame
5433    */
5434   public List<? extends AlignmentViewPanel> getAlignPanels()
5435   {
5436     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5437   }
5438
5439   /**
5440    * Open a new alignment window, with the cDNA associated with this (protein)
5441    * alignment, aligned as is the protein.
5442    */
5443   protected void viewAsCdna_actionPerformed()
5444   {
5445     // TODO no longer a menu action - refactor as required
5446     final AlignmentI alignment = getViewport().getAlignment();
5447     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5448     if (mappings == null)
5449     {
5450       return;
5451     }
5452     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5453     for (SequenceI aaSeq : alignment.getSequences())
5454     {
5455       for (AlignedCodonFrame acf : mappings)
5456       {
5457         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5458         if (dnaSeq != null)
5459         {
5460           /*
5461            * There is a cDNA mapping for this protein sequence - add to new
5462            * alignment. It will share the same dataset sequence as other mapped
5463            * cDNA (no new mappings need to be created).
5464            */
5465           final Sequence newSeq = new Sequence(dnaSeq);
5466           newSeq.setDatasetSequence(dnaSeq);
5467           cdnaSeqs.add(newSeq);
5468         }
5469       }
5470     }
5471     if (cdnaSeqs.size() == 0)
5472     {
5473       // show a warning dialog no mapped cDNA
5474       return;
5475     }
5476     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5477             .size()]));
5478     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5479             AlignFrame.DEFAULT_HEIGHT);
5480     cdna.alignAs(alignment);
5481     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5482             + this.title;
5483     Desktop.addInternalFrame(alignFrame, newtitle,
5484             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5485   }
5486
5487   /**
5488    * Set visibility of dna/protein complement view (available when shown in a
5489    * split frame).
5490    *
5491    * @param show
5492    */
5493   @Override
5494   protected void showComplement_actionPerformed(boolean show)
5495   {
5496     SplitContainerI sf = getSplitViewContainer();
5497     if (sf != null)
5498     {
5499       sf.setComplementVisible(this, show);
5500     }
5501   }
5502
5503   /**
5504    * Generate the reverse (optionally complemented) of the selected sequences,
5505    * and add them to the alignment
5506    */
5507   @Override
5508   protected void showReverse_actionPerformed(boolean complement)
5509   {
5510     AlignmentI al = null;
5511     try
5512     {
5513       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5514       al = dna.reverseCdna(complement);
5515       viewport.addAlignment(al, "");
5516       addHistoryItem(new EditCommand(
5517               MessageManager.getString("label.add_sequences"),
5518               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5519               viewport.getAlignment()));
5520     } catch (Exception ex)
5521     {
5522       System.err.println(ex.getMessage());
5523       return;
5524     }
5525   }
5526
5527   /**
5528    * Try to run a script in the Groovy console, having first ensured that this
5529    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5530    * be targeted at this alignment.
5531    */
5532   @Override
5533   protected void runGroovy_actionPerformed()
5534   {
5535     Jalview.setCurrentAlignFrame(this);
5536     groovy.ui.Console console = Desktop.getGroovyConsole();
5537     if (console != null)
5538     {
5539       try
5540       {
5541         console.runScript();
5542       } catch (Exception ex)
5543       {
5544         System.err.println((ex.toString()));
5545         JvOptionPane
5546                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5547                         .getString("label.couldnt_run_groovy_script"),
5548                         MessageManager
5549                                 .getString("label.groovy_support_failed"),
5550                         JvOptionPane.ERROR_MESSAGE);
5551       }
5552     }
5553     else
5554     {
5555       System.err.println("Can't run Groovy script as console not found");
5556     }
5557   }
5558
5559   /**
5560    * Hides columns containing (or not containing) a specified feature, provided
5561    * that would not leave all columns hidden
5562    *
5563    * @param featureType
5564    * @param columnsContaining
5565    * @return
5566    */
5567   public boolean hideFeatureColumns(String featureType,
5568           boolean columnsContaining)
5569   {
5570     boolean notForHiding = avc.markColumnsContainingFeatures(
5571             columnsContaining, false, false, featureType);
5572     if (notForHiding)
5573     {
5574       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5575               false, featureType))
5576       {
5577         getViewport().hideSelectedColumns();
5578         return true;
5579       }
5580     }
5581     return false;
5582   }
5583
5584   @Override
5585   protected void selectHighlightedColumns_actionPerformed(
5586           ActionEvent actionEvent)
5587   {
5588     // include key modifier check in case user selects from menu
5589     avc.markHighlightedColumns(
5590             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5591             true,
5592             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5593   }
5594
5595   /**
5596    * Rebuilds the Colour menu, including any user-defined colours which have
5597    * been loaded either on startup or during the session
5598    */
5599   public void buildColourMenu()
5600   {
5601     colourMenu.removeAll();
5602
5603     colourMenu.add(applyToAllGroups);
5604     colourMenu.add(textColour);
5605     colourMenu.addSeparator();
5606
5607     ColourMenuHelper.addMenuItems(colourMenu, this,
5608             viewport.getAlignment(), false);
5609
5610     colourMenu.addSeparator();
5611     colourMenu.add(conservationMenuItem);
5612     colourMenu.add(modifyConservation);
5613     colourMenu.add(abovePIDThreshold);
5614     colourMenu.add(modifyPID);
5615     colourMenu.add(annotationColour);
5616
5617     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5618     String schemeName = colourScheme == null ? null : colourScheme
5619             .getSchemeName();
5620
5621     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5622   }
5623
5624   public void newTreePanel(String treeType, ScoreModelI sm)
5625   {
5626     String treecalcnm = MessageManager.getString("label.tree_calc_"
5627             + treeType.toLowerCase());
5628     String smn = MessageManager.getStringOrReturn("label.score_model_",
5629             sm.getName());
5630     final String ttl = MessageManager.formatMessage("label.treecalc_title",
5631             treecalcnm, smn);
5632     newTreePanel(treeType, sm.getName(), ttl);
5633   }
5634 }
5635
5636 class PrintThread extends Thread
5637 {
5638   AlignmentPanel ap;
5639
5640   public PrintThread(AlignmentPanel ap)
5641   {
5642     this.ap = ap;
5643   }
5644
5645   static PageFormat pf;
5646
5647   @Override
5648   public void run()
5649   {
5650     PrinterJob printJob = PrinterJob.getPrinterJob();
5651
5652     if (pf != null)
5653     {
5654       printJob.setPrintable(ap, pf);
5655     }
5656     else
5657     {
5658       printJob.setPrintable(ap);
5659     }
5660
5661     if (printJob.printDialog())
5662     {
5663       try
5664       {
5665         printJob.print();
5666       } catch (Exception PrintException)
5667       {
5668         PrintException.printStackTrace();
5669       }
5670     }
5671   }
5672 }