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.analysis.TreeModel;
  30 import jalview.api.AlignExportSettingI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  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.HiddenColumns;
  57 import jalview.datamodel.HiddenSequences;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.ext.archaeopteryx.AptxInit;
  64 import jalview.ext.forester.io.SupportedTreeFileFilter;
  65 import jalview.ext.forester.io.TreeParser;
  66 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  67 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  68 import jalview.io.AlignmentProperties;
  69 import jalview.io.AnnotationFile;
  70 import jalview.io.BioJsHTMLOutput;
  71 import jalview.io.DataSourceType;
  72 import jalview.io.FileFormat;
  73 import jalview.io.FileFormatI;
  74 import jalview.io.FileFormats;
  75 import jalview.io.FileLoader;
  76 import jalview.io.FileParse;
  77 import jalview.io.FormatAdapter;
  78 import jalview.io.HtmlSvgOutput;
  79 import jalview.io.IdentifyFile;
  80 import jalview.io.JPredFile;
  81 import jalview.io.JalviewFileChooser;
  82 import jalview.io.JalviewFileView;
  83 import jalview.io.JnetAnnotationMaker;
  84 import jalview.io.NewickFile;
  85 import jalview.io.ScoreMatrixFile;
  86 import jalview.io.TCoffeeScoreFile;
  87 import jalview.jbgui.GAlignFrame;
  88 import jalview.schemes.ColourSchemeI;
  89 import jalview.schemes.ColourSchemes;
  90 import jalview.schemes.ResidueColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.util.MessageManager;
  93 import jalview.viewmodel.AlignmentViewport;
  94 import jalview.viewmodel.ViewportRanges;
  95 import jalview.ws.DBRefFetcher;
  96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Component;
 104 import java.awt.Dimension;
 105 import java.awt.GridLayout;
 106 import java.awt.Rectangle;
 107 import java.awt.Toolkit;
 108 import java.awt.datatransfer.Clipboard;
 109 import java.awt.datatransfer.DataFlavor;
 110 import java.awt.datatransfer.StringSelection;
 111 import java.awt.datatransfer.Transferable;
 112 import java.awt.dnd.DnDConstants;
 113 import java.awt.dnd.DropTargetDragEvent;
 114 import java.awt.dnd.DropTargetDropEvent;
 115 import java.awt.dnd.DropTargetEvent;
 116 import java.awt.dnd.DropTargetListener;
 117 import java.awt.event.ActionEvent;
 118 import java.awt.event.ActionListener;
 119 import java.awt.event.FocusAdapter;
 120 import java.awt.event.FocusEvent;
 121 import java.awt.event.ItemEvent;
 122 import java.awt.event.ItemListener;
 123 import java.awt.event.KeyAdapter;
 124 import java.awt.event.KeyEvent;
 125 import java.awt.event.MouseEvent;
 126 import java.awt.print.PageFormat;
 127 import java.awt.print.PrinterJob;
 128 import java.beans.PropertyChangeEvent;
 129 import java.io.File;
 130 import java.io.FileWriter;
 131 import java.io.IOException;
 132 import java.io.PrintWriter;
 133 import java.net.URL;
 134 import java.util.ArrayList;
 135 import java.util.Arrays;
 136 import java.util.Deque;
 137 import java.util.Enumeration;
 138 import java.util.Hashtable;
 139 import java.util.List;
 140 import java.util.StringTokenizer;
 141 import java.util.Vector;
 142
 143 import javax.swing.JCheckBoxMenuItem;
 144 import javax.swing.JComboBox;
 145 import javax.swing.JEditorPane;
 146 import javax.swing.JInternalFrame;
 147 import javax.swing.JLabel;
 148 import javax.swing.JLayeredPane;
 149 import javax.swing.JMenu;
 150 import javax.swing.JMenuItem;
 151 import javax.swing.JPanel;
 152 import javax.swing.JScrollPane;
 153 import javax.swing.SwingUtilities;
 154
 155 /**
 156  * DOCUMENT ME!
 157  *
 158  * @author $author$
 159  * @version $Revision$
 160  */
 161 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 162         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 163 {
 164
 165   public static final int DEFAULT_WIDTH = 700;
 166
 167   public static final int DEFAULT_HEIGHT = 500;
 168
 169   /*
 170    * The currently displayed panel (selected tabbed view if more than one)
 171    */
 172   public AlignmentPanel alignPanel;
 173
 174   AlignViewport viewport;
 175
 176   public AlignViewControllerI avc;
 177
 178   List<AlignmentPanel> alignPanels = new ArrayList<>();
 179
 180   /**
 181    * Last format used to load or save alignments in this window
 182    */
 183   FileFormatI currentFileFormat = null;
 184
 185   /**
 186    * Current filename for this alignment
 187    */
 188   String fileName = null;
 189
 190   /**
 191    * Creates a new AlignFrame object with specific width and height.
 192    *
 193    * @param al
 194    * @param width
 195    * @param height
 196    */
 197   public AlignFrame(AlignmentI al, int width, int height)
 198   {
 199     this(al, null, width, height);
 200   }
 201
 202   /**
 203    * Creates a new AlignFrame object with specific width, height and
 204    * sequenceSetId
 205    *
 206    * @param al
 207    * @param width
 208    * @param height
 209    * @param sequenceSetId
 210    */
 211   public AlignFrame(AlignmentI al, int width, int height,
 212           String sequenceSetId)
 213   {
 214     this(al, null, width, height, sequenceSetId);
 215   }
 216
 217   /**
 218    * Creates a new AlignFrame object with specific width, height and
 219    * sequenceSetId
 220    *
 221    * @param al
 222    * @param width
 223    * @param height
 224    * @param sequenceSetId
 225    * @param viewId
 226    */
 227   public AlignFrame(AlignmentI al, int width, int height,
 228           String sequenceSetId, String viewId)
 229   {
 230     this(al, null, width, height, sequenceSetId, viewId);
 231   }
 232
 233   /**
 234    * new alignment window with hidden columns
 235    *
 236    * @param al
 237    *          AlignmentI
 238    * @param hiddenColumns
 239    *          ColumnSelection or null
 240    * @param width
 241    *          Width of alignment frame
 242    * @param height
 243    *          height of frame.
 244    */
 245   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 246           int height)
 247   {
 248     this(al, hiddenColumns, width, height, null);
 249   }
 250
 251   /**
 252    * Create alignment frame for al with hiddenColumns, a specific width and
 253    * height, and specific sequenceId
 254    *
 255    * @param al
 256    * @param hiddenColumns
 257    * @param width
 258    * @param height
 259    * @param sequenceSetId
 260    *          (may be null)
 261    */
 262   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 263           int height, String sequenceSetId)
 264   {
 265     this(al, hiddenColumns, width, height, sequenceSetId, null);
 266   }
 267
 268   /**
 269    * Create alignment frame for al with hiddenColumns, a specific width and
 270    * height, and specific sequenceId
 271    *
 272    * @param al
 273    * @param hiddenColumns
 274    * @param width
 275    * @param height
 276    * @param sequenceSetId
 277    *          (may be null)
 278    * @param viewId
 279    *          (may be null)
 280    */
 281   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 282           int height, String sequenceSetId, String viewId)
 283   {
 284     setSize(width, height);
 285
 286     if (al.getDataset() == null)
 287     {
 288       al.setDataset(null);
 289     }
 290
 291     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 292
 293     alignPanel = new AlignmentPanel(this, viewport);
 294
 295     addAlignmentPanel(alignPanel, true);
 296     init();
 297   }
 298
 299   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 300           HiddenColumns hiddenColumns, int width, int height)
 301   {
 302     setSize(width, height);
 303
 304     if (al.getDataset() == null)
 305     {
 306       al.setDataset(null);
 307     }
 308
 309     viewport = new AlignViewport(al, hiddenColumns);
 310
 311     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 312     {
 313       viewport.hideSequence(hiddenSeqs);
 314     }
 315     alignPanel = new AlignmentPanel(this, viewport);
 316     addAlignmentPanel(alignPanel, true);
 317     init();
 318   }
 319
 320   /**
 321    * Make a new AlignFrame from existing alignmentPanels
 322    *
 323    * @param ap
 324    *          AlignmentPanel
 325    * @param av
 326    *          AlignViewport
 327    */
 328   public AlignFrame(AlignmentPanel ap)
 329   {
 330     viewport = ap.av;
 331     alignPanel = ap;
 332     addAlignmentPanel(ap, false);
 333     init();
 334   }
 335
 336   /**
 337    * initalise the alignframe from the underlying viewport data and the
 338    * configurations
 339    */
 340   void init()
 341   {
 342     if (!Jalview.isHeadlessMode())
 343     {
 344       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 345     }
 346
 347     avc = new jalview.controller.AlignViewController(this, viewport,
 348             alignPanel);
 349     if (viewport.getAlignmentConservationAnnotation() == null)
 350     {
 351       // BLOSUM62Colour.setEnabled(false);
 352       conservationMenuItem.setEnabled(false);
 353       modifyConservation.setEnabled(false);
 354       // PIDColour.setEnabled(false);
 355       // abovePIDThreshold.setEnabled(false);
 356       // modifyPID.setEnabled(false);
 357     }
 358
 359     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 360             "No sort");
 361
 362     if (sortby.equals("Id"))
 363     {
 364       sortIDMenuItem_actionPerformed(null);
 365     }
 366     else if (sortby.equals("Pairwise Identity"))
 367     {
 368       sortPairwiseMenuItem_actionPerformed(null);
 369     }
 370
 371     this.alignPanel.av
 372             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 373
 374     setMenusFromViewport(viewport);
 375     buildSortByAnnotationScoresMenu();
 376     calculateTree.addActionListener(new ActionListener()
 377     {
 378
 379       @Override
 380       public void actionPerformed(ActionEvent e)
 381       {
 382         openTreePcaDialog();
 383       }
 384     });
 385     buildColourMenu();
 386
 387     if (Desktop.desktop != null)
 388     {
 389       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 390       addServiceListeners();
 391       setGUINucleotide();
 392     }
 393
 394     if (viewport.getWrapAlignment())
 395     {
 396       wrapMenuItem_actionPerformed(null);
 397     }
 398
 399     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 400     {
 401       this.overviewMenuItem_actionPerformed(null);
 402     }
 403
 404     addKeyListener();
 405
 406     final List<AlignmentPanel> selviews = new ArrayList<>();
 407     final List<AlignmentPanel> origview = new ArrayList<>();
 408     final String menuLabel = MessageManager
 409             .getString("label.copy_format_from");
 410     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 411             new ViewSetProvider()
 412             {
 413
 414               @Override
 415               public AlignmentPanel[] getAllAlignmentPanels()
 416               {
 417                 origview.clear();
 418                 origview.add(alignPanel);
 419                 // make an array of all alignment panels except for this one
 420                 List<AlignmentPanel> aps = new ArrayList<>(
 421                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 422                 aps.remove(AlignFrame.this.alignPanel);
 423                 return aps.toArray(new AlignmentPanel[aps.size()]);
 424               }
 425             }, selviews, new ItemListener()
 426             {
 427
 428               @Override
 429               public void itemStateChanged(ItemEvent e)
 430               {
 431                 if (origview.size() > 0)
 432                 {
 433                   final AlignmentPanel ap = origview.get(0);
 434
 435                   /*
 436                    * Copy the ViewStyle of the selected panel to 'this one'.
 437                    * Don't change value of 'scaleProteinAsCdna' unless copying
 438                    * from a SplitFrame.
 439                    */
 440                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 441                           .getViewStyle();
 442                   boolean fromSplitFrame = selviews.get(0)
 443                           .getAlignViewport().getCodingComplement() != null;
 444                   if (!fromSplitFrame)
 445                   {
 446                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 447                             .getViewStyle().isScaleProteinAsCdna());
 448                   }
 449                   ap.getAlignViewport().setViewStyle(vs);
 450
 451                   /*
 452                    * Also rescale ViewStyle of SplitFrame complement if there is
 453                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 454                    * the whole ViewStyle (allow cDNA protein to have different
 455                    * fonts)
 456                    */
 457                   AlignViewportI complement = ap.getAlignViewport()
 458                           .getCodingComplement();
 459                   if (complement != null && vs.isScaleProteinAsCdna())
 460                   {
 461                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 462                     ((SplitFrame) af.getSplitViewContainer())
 463                             .adjustLayout();
 464                     af.setMenusForViewport();
 465                   }
 466
 467                   ap.updateLayout();
 468                   ap.setSelected(true);
 469                   ap.alignFrame.setMenusForViewport();
 470
 471                 }
 472               }
 473             });
 474     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 475             .indexOf("devel") > -1
 476             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 477                     .indexOf("test") > -1)
 478     {
 479       formatMenu.add(vsel);
 480     }
 481     addFocusListener(new FocusAdapter()
 482     {
 483       @Override
 484       public void focusGained(FocusEvent e)
 485       {
 486         Jalview.setCurrentAlignFrame(AlignFrame.this);
 487       }
 488     });
 489
 490   }
 491
 492   /**
 493    * Change the filename and format for the alignment, and enable the 'reload'
 494    * button functionality.
 495    *
 496    * @param file
 497    *          valid filename
 498    * @param format
 499    *          format of file
 500    */
 501   public void setFileName(String file, FileFormatI format)
 502   {
 503     fileName = file;
 504     setFileFormat(format);
 505     reload.setEnabled(true);
 506   }
 507
 508   /**
 509    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 510    * events
 511    */
 512   void addKeyListener()
 513   {
 514     addKeyListener(new KeyAdapter()
 515     {
 516       @Override
 517       public void keyPressed(KeyEvent evt)
 518       {
 519         if (viewport.cursorMode
 520                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 521                         && evt.getKeyCode() <= KeyEvent.VK_9)
 522                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 523                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 524                 && Character.isDigit(evt.getKeyChar()))
 525         {
 526           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 527         }
 528
 529         switch (evt.getKeyCode())
 530         {
 531
 532         case 27: // escape key
 533           deselectAllSequenceMenuItem_actionPerformed(null);
 534
 535           break;
 536
 537         case KeyEvent.VK_DOWN:
 538           if (evt.isAltDown() || !viewport.cursorMode)
 539           {
 540             moveSelectedSequences(false);
 541           }
 542           if (viewport.cursorMode)
 543           {
 544             alignPanel.getSeqPanel().moveCursor(0, 1);
 545           }
 546           break;
 547
 548         case KeyEvent.VK_UP:
 549           if (evt.isAltDown() || !viewport.cursorMode)
 550           {
 551             moveSelectedSequences(true);
 552           }
 553           if (viewport.cursorMode)
 554           {
 555             alignPanel.getSeqPanel().moveCursor(0, -1);
 556           }
 557
 558           break;
 559
 560         case KeyEvent.VK_LEFT:
 561           if (evt.isAltDown() || !viewport.cursorMode)
 562           {
 563             slideSequences(false,
 564                     alignPanel.getSeqPanel().getKeyboardNo1());
 565           }
 566           else
 567           {
 568             alignPanel.getSeqPanel().moveCursor(-1, 0);
 569           }
 570
 571           break;
 572
 573         case KeyEvent.VK_RIGHT:
 574           if (evt.isAltDown() || !viewport.cursorMode)
 575           {
 576             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 577           }
 578           else
 579           {
 580             alignPanel.getSeqPanel().moveCursor(1, 0);
 581           }
 582           break;
 583
 584         case KeyEvent.VK_SPACE:
 585           if (viewport.cursorMode)
 586           {
 587             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 588                     || evt.isShiftDown() || evt.isAltDown());
 589           }
 590           break;
 591
 592         // case KeyEvent.VK_A:
 593         // if (viewport.cursorMode)
 594         // {
 595         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 596         // //System.out.println("A");
 597         // }
 598         // break;
 599         /*
 600          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 601          * System.out.println("closing bracket"); } break;
 602          */
 603         case KeyEvent.VK_DELETE:
 604         case KeyEvent.VK_BACK_SPACE:
 605           if (!viewport.cursorMode)
 606           {
 607             cut_actionPerformed(null);
 608           }
 609           else
 610           {
 611             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 612                     || evt.isShiftDown() || evt.isAltDown());
 613           }
 614
 615           break;
 616
 617         case KeyEvent.VK_S:
 618           if (viewport.cursorMode)
 619           {
 620             alignPanel.getSeqPanel().setCursorRow();
 621           }
 622           break;
 623         case KeyEvent.VK_C:
 624           if (viewport.cursorMode && !evt.isControlDown())
 625           {
 626             alignPanel.getSeqPanel().setCursorColumn();
 627           }
 628           break;
 629         case KeyEvent.VK_P:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setCursorPosition();
 633           }
 634           break;
 635
 636         case KeyEvent.VK_ENTER:
 637         case KeyEvent.VK_COMMA:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setCursorRowAndColumn();
 641           }
 642           break;
 643
 644         case KeyEvent.VK_Q:
 645           if (viewport.cursorMode)
 646           {
 647             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 648           }
 649           break;
 650         case KeyEvent.VK_M:
 651           if (viewport.cursorMode)
 652           {
 653             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 654           }
 655           break;
 656
 657         case KeyEvent.VK_F2:
 658           viewport.cursorMode = !viewport.cursorMode;
 659           statusBar.setText(MessageManager
 660                   .formatMessage("label.keyboard_editing_mode", new String[]
 661                   { (viewport.cursorMode ? "on" : "off") }));
 662           if (viewport.cursorMode)
 663           {
 664             ViewportRanges ranges = viewport.getRanges();
 665             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 666                     .getStartRes();
 667             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 668                     .getStartSeq();
 669           }
 670           alignPanel.getSeqPanel().seqCanvas.repaint();
 671           break;
 672
 673         case KeyEvent.VK_F1:
 674           try
 675           {
 676             Help.showHelpWindow();
 677           } catch (Exception ex)
 678           {
 679             ex.printStackTrace();
 680           }
 681           break;
 682         case KeyEvent.VK_H:
 683         {
 684           boolean toggleSeqs = !evt.isControlDown();
 685           boolean toggleCols = !evt.isShiftDown();
 686           toggleHiddenRegions(toggleSeqs, toggleCols);
 687           break;
 688         }
 689         case KeyEvent.VK_B:
 690         {
 691           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 692           boolean modifyExisting = true; // always modify, don't clear
 693                                          // evt.isShiftDown();
 694           boolean invertHighlighted = evt.isAltDown();
 695           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 696                   toggleSel);
 697           break;
 698         }
 699         case KeyEvent.VK_PAGE_UP:
 700           viewport.getRanges().pageUp();
 701           break;
 702         case KeyEvent.VK_PAGE_DOWN:
 703           viewport.getRanges().pageDown();
 704           break;
 705         }
 706       }
 707
 708       @Override
 709       public void keyReleased(KeyEvent evt)
 710       {
 711         switch (evt.getKeyCode())
 712         {
 713         case KeyEvent.VK_LEFT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null,
 717                     viewport.getAlignment().getSequences());
 718           }
 719           break;
 720
 721         case KeyEvent.VK_RIGHT:
 722           if (evt.isAltDown() || !viewport.cursorMode)
 723           {
 724             viewport.firePropertyChange("alignment", null,
 725                     viewport.getAlignment().getSequences());
 726           }
 727           break;
 728         }
 729       }
 730     });
 731   }
 732
 733   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 734   {
 735     ap.alignFrame = this;
 736     avc = new jalview.controller.AlignViewController(this, viewport,
 737             alignPanel);
 738
 739     alignPanels.add(ap);
 740
 741     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 742
 743     int aSize = alignPanels.size();
 744
 745     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 746
 747     if (aSize == 1 && ap.av.viewName == null)
 748     {
 749       this.getContentPane().add(ap, BorderLayout.CENTER);
 750     }
 751     else
 752     {
 753       if (aSize == 2)
 754       {
 755         setInitialTabVisible();
 756       }
 757
 758       expandViews.setEnabled(true);
 759       gatherViews.setEnabled(true);
 760       tabbedPane.addTab(ap.av.viewName, ap);
 761
 762       ap.setVisible(false);
 763     }
 764
 765     if (newPanel)
 766     {
 767       if (ap.av.isPadGaps())
 768       {
 769         ap.av.getAlignment().padGaps();
 770       }
 771       ap.av.updateConservation(ap);
 772       ap.av.updateConsensus(ap);
 773       ap.av.updateStrucConsensus(ap);
 774     }
 775   }
 776
 777   public void setInitialTabVisible()
 778   {
 779     expandViews.setEnabled(true);
 780     gatherViews.setEnabled(true);
 781     tabbedPane.setVisible(true);
 782     AlignmentPanel first = alignPanels.get(0);
 783     tabbedPane.addTab(first.av.viewName, first);
 784     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 785   }
 786
 787   public AlignViewport getViewport()
 788   {
 789     return viewport;
 790   }
 791
 792   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 793   private void addServiceListeners()
 794   {
 795     final java.beans.PropertyChangeListener thisListener;
 796     Desktop.instance.addJalviewPropertyChangeListener("services",
 797             thisListener = new java.beans.PropertyChangeListener()
 798             {
 799               @Override
 800               public void propertyChange(PropertyChangeEvent evt)
 801               {
 802                 // // System.out.println("Discoverer property change.");
 803                 // if (evt.getPropertyName().equals("services"))
 804                 {
 805                   SwingUtilities.invokeLater(new Runnable()
 806                   {
 807
 808                     @Override
 809                     public void run()
 810                     {
 811                       System.err.println(
 812                               "Rebuild WS Menu for service change");
 813                       BuildWebServiceMenu();
 814                     }
 815
 816                   });
 817                 }
 818               }
 819             });
 820     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 821     {
 822       @Override
 823       public void internalFrameClosed(
 824               javax.swing.event.InternalFrameEvent evt)
 825       {
 826         // System.out.println("deregistering discoverer listener");
 827         Desktop.instance.removeJalviewPropertyChangeListener("services",
 828                 thisListener);
 829         closeMenuItem_actionPerformed(true);
 830       };
 831     });
 832     // Finally, build the menu once to get current service state
 833     new Thread(new Runnable()
 834     {
 835       @Override
 836       public void run()
 837       {
 838         BuildWebServiceMenu();
 839       }
 840     }).start();
 841   }
 842
 843   /**
 844    * Configure menu items that vary according to whether the alignment is
 845    * nucleotide or protein
 846    */
 847   public void setGUINucleotide()
 848   {
 849     AlignmentI al = getViewport().getAlignment();
 850     boolean nucleotide = al.isNucleotide();
 851
 852     showTranslation.setVisible(nucleotide);
 853     showReverse.setVisible(nucleotide);
 854     showReverseComplement.setVisible(nucleotide);
 855     conservationMenuItem.setEnabled(!nucleotide);
 856     modifyConservation
 857             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 858     showGroupConservation.setEnabled(!nucleotide);
 859
 860     showComplementMenuItem
 861             .setText(nucleotide ? MessageManager.getString("label.protein")
 862                     : MessageManager.getString("label.nucleotide"));
 863   }
 864
 865   /**
 866    * set up menus for the current viewport. This may be called after any
 867    * operation that affects the data in the current view (selection changed,
 868    * etc) to update the menus to reflect the new state.
 869    */
 870   @Override
 871   public void setMenusForViewport()
 872   {
 873     setMenusFromViewport(viewport);
 874   }
 875
 876   /**
 877    * Need to call this method when tabs are selected for multiple views, or when
 878    * loading from Jalview2XML.java
 879    *
 880    * @param av
 881    *          AlignViewport
 882    */
 883   void setMenusFromViewport(AlignViewport av)
 884   {
 885     padGapsMenuitem.setSelected(av.isPadGaps());
 886     colourTextMenuItem.setSelected(av.isShowColourText());
 887     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 888     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 889     conservationMenuItem.setSelected(av.getConservationSelected());
 890     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 891     seqLimits.setSelected(av.getShowJVSuffix());
 892     idRightAlign.setSelected(av.isRightAlignIds());
 893     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 894     renderGapsMenuItem.setSelected(av.isRenderGaps());
 895     wrapMenuItem.setSelected(av.getWrapAlignment());
 896     scaleAbove.setVisible(av.getWrapAlignment());
 897     scaleLeft.setVisible(av.getWrapAlignment());
 898     scaleRight.setVisible(av.getWrapAlignment());
 899     annotationPanelMenuItem.setState(av.isShowAnnotation());
 900     /*
 901      * Show/hide annotations only enabled if annotation panel is shown
 902      */
 903     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 904     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 905     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 906     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 907     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 908     viewTextMenuItem.setSelected(av.getShowText());
 909     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 910     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 911     showGroupConservation.setSelected(av.isShowGroupConservation());
 912     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 913     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 914     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 915
 916     ColourMenuHelper.setColourSelected(colourMenu,
 917             av.getGlobalColourScheme());
 918
 919     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 920     hiddenMarkers.setState(av.getShowHiddenMarkers());
 921     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 922     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 923     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 924     autoCalculate.setSelected(av.autoCalculateConsensus);
 925     sortByTree.setSelected(av.sortByTree);
 926     listenToViewSelections.setSelected(av.followSelection);
 927
 928     showProducts.setEnabled(canShowProducts());
 929     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 930
 931     updateEditMenuBar();
 932   }
 933
 934   /**
 935    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 936    *
 937    * @param b
 938    */
 939   public void setGroovyEnabled(boolean b)
 940   {
 941     runGroovy.setEnabled(b);
 942   }
 943
 944   private IProgressIndicator progressBar;
 945
 946   /*
 947    * (non-Javadoc)
 948    *
 949    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 950    */
 951   @Override
 952   public void setProgressBar(String message, long id)
 953   {
 954     progressBar.setProgressBar(message, id);
 955   }
 956
 957   @Override
 958   public void registerHandler(final long id,
 959           final IProgressIndicatorHandler handler)
 960   {
 961     progressBar.registerHandler(id, handler);
 962   }
 963
 964   /**
 965    *
 966    * @return true if any progress bars are still active
 967    */
 968   @Override
 969   public boolean operationInProgress()
 970   {
 971     return progressBar.operationInProgress();
 972   }
 973
 974   @Override
 975   public void setStatus(String text)
 976   {
 977     statusBar.setText(text);
 978   }
 979
 980   /*
 981    * Added so Castor Mapping file can obtain Jalview Version
 982    */
 983   public String getVersion()
 984   {
 985     return jalview.bin.Cache.getProperty("VERSION");
 986   }
 987
 988   public FeatureRenderer getFeatureRenderer()
 989   {
 990     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 991   }
 992
 993   @Override
 994   public void fetchSequence_actionPerformed(ActionEvent e)
 995   {
 996     new jalview.gui.SequenceFetcher(this);
 997   }
 998
 999   @Override
1000   public void addFromFile_actionPerformed(ActionEvent e)
1001   {
1002     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1003   }
1004
1005   @Override
1006   public void reload_actionPerformed(ActionEvent e)
1007   {
1008     if (fileName != null)
1009     {
1010       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1011       // originating file's format
1012       // TODO: work out how to recover feature settings for correct view(s) when
1013       // file is reloaded.
1014       if (FileFormat.Jalview.equals(currentFileFormat))
1015       {
1016         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1017         for (int i = 0; i < frames.length; i++)
1018         {
1019           if (frames[i] instanceof AlignFrame && frames[i] != this
1020                   && ((AlignFrame) frames[i]).fileName != null
1021                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1022           {
1023             try
1024             {
1025               frames[i].setSelected(true);
1026               Desktop.instance.closeAssociatedWindows();
1027             } catch (java.beans.PropertyVetoException ex)
1028             {
1029             }
1030           }
1031
1032         }
1033         Desktop.instance.closeAssociatedWindows();
1034
1035         FileLoader loader = new FileLoader();
1036         DataSourceType protocol = fileName.startsWith("http:")
1037                 ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1040       }
1041       else
1042       {
1043         Rectangle bounds = this.getBounds();
1044
1045         FileLoader loader = new FileLoader();
1046         DataSourceType protocol = fileName.startsWith("http:")
1047                 ? DataSourceType.URL
1048                 : DataSourceType.FILE;
1049         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1050                 protocol, currentFileFormat);
1051
1052         newframe.setBounds(bounds);
1053         if (featureSettings != null && featureSettings.isShowing())
1054         {
1055           final Rectangle fspos = featureSettings.frame.getBounds();
1056           // TODO: need a 'show feature settings' function that takes bounds -
1057           // need to refactor Desktop.addFrame
1058           newframe.featureSettings_actionPerformed(null);
1059           final FeatureSettings nfs = newframe.featureSettings;
1060           SwingUtilities.invokeLater(new Runnable()
1061           {
1062             @Override
1063             public void run()
1064             {
1065               nfs.frame.setBounds(fspos);
1066             }
1067           });
1068           this.featureSettings.close();
1069           this.featureSettings = null;
1070         }
1071         this.closeMenuItem_actionPerformed(true);
1072       }
1073     }
1074   }
1075
1076   @Override
1077   public void addFromText_actionPerformed(ActionEvent e)
1078   {
1079     Desktop.instance
1080             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1081   }
1082
1083   @Override
1084   public void addFromURL_actionPerformed(ActionEvent e)
1085   {
1086     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1087   }
1088
1089   @Override
1090   public void save_actionPerformed(ActionEvent e)
1091   {
1092     if (fileName == null || (currentFileFormat == null)
1093             || fileName.startsWith("http"))
1094     {
1095       saveAs_actionPerformed(null);
1096     }
1097     else
1098     {
1099       saveAlignment(fileName, currentFileFormat);
1100     }
1101   }
1102
1103   /**
1104    * DOCUMENT ME!
1105    *
1106    * @param e
1107    *          DOCUMENT ME!
1108    */
1109   @Override
1110   public void saveAs_actionPerformed(ActionEvent e)
1111   {
1112     String format = currentFileFormat == null ? null
1113             : currentFileFormat.getName();
1114     JalviewFileChooser chooser = JalviewFileChooser
1115             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1116
1117     chooser.setFileView(new JalviewFileView());
1118     chooser.setDialogTitle(
1119             MessageManager.getString("label.save_alignment_to_file"));
1120     chooser.setToolTipText(MessageManager.getString("action.save"));
1121
1122     int value = chooser.showSaveDialog(this);
1123
1124     if (value == JalviewFileChooser.APPROVE_OPTION)
1125     {
1126       currentFileFormat = chooser.getSelectedFormat();
1127       while (currentFileFormat == null)
1128       {
1129         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1130                 MessageManager.getString(
1131                         "label.select_file_format_before_saving"),
1132                 MessageManager.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(
1162                 shortName.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(format, exportData.getAlignment(), // class
1183                                                                            // cast
1184                                                                            // exceptions
1185                                                                            // will
1186               // occur in the distant future
1187               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1188               f.getCacheSuffixDefault(format),
1189               viewport.getAlignment().getHiddenColumns());
1190
1191       if (output == null)
1192       {
1193         success = false;
1194       }
1195       else
1196       {
1197         try
1198         {
1199           PrintWriter out = new PrintWriter(new FileWriter(file));
1200
1201           out.print(output);
1202           out.close();
1203           this.setTitle(file);
1204           statusBar.setText(MessageManager.formatMessage(
1205                   "label.successfully_saved_to_file_in_format", new Object[]
1206                   { fileName, format.getName() }));
1207         } catch (Exception ex)
1208         {
1209           success = false;
1210           ex.printStackTrace();
1211         }
1212       }
1213     }
1214
1215     if (!success)
1216     {
1217       JvOptionPane.showInternalMessageDialog(this, MessageManager
1218               .formatMessage("label.couldnt_save_file", new Object[]
1219               { fileName }),
1220               MessageManager.getString("label.error_saving_file"),
1221               JvOptionPane.WARNING_MESSAGE);
1222     }
1223
1224     return success;
1225   }
1226
1227   private void warningMessage(String warning, String title)
1228   {
1229     if (new jalview.util.Platform().isHeadless())
1230     {
1231       System.err.println("Warning: " + title + "\nWarning: " + warning);
1232
1233     }
1234     else
1235     {
1236       JvOptionPane.showInternalMessageDialog(this, warning, title,
1237               JvOptionPane.WARNING_MESSAGE);
1238     }
1239     return;
1240   }
1241
1242   /**
1243    * DOCUMENT ME!
1244    *
1245    * @param e
1246    *          DOCUMENT ME!
1247    */
1248   @Override
1249   protected void outputText_actionPerformed(ActionEvent e)
1250   {
1251     FileFormatI fileFormat = FileFormats.getInstance()
1252             .forName(e.getActionCommand());
1253     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1254             viewport, null);
1255     if (exportData.getSettings().isCancelled())
1256     {
1257       return;
1258     }
1259     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1260     cap.setForInput(null);
1261     try
1262     {
1263       FileFormatI format = fileFormat;
1264       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1265               .formatSequences(format, exportData.getAlignment(),
1266                       exportData.getOmitHidden(),
1267                       exportData.getStartEndPostions(),
1268                       viewport.getAlignment().getHiddenColumns()));
1269       Desktop.addInternalFrame(cap, MessageManager
1270               .formatMessage("label.alignment_output_command", new Object[]
1271               { e.getActionCommand() }), 600, 500);
1272     } catch (OutOfMemoryError oom)
1273     {
1274       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1275               oom);
1276       cap.dispose();
1277     }
1278
1279   }
1280
1281   public static AlignmentExportData getAlignmentForExport(
1282           FileFormatI format, AlignViewportI viewport,
1283           AlignExportSettingI exportSettings)
1284   {
1285     AlignmentI alignmentToExport = null;
1286     AlignExportSettingI settings = exportSettings;
1287     String[] omitHidden = null;
1288
1289     HiddenSequences hiddenSeqs = viewport.getAlignment()
1290             .getHiddenSequences();
1291
1292     alignmentToExport = viewport.getAlignment();
1293
1294     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1295     if (settings == null)
1296     {
1297       settings = new AlignExportSettings(hasHiddenSeqs,
1298               viewport.hasHiddenColumns(), format);
1299     }
1300     // settings.isExportAnnotations();
1301
1302     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1303     {
1304       omitHidden = viewport.getViewAsString(false,
1305               settings.isExportHiddenSequences());
1306     }
1307
1308     int[] alignmentStartEnd = new int[2];
1309     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1310     {
1311       alignmentToExport = hiddenSeqs.getFullAlignment();
1312     }
1313     else
1314     {
1315       alignmentToExport = viewport.getAlignment();
1316     }
1317     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1318             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1319     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1320             omitHidden, alignmentStartEnd, settings);
1321     return ed;
1322   }
1323
1324   /**
1325    * DOCUMENT ME!
1326    *
1327    * @param e
1328    *          DOCUMENT ME!
1329    */
1330   @Override
1331   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1332   {
1333     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1334     htmlSVG.exportHTML(null);
1335   }
1336
1337   @Override
1338   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1339   {
1340     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1341     bjs.exportHTML(null);
1342   }
1343
1344   public void createImageMap(File file, String image)
1345   {
1346     alignPanel.makePNGImageMap(file, image);
1347   }
1348
1349   /**
1350    * DOCUMENT ME!
1351    *
1352    * @param e
1353    *          DOCUMENT ME!
1354    */
1355   @Override
1356   public void createPNG(File f)
1357   {
1358     alignPanel.makePNG(f);
1359   }
1360
1361   /**
1362    * DOCUMENT ME!
1363    *
1364    * @param e
1365    *          DOCUMENT ME!
1366    */
1367   @Override
1368   public void createEPS(File f)
1369   {
1370     alignPanel.makeEPS(f);
1371   }
1372
1373   @Override
1374   public void createSVG(File f)
1375   {
1376     alignPanel.makeSVG(f);
1377   }
1378
1379   @Override
1380   public void pageSetup_actionPerformed(ActionEvent e)
1381   {
1382     PrinterJob printJob = PrinterJob.getPrinterJob();
1383     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1384   }
1385
1386   /**
1387    * DOCUMENT ME!
1388    *
1389    * @param e
1390    *          DOCUMENT ME!
1391    */
1392   @Override
1393   public void printMenuItem_actionPerformed(ActionEvent e)
1394   {
1395     // Putting in a thread avoids Swing painting problems
1396     PrintThread thread = new PrintThread(alignPanel);
1397     thread.start();
1398   }
1399
1400   @Override
1401   public void exportFeatures_actionPerformed(ActionEvent e)
1402   {
1403     new AnnotationExporter().exportFeatures(alignPanel);
1404   }
1405
1406   @Override
1407   public void exportAnnotations_actionPerformed(ActionEvent e)
1408   {
1409     new AnnotationExporter().exportAnnotations(alignPanel);
1410   }
1411
1412   @Override
1413   public void associatedData_actionPerformed(ActionEvent e)
1414   {
1415     // Pick the tree file
1416     JalviewFileChooser chooser = new JalviewFileChooser(
1417             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1418     chooser.setFileView(new JalviewFileView());
1419     chooser.setDialogTitle(
1420             MessageManager.getString("label.load_jalview_annotations"));
1421     chooser.setToolTipText(
1422             MessageManager.getString("label.load_jalview_annotations"));
1423
1424     int value = chooser.showOpenDialog(null);
1425
1426     if (value == JalviewFileChooser.APPROVE_OPTION)
1427     {
1428       String choice = chooser.getSelectedFile().getPath();
1429       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1430       loadJalviewDataFile(choice, null, null, null);
1431     }
1432
1433   }
1434
1435   /**
1436    * Close the current view or all views in the alignment frame. If the frame
1437    * only contains one view then the alignment will be removed from memory.
1438    *
1439    * @param closeAllTabs
1440    */
1441   @Override
1442   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1443   {
1444     if (alignPanels != null && alignPanels.size() < 2)
1445     {
1446       closeAllTabs = true;
1447     }
1448
1449     try
1450     {
1451       if (alignPanels != null)
1452       {
1453         if (closeAllTabs)
1454         {
1455           if (this.isClosed())
1456           {
1457             // really close all the windows - otherwise wait till
1458             // setClosed(true) is called
1459             for (int i = 0; i < alignPanels.size(); i++)
1460             {
1461               AlignmentPanel ap = alignPanels.get(i);
1462               ap.closePanel();
1463             }
1464           }
1465         }
1466         else
1467         {
1468           closeView(alignPanel);
1469         }
1470       }
1471
1472       if (closeAllTabs)
1473       {
1474         /*
1475          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1476          * be called recursively, with the frame now in 'closed' state
1477          */
1478         this.setClosed(true);
1479       }
1480     } catch (Exception ex)
1481     {
1482       ex.printStackTrace();
1483     }
1484   }
1485
1486   /**
1487    * Close the specified panel and close up tabs appropriately.
1488    *
1489    * @param panelToClose
1490    */
1491   public void closeView(AlignmentPanel panelToClose)
1492   {
1493     int index = tabbedPane.getSelectedIndex();
1494     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1495     alignPanels.remove(panelToClose);
1496     panelToClose.closePanel();
1497     panelToClose = null;
1498
1499     tabbedPane.removeTabAt(closedindex);
1500     tabbedPane.validate();
1501
1502     if (index > closedindex || index == tabbedPane.getTabCount())
1503     {
1504       // modify currently selected tab index if necessary.
1505       index--;
1506     }
1507
1508     this.tabSelectionChanged(index);
1509   }
1510
1511   /**
1512    * DOCUMENT ME!
1513    */
1514   void updateEditMenuBar()
1515   {
1516
1517     if (viewport.getHistoryList().size() > 0)
1518     {
1519       undoMenuItem.setEnabled(true);
1520       CommandI command = viewport.getHistoryList().peek();
1521       undoMenuItem.setText(MessageManager
1522               .formatMessage("label.undo_command", new Object[]
1523               { command.getDescription() }));
1524     }
1525     else
1526     {
1527       undoMenuItem.setEnabled(false);
1528       undoMenuItem.setText(MessageManager.getString("action.undo"));
1529     }
1530
1531     if (viewport.getRedoList().size() > 0)
1532     {
1533       redoMenuItem.setEnabled(true);
1534
1535       CommandI command = viewport.getRedoList().peek();
1536       redoMenuItem.setText(MessageManager
1537               .formatMessage("label.redo_command", new Object[]
1538               { command.getDescription() }));
1539     }
1540     else
1541     {
1542       redoMenuItem.setEnabled(false);
1543       redoMenuItem.setText(MessageManager.getString("action.redo"));
1544     }
1545   }
1546
1547   @Override
1548   public void addHistoryItem(CommandI command)
1549   {
1550     if (command.getSize() > 0)
1551     {
1552       viewport.addToHistoryList(command);
1553       viewport.clearRedoList();
1554       updateEditMenuBar();
1555       viewport.updateHiddenColumns();
1556       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1557       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1558       // viewport.getColumnSelection()
1559       // .getHiddenColumns().size() > 0);
1560     }
1561   }
1562
1563   /**
1564    *
1565    * @return alignment objects for all views
1566    */
1567   AlignmentI[] getViewAlignments()
1568   {
1569     if (alignPanels != null)
1570     {
1571       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1572       int i = 0;
1573       for (AlignmentPanel ap : alignPanels)
1574       {
1575         als[i++] = ap.av.getAlignment();
1576       }
1577       return als;
1578     }
1579     if (viewport != null)
1580     {
1581       return new AlignmentI[] { viewport.getAlignment() };
1582     }
1583     return null;
1584   }
1585
1586   /**
1587    * DOCUMENT ME!
1588    *
1589    * @param e
1590    *          DOCUMENT ME!
1591    */
1592   @Override
1593   protected void undoMenuItem_actionPerformed(ActionEvent e)
1594   {
1595     if (viewport.getHistoryList().isEmpty())
1596     {
1597       return;
1598     }
1599     CommandI command = viewport.getHistoryList().pop();
1600     viewport.addToRedoList(command);
1601     command.undoCommand(getViewAlignments());
1602
1603     AlignmentViewport originalSource = getOriginatingSource(command);
1604     updateEditMenuBar();
1605
1606     if (originalSource != null)
1607     {
1608       if (originalSource != viewport)
1609       {
1610         Cache.log.warn(
1611                 "Implementation worry: mismatch of viewport origin for undo");
1612       }
1613       originalSource.updateHiddenColumns();
1614       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1615       // null
1616       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1617       // viewport.getColumnSelection()
1618       // .getHiddenColumns().size() > 0);
1619       originalSource.firePropertyChange("alignment", null,
1620               originalSource.getAlignment().getSequences());
1621     }
1622   }
1623
1624   /**
1625    * DOCUMENT ME!
1626    *
1627    * @param e
1628    *          DOCUMENT ME!
1629    */
1630   @Override
1631   protected void redoMenuItem_actionPerformed(ActionEvent e)
1632   {
1633     if (viewport.getRedoList().size() < 1)
1634     {
1635       return;
1636     }
1637
1638     CommandI command = viewport.getRedoList().pop();
1639     viewport.addToHistoryList(command);
1640     command.doCommand(getViewAlignments());
1641
1642     AlignmentViewport originalSource = getOriginatingSource(command);
1643     updateEditMenuBar();
1644
1645     if (originalSource != null)
1646     {
1647
1648       if (originalSource != viewport)
1649       {
1650         Cache.log.warn(
1651                 "Implementation worry: mismatch of viewport origin for redo");
1652       }
1653       originalSource.updateHiddenColumns();
1654       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1655       // null
1656       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657       // viewport.getColumnSelection()
1658       // .getHiddenColumns().size() > 0);
1659       originalSource.firePropertyChange("alignment", null,
1660               originalSource.getAlignment().getSequences());
1661     }
1662   }
1663
1664   AlignmentViewport getOriginatingSource(CommandI command)
1665   {
1666     AlignmentViewport originalSource = null;
1667     // For sequence removal and addition, we need to fire
1668     // the property change event FROM the viewport where the
1669     // original alignment was altered
1670     AlignmentI al = null;
1671     if (command instanceof EditCommand)
1672     {
1673       EditCommand editCommand = (EditCommand) command;
1674       al = editCommand.getAlignment();
1675       List<Component> comps = PaintRefresher.components
1676               .get(viewport.getSequenceSetId());
1677
1678       for (Component comp : comps)
1679       {
1680         if (comp instanceof AlignmentPanel)
1681         {
1682           if (al == ((AlignmentPanel) comp).av.getAlignment())
1683           {
1684             originalSource = ((AlignmentPanel) comp).av;
1685             break;
1686           }
1687         }
1688       }
1689     }
1690
1691     if (originalSource == null)
1692     {
1693       // The original view is closed, we must validate
1694       // the current view against the closed view first
1695       if (al != null)
1696       {
1697         PaintRefresher.validateSequences(al, viewport.getAlignment());
1698       }
1699
1700       originalSource = viewport;
1701     }
1702
1703     return originalSource;
1704   }
1705
1706   /**
1707    * DOCUMENT ME!
1708    *
1709    * @param up
1710    *          DOCUMENT ME!
1711    */
1712   public void moveSelectedSequences(boolean up)
1713   {
1714     SequenceGroup sg = viewport.getSelectionGroup();
1715
1716     if (sg == null)
1717     {
1718       return;
1719     }
1720     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1721             viewport.getHiddenRepSequences(), up);
1722     alignPanel.paintAlignment(true, false);
1723   }
1724
1725   synchronized void slideSequences(boolean right, int size)
1726   {
1727     List<SequenceI> sg = new ArrayList<>();
1728     if (viewport.cursorMode)
1729     {
1730       sg.add(viewport.getAlignment()
1731               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1732     }
1733     else if (viewport.getSelectionGroup() != null
1734             && viewport.getSelectionGroup().getSize() != viewport
1735                     .getAlignment().getHeight())
1736     {
1737       sg = viewport.getSelectionGroup()
1738               .getSequences(viewport.getHiddenRepSequences());
1739     }
1740
1741     if (sg.size() < 1)
1742     {
1743       return;
1744     }
1745
1746     List<SequenceI> invertGroup = new ArrayList<>();
1747
1748     for (SequenceI seq : viewport.getAlignment().getSequences())
1749     {
1750       if (!sg.contains(seq))
1751       {
1752         invertGroup.add(seq);
1753       }
1754     }
1755
1756     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1757
1758     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1759     for (int i = 0; i < invertGroup.size(); i++)
1760     {
1761       seqs2[i] = invertGroup.get(i);
1762     }
1763
1764     SlideSequencesCommand ssc;
1765     if (right)
1766     {
1767       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1768               viewport.getGapCharacter());
1769     }
1770     else
1771     {
1772       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1773               viewport.getGapCharacter());
1774     }
1775
1776     int groupAdjustment = 0;
1777     if (ssc.getGapsInsertedBegin() && right)
1778     {
1779       if (viewport.cursorMode)
1780       {
1781         alignPanel.getSeqPanel().moveCursor(size, 0);
1782       }
1783       else
1784       {
1785         groupAdjustment = size;
1786       }
1787     }
1788     else if (!ssc.getGapsInsertedBegin() && !right)
1789     {
1790       if (viewport.cursorMode)
1791       {
1792         alignPanel.getSeqPanel().moveCursor(-size, 0);
1793       }
1794       else
1795       {
1796         groupAdjustment = -size;
1797       }
1798     }
1799
1800     if (groupAdjustment != 0)
1801     {
1802       viewport.getSelectionGroup().setStartRes(
1803               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1804       viewport.getSelectionGroup().setEndRes(
1805               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1806     }
1807
1808     /*
1809      * just extend the last slide command if compatible; but not if in
1810      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1811      */
1812     boolean appendHistoryItem = false;
1813     Deque<CommandI> historyList = viewport.getHistoryList();
1814     boolean inSplitFrame = getSplitViewContainer() != null;
1815     if (!inSplitFrame && historyList != null && historyList.size() > 0
1816             && historyList.peek() instanceof SlideSequencesCommand)
1817     {
1818       appendHistoryItem = ssc.appendSlideCommand(
1819               (SlideSequencesCommand) historyList.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().setContents(ss,
1868               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<>();
1879       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1880       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1881       ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1882               .getHiddenColumns().getHiddenColumnsCopy();
1883       for (int[] region : hiddenRegions)
1884       {
1885         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1886         {
1887           hiddenColumns
1888                   .add(new int[]
1889                   { region[0] - hiddenOffset, region[1] - hiddenOffset });
1890         }
1891       }
1892     }
1893
1894     Desktop.jalviewClipboard = new Object[] { seqs,
1895         viewport.getAlignment().getDataset(), hiddenColumns };
1896     statusBar.setText(MessageManager.formatMessage(
1897             "label.copied_sequences_to_clipboard", new Object[]
1898             { Integer.valueOf(seqs.length).toString() }));
1899   }
1900
1901   /**
1902    * DOCUMENT ME!
1903    *
1904    * @param e
1905    *          DOCUMENT ME!
1906    */
1907   @Override
1908   protected void pasteNew_actionPerformed(ActionEvent e)
1909   {
1910     paste(true);
1911   }
1912
1913   /**
1914    * DOCUMENT ME!
1915    *
1916    * @param e
1917    *          DOCUMENT ME!
1918    */
1919   @Override
1920   protected void pasteThis_actionPerformed(ActionEvent e)
1921   {
1922     paste(false);
1923   }
1924
1925   /**
1926    * Paste contents of Jalview clipboard
1927    *
1928    * @param newAlignment
1929    *          true to paste to a new alignment, otherwise add to this.
1930    */
1931   void paste(boolean newAlignment)
1932   {
1933     boolean externalPaste = true;
1934     try
1935     {
1936       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1937       Transferable contents = c.getContents(this);
1938
1939       if (contents == null)
1940       {
1941         return;
1942       }
1943
1944       String str;
1945       FileFormatI format;
1946       try
1947       {
1948         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1949         if (str.length() < 1)
1950         {
1951           return;
1952         }
1953
1954         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1955
1956       } catch (OutOfMemoryError er)
1957       {
1958         new OOMWarning("Out of memory pasting sequences!!", er);
1959         return;
1960       }
1961
1962       SequenceI[] sequences;
1963       boolean annotationAdded = false;
1964       AlignmentI alignment = null;
1965
1966       if (Desktop.jalviewClipboard != null)
1967       {
1968         // The clipboard was filled from within Jalview, we must use the
1969         // sequences
1970         // And dataset from the copied alignment
1971         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1972         // be doubly sure that we create *new* sequence objects.
1973         sequences = new SequenceI[newseq.length];
1974         for (int i = 0; i < newseq.length; i++)
1975         {
1976           sequences[i] = new Sequence(newseq[i]);
1977         }
1978         alignment = new Alignment(sequences);
1979         externalPaste = false;
1980       }
1981       else
1982       {
1983         // parse the clipboard as an alignment.
1984         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1985                 format);
1986         sequences = alignment.getSequencesArray();
1987       }
1988
1989       int alwidth = 0;
1990       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1991       int fgroup = -1;
1992
1993       if (newAlignment)
1994       {
1995
1996         if (Desktop.jalviewClipboard != null)
1997         {
1998           // dataset is inherited
1999           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2000         }
2001         else
2002         {
2003           // new dataset is constructed
2004           alignment.setDataset(null);
2005         }
2006         alwidth = alignment.getWidth() + 1;
2007       }
2008       else
2009       {
2010         AlignmentI pastedal = alignment; // preserve pasted alignment object
2011         // Add pasted sequences and dataset into existing alignment.
2012         alignment = viewport.getAlignment();
2013         alwidth = alignment.getWidth() + 1;
2014         // decide if we need to import sequences from an existing dataset
2015         boolean importDs = Desktop.jalviewClipboard != null
2016                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2017         // importDs==true instructs us to copy over new dataset sequences from
2018         // an existing alignment
2019         Vector newDs = (importDs) ? new Vector() : null; // used to create
2020         // minimum dataset set
2021
2022         for (int i = 0; i < sequences.length; i++)
2023         {
2024           if (importDs)
2025           {
2026             newDs.addElement(null);
2027           }
2028           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2029           // paste
2030           if (importDs && ds != null)
2031           {
2032             if (!newDs.contains(ds))
2033             {
2034               newDs.setElementAt(ds, i);
2035               ds = new Sequence(ds);
2036               // update with new dataset sequence
2037               sequences[i].setDatasetSequence(ds);
2038             }
2039             else
2040             {
2041               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2042             }
2043           }
2044           else
2045           {
2046             // copy and derive new dataset sequence
2047             sequences[i] = sequences[i].deriveSequence();
2048             alignment.getDataset()
2049                     .addSequence(sequences[i].getDatasetSequence());
2050             // TODO: avoid creation of duplicate dataset sequences with a
2051             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2052           }
2053           alignment.addSequence(sequences[i]); // merges dataset
2054         }
2055         if (newDs != null)
2056         {
2057           newDs.clear(); // tidy up
2058         }
2059         if (alignment.getAlignmentAnnotation() != null)
2060         {
2061           for (AlignmentAnnotation alan : alignment
2062                   .getAlignmentAnnotation())
2063           {
2064             if (alan.graphGroup > fgroup)
2065             {
2066               fgroup = alan.graphGroup;
2067             }
2068           }
2069         }
2070         if (pastedal.getAlignmentAnnotation() != null)
2071         {
2072           // Add any annotation attached to alignment.
2073           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2074           for (int i = 0; i < alann.length; i++)
2075           {
2076             annotationAdded = true;
2077             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2078             {
2079               AlignmentAnnotation newann = new AlignmentAnnotation(
2080                       alann[i]);
2081               if (newann.graphGroup > -1)
2082               {
2083                 if (newGraphGroups.size() <= newann.graphGroup
2084                         || newGraphGroups.get(newann.graphGroup) == null)
2085                 {
2086                   for (int q = newGraphGroups
2087                           .size(); q <= newann.graphGroup; q++)
2088                   {
2089                     newGraphGroups.add(q, null);
2090                   }
2091                   newGraphGroups.set(newann.graphGroup,
2092                           new Integer(++fgroup));
2093                 }
2094                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2095                         .intValue();
2096               }
2097
2098               newann.padAnnotation(alwidth);
2099               alignment.addAnnotation(newann);
2100             }
2101           }
2102         }
2103       }
2104       if (!newAlignment)
2105       {
2106         // /////
2107         // ADD HISTORY ITEM
2108         //
2109         addHistoryItem(new EditCommand(
2110                 MessageManager.getString("label.add_sequences"),
2111                 Action.PASTE, sequences, 0, alignment.getWidth(),
2112                 alignment));
2113       }
2114       // Add any annotations attached to sequences
2115       for (int i = 0; i < sequences.length; i++)
2116       {
2117         if (sequences[i].getAnnotation() != null)
2118         {
2119           AlignmentAnnotation newann;
2120           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2121           {
2122             annotationAdded = true;
2123             newann = sequences[i].getAnnotation()[a];
2124             newann.adjustForAlignment();
2125             newann.padAnnotation(alwidth);
2126             if (newann.graphGroup > -1)
2127             {
2128               if (newann.graphGroup > -1)
2129               {
2130                 if (newGraphGroups.size() <= newann.graphGroup
2131                         || newGraphGroups.get(newann.graphGroup) == null)
2132                 {
2133                   for (int q = newGraphGroups
2134                           .size(); q <= newann.graphGroup; q++)
2135                   {
2136                     newGraphGroups.add(q, null);
2137                   }
2138                   newGraphGroups.set(newann.graphGroup,
2139                           new Integer(++fgroup));
2140                 }
2141                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2142                         .intValue();
2143               }
2144             }
2145             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2146             // was
2147             // duplicated
2148             // earlier
2149             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2150                     a);
2151           }
2152         }
2153       }
2154       if (!newAlignment)
2155       {
2156
2157         // propagate alignment changed.
2158         viewport.getRanges().setEndSeq(alignment.getHeight());
2159         if (annotationAdded)
2160         {
2161           // Duplicate sequence annotation in all views.
2162           AlignmentI[] alview = this.getViewAlignments();
2163           for (int i = 0; i < sequences.length; i++)
2164           {
2165             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2166             if (sann == null)
2167             {
2168               continue;
2169             }
2170             for (int avnum = 0; avnum < alview.length; avnum++)
2171             {
2172               if (alview[avnum] != alignment)
2173               {
2174                 // duplicate in a view other than the one with input focus
2175                 int avwidth = alview[avnum].getWidth() + 1;
2176                 // this relies on sann being preserved after we
2177                 // modify the sequence's annotation array for each duplication
2178                 for (int a = 0; a < sann.length; a++)
2179                 {
2180                   AlignmentAnnotation newann = new AlignmentAnnotation(
2181                           sann[a]);
2182                   sequences[i].addAlignmentAnnotation(newann);
2183                   newann.padAnnotation(avwidth);
2184                   alview[avnum].addAnnotation(newann); // annotation was
2185                   // duplicated earlier
2186                   // TODO JAL-1145 graphGroups are not updated for sequence
2187                   // annotation added to several views. This may cause
2188                   // strangeness
2189                   alview[avnum].setAnnotationIndex(newann, a);
2190                 }
2191               }
2192             }
2193           }
2194           buildSortByAnnotationScoresMenu();
2195         }
2196         viewport.firePropertyChange("alignment", null,
2197                 alignment.getSequences());
2198         if (alignPanels != null)
2199         {
2200           for (AlignmentPanel ap : alignPanels)
2201           {
2202             ap.validateAnnotationDimensions(false);
2203           }
2204         }
2205         else
2206         {
2207           alignPanel.validateAnnotationDimensions(false);
2208         }
2209
2210       }
2211       else
2212       {
2213         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2214                 DEFAULT_HEIGHT);
2215         String newtitle = new String("Copied sequences");
2216
2217         if (Desktop.jalviewClipboard != null
2218                 && Desktop.jalviewClipboard[2] != null)
2219         {
2220           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2221           for (int[] region : hc)
2222           {
2223             af.viewport.hideColumns(region[0], region[1]);
2224           }
2225         }
2226
2227         // >>>This is a fix for the moment, until a better solution is
2228         // found!!<<<
2229         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2230                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2231                         .getFeatureRenderer());
2232
2233         // TODO: maintain provenance of an alignment, rather than just make the
2234         // title a concatenation of operations.
2235         if (!externalPaste)
2236         {
2237           if (title.startsWith("Copied sequences"))
2238           {
2239             newtitle = title;
2240           }
2241           else
2242           {
2243             newtitle = newtitle.concat("- from " + title);
2244           }
2245         }
2246         else
2247         {
2248           newtitle = new String("Pasted sequences");
2249         }
2250
2251         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2252                 DEFAULT_HEIGHT);
2253
2254       }
2255
2256     } catch (Exception ex)
2257     {
2258       ex.printStackTrace();
2259       System.out.println("Exception whilst pasting: " + ex);
2260       // could be anything being pasted in here
2261     }
2262
2263   }
2264
2265   @Override
2266   protected void expand_newalign(ActionEvent e)
2267   {
2268     try
2269     {
2270       AlignmentI alignment = AlignmentUtils
2271               .expandContext(getViewport().getAlignment(), -1);
2272       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2273               DEFAULT_HEIGHT);
2274       String newtitle = new String("Flanking alignment");
2275
2276       if (Desktop.jalviewClipboard != null
2277               && Desktop.jalviewClipboard[2] != null)
2278       {
2279         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2280         for (int region[] : hc)
2281         {
2282           af.viewport.hideColumns(region[0], region[1]);
2283         }
2284       }
2285
2286       // >>>This is a fix for the moment, until a better solution is
2287       // found!!<<<
2288       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2289               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2290                       .getFeatureRenderer());
2291
2292       // TODO: maintain provenance of an alignment, rather than just make the
2293       // title a concatenation of operations.
2294       {
2295         if (title.startsWith("Copied sequences"))
2296         {
2297           newtitle = title;
2298         }
2299         else
2300         {
2301           newtitle = newtitle.concat("- from " + title);
2302         }
2303       }
2304
2305       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2306
2307     } catch (Exception ex)
2308     {
2309       ex.printStackTrace();
2310       System.out.println("Exception whilst pasting: " + ex);
2311       // could be anything being pasted in here
2312     } catch (OutOfMemoryError oom)
2313     {
2314       new OOMWarning("Viewing flanking region of alignment", oom);
2315     }
2316   }
2317
2318   /**
2319    * DOCUMENT ME!
2320    *
2321    * @param e
2322    *          DOCUMENT ME!
2323    */
2324   @Override
2325   protected void cut_actionPerformed(ActionEvent e)
2326   {
2327     copy_actionPerformed(null);
2328     delete_actionPerformed(null);
2329   }
2330
2331   /**
2332    * DOCUMENT ME!
2333    *
2334    * @param e
2335    *          DOCUMENT ME!
2336    */
2337   @Override
2338   protected void delete_actionPerformed(ActionEvent evt)
2339   {
2340
2341     SequenceGroup sg = viewport.getSelectionGroup();
2342     if (sg == null)
2343     {
2344       return;
2345     }
2346
2347     /*
2348      * If the cut affects all sequences, warn, remove highlighted columns
2349      */
2350     if (sg.getSize() == viewport.getAlignment().getHeight())
2351     {
2352       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2353               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2354       if (isEntireAlignWidth)
2355       {
2356         int confirm = JvOptionPane.showConfirmDialog(this,
2357                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2358                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2359                 JvOptionPane.OK_CANCEL_OPTION);
2360
2361         if (confirm == JvOptionPane.CANCEL_OPTION
2362                 || confirm == JvOptionPane.CLOSED_OPTION)
2363         {
2364           return;
2365         }
2366       }
2367       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2368               sg.getEndRes() + 1);
2369     }
2370     SequenceI[] cut = sg.getSequences()
2371             .toArray(new SequenceI[sg.getSize()]);
2372
2373     addHistoryItem(new EditCommand(
2374             MessageManager.getString("label.cut_sequences"), Action.CUT,
2375             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2376             viewport.getAlignment()));
2377
2378     viewport.setSelectionGroup(null);
2379     viewport.sendSelection();
2380     viewport.getAlignment().deleteGroup(sg);
2381
2382     viewport.firePropertyChange("alignment", null,
2383             viewport.getAlignment().getSequences());
2384     if (viewport.getAlignment().getHeight() < 1)
2385     {
2386       try
2387       {
2388         this.setClosed(true);
2389       } catch (Exception ex)
2390       {
2391       }
2392     }
2393   }
2394
2395   /**
2396    * DOCUMENT ME!
2397    *
2398    * @param e
2399    *          DOCUMENT ME!
2400    */
2401   @Override
2402   protected void deleteGroups_actionPerformed(ActionEvent e)
2403   {
2404     if (avc.deleteGroups())
2405     {
2406       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2407       alignPanel.updateAnnotation();
2408       alignPanel.paintAlignment(true, true);
2409     }
2410   }
2411
2412   /**
2413    * DOCUMENT ME!
2414    *
2415    * @param e
2416    *          DOCUMENT ME!
2417    */
2418   @Override
2419   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2420   {
2421     SequenceGroup sg = new SequenceGroup();
2422
2423     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2424     {
2425       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2426     }
2427
2428     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2429     viewport.setSelectionGroup(sg);
2430     viewport.sendSelection();
2431     // JAL-2034 - should delegate to
2432     // alignPanel to decide if overview needs
2433     // updating.
2434     alignPanel.paintAlignment(false, false);
2435     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2436   }
2437
2438   /**
2439    * DOCUMENT ME!
2440    *
2441    * @param e
2442    *          DOCUMENT ME!
2443    */
2444   @Override
2445   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2446   {
2447     if (viewport.cursorMode)
2448     {
2449       alignPanel.getSeqPanel().keyboardNo1 = null;
2450       alignPanel.getSeqPanel().keyboardNo2 = null;
2451     }
2452     viewport.setSelectionGroup(null);
2453     viewport.getColumnSelection().clear();
2454     viewport.setSelectionGroup(null);
2455     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2456     // JAL-2034 - should delegate to
2457     // alignPanel to decide if overview needs
2458     // updating.
2459     alignPanel.paintAlignment(false, false);
2460     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2461     viewport.sendSelection();
2462   }
2463
2464   /**
2465    * DOCUMENT ME!
2466    *
2467    * @param e
2468    *          DOCUMENT ME!
2469    */
2470   @Override
2471   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2472   {
2473     SequenceGroup sg = viewport.getSelectionGroup();
2474
2475     if (sg == null)
2476     {
2477       selectAllSequenceMenuItem_actionPerformed(null);
2478
2479       return;
2480     }
2481
2482     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2483     {
2484       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2485     }
2486     // JAL-2034 - should delegate to
2487     // alignPanel to decide if overview needs
2488     // updating.
2489
2490     alignPanel.paintAlignment(true, false);
2491     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2492     viewport.sendSelection();
2493   }
2494
2495   @Override
2496   public void invertColSel_actionPerformed(ActionEvent e)
2497   {
2498     viewport.invertColumnSelection();
2499     alignPanel.paintAlignment(true, false);
2500     viewport.sendSelection();
2501   }
2502
2503   /**
2504    * DOCUMENT ME!
2505    *
2506    * @param e
2507    *          DOCUMENT ME!
2508    */
2509   @Override
2510   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2511   {
2512     trimAlignment(true);
2513   }
2514
2515   /**
2516    * DOCUMENT ME!
2517    *
2518    * @param e
2519    *          DOCUMENT ME!
2520    */
2521   @Override
2522   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2523   {
2524     trimAlignment(false);
2525   }
2526
2527   void trimAlignment(boolean trimLeft)
2528   {
2529     ColumnSelection colSel = viewport.getColumnSelection();
2530     int column;
2531
2532     if (!colSel.isEmpty())
2533     {
2534       if (trimLeft)
2535       {
2536         column = colSel.getMin();
2537       }
2538       else
2539       {
2540         column = colSel.getMax();
2541       }
2542
2543       SequenceI[] seqs;
2544       if (viewport.getSelectionGroup() != null)
2545       {
2546         seqs = viewport.getSelectionGroup()
2547                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2548       }
2549       else
2550       {
2551         seqs = viewport.getAlignment().getSequencesArray();
2552       }
2553
2554       TrimRegionCommand trimRegion;
2555       if (trimLeft)
2556       {
2557         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2558                 column, viewport.getAlignment());
2559         viewport.getRanges().setStartRes(0);
2560       }
2561       else
2562       {
2563         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2564                 column, viewport.getAlignment());
2565       }
2566
2567       statusBar.setText(MessageManager
2568               .formatMessage("label.removed_columns", new String[]
2569               { Integer.valueOf(trimRegion.getSize()).toString() }));
2570
2571       addHistoryItem(trimRegion);
2572
2573       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2574       {
2575         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2576                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2577         {
2578           viewport.getAlignment().deleteGroup(sg);
2579         }
2580       }
2581
2582       viewport.firePropertyChange("alignment", null,
2583               viewport.getAlignment().getSequences());
2584     }
2585   }
2586
2587   /**
2588    * DOCUMENT ME!
2589    *
2590    * @param e
2591    *          DOCUMENT ME!
2592    */
2593   @Override
2594   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2595   {
2596     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2597
2598     SequenceI[] seqs;
2599     if (viewport.getSelectionGroup() != null)
2600     {
2601       seqs = viewport.getSelectionGroup()
2602               .getSequencesAsArray(viewport.getHiddenRepSequences());
2603       start = viewport.getSelectionGroup().getStartRes();
2604       end = viewport.getSelectionGroup().getEndRes();
2605     }
2606     else
2607     {
2608       seqs = viewport.getAlignment().getSequencesArray();
2609     }
2610
2611     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2612             "Remove Gapped Columns", seqs, start, end,
2613             viewport.getAlignment());
2614
2615     addHistoryItem(removeGapCols);
2616
2617     statusBar.setText(MessageManager
2618             .formatMessage("label.removed_empty_columns", new Object[]
2619             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2620
2621     // This is to maintain viewport position on first residue
2622     // of first sequence
2623     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2624     ViewportRanges ranges = viewport.getRanges();
2625     int startRes = seq.findPosition(ranges.getStartRes());
2626     // ShiftList shifts;
2627     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2628     // edit.alColumnChanges=shifts.getInverse();
2629     // if (viewport.hasHiddenColumns)
2630     // viewport.getColumnSelection().compensateForEdits(shifts);
2631     ranges.setStartRes(seq.findIndex(startRes) - 1);
2632     viewport.firePropertyChange("alignment", null,
2633             viewport.getAlignment().getSequences());
2634
2635   }
2636
2637   /**
2638    * DOCUMENT ME!
2639    *
2640    * @param e
2641    *          DOCUMENT ME!
2642    */
2643   @Override
2644   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2645   {
2646     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2647
2648     SequenceI[] seqs;
2649     if (viewport.getSelectionGroup() != null)
2650     {
2651       seqs = viewport.getSelectionGroup()
2652               .getSequencesAsArray(viewport.getHiddenRepSequences());
2653       start = viewport.getSelectionGroup().getStartRes();
2654       end = viewport.getSelectionGroup().getEndRes();
2655     }
2656     else
2657     {
2658       seqs = viewport.getAlignment().getSequencesArray();
2659     }
2660
2661     // This is to maintain viewport position on first residue
2662     // of first sequence
2663     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2664     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2665
2666     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2667             viewport.getAlignment()));
2668
2669     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2670
2671     viewport.firePropertyChange("alignment", null,
2672             viewport.getAlignment().getSequences());
2673
2674   }
2675
2676   /**
2677    * DOCUMENT ME!
2678    *
2679    * @param e
2680    *          DOCUMENT ME!
2681    */
2682   @Override
2683   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2684   {
2685     viewport.setPadGaps(padGapsMenuitem.isSelected());
2686     viewport.firePropertyChange("alignment", null,
2687             viewport.getAlignment().getSequences());
2688   }
2689
2690   /**
2691    * DOCUMENT ME!
2692    *
2693    * @param e
2694    *          DOCUMENT ME!
2695    */
2696   @Override
2697   public void findMenuItem_actionPerformed(ActionEvent e)
2698   {
2699     new Finder();
2700   }
2701
2702   /**
2703    * Create a new view of the current alignment.
2704    */
2705   @Override
2706   public void newView_actionPerformed(ActionEvent e)
2707   {
2708     newView(null, true);
2709   }
2710
2711   /**
2712    * Creates and shows a new view of the current alignment.
2713    *
2714    * @param viewTitle
2715    *          title of newly created view; if null, one will be generated
2716    * @param copyAnnotation
2717    *          if true then duplicate all annnotation, groups and settings
2718    * @return new alignment panel, already displayed.
2719    */
2720   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2721   {
2722     /*
2723      * Create a new AlignmentPanel (with its own, new Viewport)
2724      */
2725     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2726     if (!copyAnnotation)
2727     {
2728       /*
2729        * remove all groups and annotation except for the automatic stuff
2730        */
2731       newap.av.getAlignment().deleteAllGroups();
2732       newap.av.getAlignment().deleteAllAnnotations(false);
2733     }
2734
2735     newap.av.setGatherViewsHere(false);
2736
2737     if (viewport.viewName == null)
2738     {
2739       viewport.viewName = MessageManager
2740               .getString("label.view_name_original");
2741     }
2742
2743     /*
2744      * Views share the same edits undo and redo stacks
2745      */
2746     newap.av.setHistoryList(viewport.getHistoryList());
2747     newap.av.setRedoList(viewport.getRedoList());
2748
2749     /*
2750      * Views share the same mappings; need to deregister any new mappings
2751      * created by copyAlignPanel, and register the new reference to the shared
2752      * mappings
2753      */
2754     newap.av.replaceMappings(viewport.getAlignment());
2755
2756     /*
2757      * start up cDNA consensus (if applicable) now mappings are in place
2758      */
2759     if (newap.av.initComplementConsensus())
2760     {
2761       newap.refresh(true); // adjust layout of annotations
2762     }
2763
2764     newap.av.viewName = getNewViewName(viewTitle);
2765
2766     addAlignmentPanel(newap, true);
2767     newap.alignmentChanged();
2768
2769     if (alignPanels.size() == 2)
2770     {
2771       viewport.setGatherViewsHere(true);
2772     }
2773     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2774     return newap;
2775   }
2776
2777   /**
2778    * Make a new name for the view, ensuring it is unique within the current
2779    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2780    * these now use viewId. Unique view names are still desirable for usability.)
2781    *
2782    * @param viewTitle
2783    * @return
2784    */
2785   protected String getNewViewName(String viewTitle)
2786   {
2787     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2788     boolean addFirstIndex = false;
2789     if (viewTitle == null || viewTitle.trim().length() == 0)
2790     {
2791       viewTitle = MessageManager.getString("action.view");
2792       addFirstIndex = true;
2793     }
2794     else
2795     {
2796       index = 1;// we count from 1 if given a specific name
2797     }
2798     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2799
2800     List<Component> comps = PaintRefresher.components
2801             .get(viewport.getSequenceSetId());
2802
2803     List<String> existingNames = getExistingViewNames(comps);
2804
2805     while (existingNames.contains(newViewName))
2806     {
2807       newViewName = viewTitle + " " + (++index);
2808     }
2809     return newViewName;
2810   }
2811
2812   /**
2813    * Returns a list of distinct view names found in the given list of
2814    * components. View names are held on the viewport of an AlignmentPanel.
2815    *
2816    * @param comps
2817    * @return
2818    */
2819   protected List<String> getExistingViewNames(List<Component> comps)
2820   {
2821     List<String> existingNames = new ArrayList<>();
2822     for (Component comp : comps)
2823     {
2824       if (comp instanceof AlignmentPanel)
2825       {
2826         AlignmentPanel ap = (AlignmentPanel) comp;
2827         if (!existingNames.contains(ap.av.viewName))
2828         {
2829           existingNames.add(ap.av.viewName);
2830         }
2831       }
2832     }
2833     return existingNames;
2834   }
2835
2836   /**
2837    * Explode tabbed views into separate windows.
2838    */
2839   @Override
2840   public void expandViews_actionPerformed(ActionEvent e)
2841   {
2842     Desktop.explodeViews(this);
2843   }
2844
2845   /**
2846    * Gather views in separate windows back into a tabbed presentation.
2847    */
2848   @Override
2849   public void gatherViews_actionPerformed(ActionEvent e)
2850   {
2851     Desktop.instance.gatherViews(this);
2852   }
2853
2854   /**
2855    * DOCUMENT ME!
2856    *
2857    * @param e
2858    *          DOCUMENT ME!
2859    */
2860   @Override
2861   public void font_actionPerformed(ActionEvent e)
2862   {
2863     new FontChooser(alignPanel);
2864   }
2865
2866   /**
2867    * DOCUMENT ME!
2868    *
2869    * @param e
2870    *          DOCUMENT ME!
2871    */
2872   @Override
2873   protected void seqLimit_actionPerformed(ActionEvent e)
2874   {
2875     viewport.setShowJVSuffix(seqLimits.isSelected());
2876
2877     alignPanel.getIdPanel().getIdCanvas()
2878             .setPreferredSize(alignPanel.calculateIdWidth());
2879     alignPanel.paintAlignment(true, false);
2880   }
2881
2882   @Override
2883   public void idRightAlign_actionPerformed(ActionEvent e)
2884   {
2885     viewport.setRightAlignIds(idRightAlign.isSelected());
2886     alignPanel.paintAlignment(false, false);
2887   }
2888
2889   @Override
2890   public void centreColumnLabels_actionPerformed(ActionEvent e)
2891   {
2892     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2893     alignPanel.paintAlignment(false, false);
2894   }
2895
2896   /*
2897    * (non-Javadoc)
2898    *
2899    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2900    */
2901   @Override
2902   protected void followHighlight_actionPerformed()
2903   {
2904     /*
2905      * Set the 'follow' flag on the Viewport (and scroll to position if now
2906      * true).
2907      */
2908     final boolean state = this.followHighlightMenuItem.getState();
2909     viewport.setFollowHighlight(state);
2910     if (state)
2911     {
2912       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2913     }
2914   }
2915
2916   /**
2917    * DOCUMENT ME!
2918    *
2919    * @param e
2920    *          DOCUMENT ME!
2921    */
2922   @Override
2923   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2924   {
2925     viewport.setColourText(colourTextMenuItem.isSelected());
2926     alignPanel.paintAlignment(false, false);
2927   }
2928
2929   /**
2930    * DOCUMENT ME!
2931    *
2932    * @param e
2933    *          DOCUMENT ME!
2934    */
2935   @Override
2936   public void wrapMenuItem_actionPerformed(ActionEvent e)
2937   {
2938     scaleAbove.setVisible(wrapMenuItem.isSelected());
2939     scaleLeft.setVisible(wrapMenuItem.isSelected());
2940     scaleRight.setVisible(wrapMenuItem.isSelected());
2941     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2942     alignPanel.updateLayout();
2943   }
2944
2945   @Override
2946   public void showAllSeqs_actionPerformed(ActionEvent e)
2947   {
2948     viewport.showAllHiddenSeqs();
2949   }
2950
2951   @Override
2952   public void showAllColumns_actionPerformed(ActionEvent e)
2953   {
2954     viewport.showAllHiddenColumns();
2955     alignPanel.paintAlignment(true, true);
2956     viewport.sendSelection();
2957   }
2958
2959   @Override
2960   public void hideSelSequences_actionPerformed(ActionEvent e)
2961   {
2962     viewport.hideAllSelectedSeqs();
2963   }
2964
2965   /**
2966    * called by key handler and the hide all/show all menu items
2967    *
2968    * @param toggleSeqs
2969    * @param toggleCols
2970    */
2971   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2972   {
2973
2974     boolean hide = false;
2975     SequenceGroup sg = viewport.getSelectionGroup();
2976     if (!toggleSeqs && !toggleCols)
2977     {
2978       // Hide everything by the current selection - this is a hack - we do the
2979       // invert and then hide
2980       // first check that there will be visible columns after the invert.
2981       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2982               && sg.getStartRes() <= sg.getEndRes()))
2983       {
2984         // now invert the sequence set, if required - empty selection implies
2985         // that no hiding is required.
2986         if (sg != null)
2987         {
2988           invertSequenceMenuItem_actionPerformed(null);
2989           sg = viewport.getSelectionGroup();
2990           toggleSeqs = true;
2991
2992         }
2993         viewport.expandColSelection(sg, true);
2994         // finally invert the column selection and get the new sequence
2995         // selection.
2996         invertColSel_actionPerformed(null);
2997         toggleCols = true;
2998       }
2999     }
3000
3001     if (toggleSeqs)
3002     {
3003       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3004       {
3005         hideSelSequences_actionPerformed(null);
3006         hide = true;
3007       }
3008       else if (!(toggleCols && viewport.hasSelectedColumns()))
3009       {
3010         showAllSeqs_actionPerformed(null);
3011       }
3012     }
3013
3014     if (toggleCols)
3015     {
3016       if (viewport.hasSelectedColumns())
3017       {
3018         hideSelColumns_actionPerformed(null);
3019         if (!toggleSeqs)
3020         {
3021           viewport.setSelectionGroup(sg);
3022         }
3023       }
3024       else if (!hide)
3025       {
3026         showAllColumns_actionPerformed(null);
3027       }
3028     }
3029   }
3030
3031   /*
3032    * (non-Javadoc)
3033    *
3034    * @see
3035    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3036    * event.ActionEvent)
3037    */
3038   @Override
3039   public void hideAllButSelection_actionPerformed(ActionEvent e)
3040   {
3041     toggleHiddenRegions(false, false);
3042     viewport.sendSelection();
3043   }
3044
3045   /*
3046    * (non-Javadoc)
3047    *
3048    * @see
3049    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3050    * .ActionEvent)
3051    */
3052   @Override
3053   public void hideAllSelection_actionPerformed(ActionEvent e)
3054   {
3055     SequenceGroup sg = viewport.getSelectionGroup();
3056     viewport.expandColSelection(sg, false);
3057     viewport.hideAllSelectedSeqs();
3058     viewport.hideSelectedColumns();
3059     alignPanel.paintAlignment(true, true);
3060     viewport.sendSelection();
3061   }
3062
3063   /*
3064    * (non-Javadoc)
3065    *
3066    * @see
3067    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3068    * ActionEvent)
3069    */
3070   @Override
3071   public void showAllhidden_actionPerformed(ActionEvent e)
3072   {
3073     viewport.showAllHiddenColumns();
3074     viewport.showAllHiddenSeqs();
3075     alignPanel.paintAlignment(true, true);
3076     viewport.sendSelection();
3077   }
3078
3079   @Override
3080   public void hideSelColumns_actionPerformed(ActionEvent e)
3081   {
3082     viewport.hideSelectedColumns();
3083     alignPanel.paintAlignment(true, true);
3084     viewport.sendSelection();
3085   }
3086
3087   @Override
3088   public void hiddenMarkers_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3091     repaint();
3092   }
3093
3094   /**
3095    * DOCUMENT ME!
3096    *
3097    * @param e
3098    *          DOCUMENT ME!
3099    */
3100   @Override
3101   protected void scaleAbove_actionPerformed(ActionEvent e)
3102   {
3103     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3104     // TODO: do we actually need to update overview for scale above change ?
3105     alignPanel.paintAlignment(true, false);
3106   }
3107
3108   /**
3109    * DOCUMENT ME!
3110    *
3111    * @param e
3112    *          DOCUMENT ME!
3113    */
3114   @Override
3115   protected void scaleLeft_actionPerformed(ActionEvent e)
3116   {
3117     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3118     alignPanel.paintAlignment(true, false);
3119   }
3120
3121   /**
3122    * DOCUMENT ME!
3123    *
3124    * @param e
3125    *          DOCUMENT ME!
3126    */
3127   @Override
3128   protected void scaleRight_actionPerformed(ActionEvent e)
3129   {
3130     viewport.setScaleRightWrapped(scaleRight.isSelected());
3131     alignPanel.paintAlignment(true, false);
3132   }
3133
3134   /**
3135    * DOCUMENT ME!
3136    *
3137    * @param e
3138    *          DOCUMENT ME!
3139    */
3140   @Override
3141   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3142   {
3143     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3144     alignPanel.paintAlignment(false, false);
3145   }
3146
3147   /**
3148    * DOCUMENT ME!
3149    *
3150    * @param e
3151    *          DOCUMENT ME!
3152    */
3153   @Override
3154   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3155   {
3156     viewport.setShowText(viewTextMenuItem.isSelected());
3157     alignPanel.paintAlignment(false, false);
3158   }
3159
3160   /**
3161    * DOCUMENT ME!
3162    *
3163    * @param e
3164    *          DOCUMENT ME!
3165    */
3166   @Override
3167   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3168   {
3169     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3170     alignPanel.paintAlignment(false, false);
3171   }
3172
3173   public FeatureSettings featureSettings;
3174
3175   @Override
3176   public FeatureSettingsControllerI getFeatureSettingsUI()
3177   {
3178     return featureSettings;
3179   }
3180
3181   @Override
3182   public void featureSettings_actionPerformed(ActionEvent e)
3183   {
3184     if (featureSettings != null)
3185     {
3186       featureSettings.close();
3187       featureSettings = null;
3188     }
3189     if (!showSeqFeatures.isSelected())
3190     {
3191       // make sure features are actually displayed
3192       showSeqFeatures.setSelected(true);
3193       showSeqFeatures_actionPerformed(null);
3194     }
3195     featureSettings = new FeatureSettings(this);
3196   }
3197
3198   /**
3199    * Set or clear 'Show Sequence Features'
3200    *
3201    * @param evt
3202    *          DOCUMENT ME!
3203    */
3204   @Override
3205   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3206   {
3207     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3208     alignPanel.paintAlignment(true, true);
3209   }
3210
3211   /**
3212    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3213    * the annotations panel as a whole.
3214    *
3215    * The options to show/hide all annotations should be enabled when the panel
3216    * is shown, and disabled when the panel is hidden.
3217    *
3218    * @param e
3219    */
3220   @Override
3221   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3222   {
3223     final boolean setVisible = annotationPanelMenuItem.isSelected();
3224     viewport.setShowAnnotation(setVisible);
3225     this.showAllSeqAnnotations.setEnabled(setVisible);
3226     this.hideAllSeqAnnotations.setEnabled(setVisible);
3227     this.showAllAlAnnotations.setEnabled(setVisible);
3228     this.hideAllAlAnnotations.setEnabled(setVisible);
3229     alignPanel.updateLayout();
3230   }
3231
3232   @Override
3233   public void alignmentProperties()
3234   {
3235     JEditorPane editPane = new JEditorPane("text/html", "");
3236     editPane.setEditable(false);
3237     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3238             .formatAsHtml();
3239     editPane.setText(
3240             MessageManager.formatMessage("label.html_content", new Object[]
3241             { contents.toString() }));
3242     JInternalFrame frame = new JInternalFrame();
3243     frame.getContentPane().add(new JScrollPane(editPane));
3244
3245     Desktop.addInternalFrame(frame, MessageManager
3246             .formatMessage("label.alignment_properties", new Object[]
3247             { getTitle() }), 500, 400);
3248   }
3249
3250   /**
3251    * DOCUMENT ME!
3252    *
3253    * @param e
3254    *          DOCUMENT ME!
3255    */
3256   @Override
3257   public void overviewMenuItem_actionPerformed(ActionEvent e)
3258   {
3259     if (alignPanel.overviewPanel != null)
3260     {
3261       return;
3262     }
3263
3264     JInternalFrame frame = new JInternalFrame();
3265     final OverviewPanel overview = new OverviewPanel(alignPanel);
3266     frame.setContentPane(overview);
3267     Desktop.addInternalFrame(frame, MessageManager
3268             .formatMessage("label.overview_params", new Object[]
3269             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3270             true, true);
3271     frame.pack();
3272     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3273     frame.addInternalFrameListener(
3274             new javax.swing.event.InternalFrameAdapter()
3275             {
3276               @Override
3277               public void internalFrameClosed(
3278                       javax.swing.event.InternalFrameEvent evt)
3279               {
3280                 overview.dispose();
3281                 alignPanel.setOverviewPanel(null);
3282               };
3283             });
3284
3285     alignPanel.setOverviewPanel(overview);
3286   }
3287
3288   @Override
3289   public void textColour_actionPerformed()
3290   {
3291     new TextColourChooser().chooseColour(alignPanel, null);
3292   }
3293
3294   /*
3295    * public void covariationColour_actionPerformed() {
3296    * changeColour(new
3297    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3298    * ()[0])); }
3299    */
3300   @Override
3301   public void annotationColour_actionPerformed()
3302   {
3303     new AnnotationColourChooser(viewport, alignPanel);
3304   }
3305
3306   @Override
3307   public void annotationColumn_actionPerformed(ActionEvent e)
3308   {
3309     new AnnotationColumnChooser(viewport, alignPanel);
3310   }
3311
3312   /**
3313    * Action on the user checking or unchecking the option to apply the selected
3314    * colour scheme to all groups. If unchecked, groups may have their own
3315    * independent colour schemes.
3316    *
3317    * @param selected
3318    */
3319   @Override
3320   public void applyToAllGroups_actionPerformed(boolean selected)
3321   {
3322     viewport.setColourAppliesToAllGroups(selected);
3323   }
3324
3325   /**
3326    * Action on user selecting a colour from the colour menu
3327    *
3328    * @param name
3329    *          the name (not the menu item label!) of the colour scheme
3330    */
3331   @Override
3332   public void changeColour_actionPerformed(String name)
3333   {
3334     /*
3335      * 'User Defined' opens a panel to configure or load a
3336      * user-defined colour scheme
3337      */
3338     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3339     {
3340       new UserDefinedColours(alignPanel);
3341       return;
3342     }
3343
3344     /*
3345      * otherwise set the chosen colour scheme (or null for 'None')
3346      */
3347     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3348             viewport.getAlignment(), viewport.getHiddenRepSequences());
3349     changeColour(cs);
3350   }
3351
3352   /**
3353    * Actions on setting or changing the alignment colour scheme
3354    *
3355    * @param cs
3356    */
3357   @Override
3358   public void changeColour(ColourSchemeI cs)
3359   {
3360     // TODO: pull up to controller method
3361     ColourMenuHelper.setColourSelected(colourMenu, cs);
3362
3363     viewport.setGlobalColourScheme(cs);
3364
3365     alignPanel.paintAlignment(true, true);
3366   }
3367
3368   /**
3369    * Show the PID threshold slider panel
3370    */
3371   @Override
3372   protected void modifyPID_actionPerformed()
3373   {
3374     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3375             alignPanel.getViewName());
3376     SliderPanel.showPIDSlider();
3377   }
3378
3379   /**
3380    * Show the Conservation slider panel
3381    */
3382   @Override
3383   protected void modifyConservation_actionPerformed()
3384   {
3385     SliderPanel.setConservationSlider(alignPanel,
3386             viewport.getResidueShading(), alignPanel.getViewName());
3387     SliderPanel.showConservationSlider();
3388   }
3389
3390   /**
3391    * Action on selecting or deselecting (Colour) By Conservation
3392    */
3393   @Override
3394   public void conservationMenuItem_actionPerformed(boolean selected)
3395   {
3396     modifyConservation.setEnabled(selected);
3397     viewport.setConservationSelected(selected);
3398     viewport.getResidueShading().setConservationApplied(selected);
3399
3400     changeColour(viewport.getGlobalColourScheme());
3401     if (selected)
3402     {
3403       modifyConservation_actionPerformed();
3404     }
3405     else
3406     {
3407       SliderPanel.hideConservationSlider();
3408     }
3409   }
3410
3411   /**
3412    * Action on selecting or deselecting (Colour) Above PID Threshold
3413    */
3414   @Override
3415   public void abovePIDThreshold_actionPerformed(boolean selected)
3416   {
3417     modifyPID.setEnabled(selected);
3418     viewport.setAbovePIDThreshold(selected);
3419     if (!selected)
3420     {
3421       viewport.getResidueShading().setThreshold(0,
3422               viewport.isIgnoreGapsConsensus());
3423     }
3424
3425     changeColour(viewport.getGlobalColourScheme());
3426     if (selected)
3427     {
3428       modifyPID_actionPerformed();
3429     }
3430     else
3431     {
3432       SliderPanel.hidePIDSlider();
3433     }
3434   }
3435
3436   /**
3437    * DOCUMENT ME!
3438    *
3439    * @param e
3440    *          DOCUMENT ME!
3441    */
3442   @Override
3443   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3444   {
3445     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3446     AlignmentSorter.sortByPID(viewport.getAlignment(),
3447             viewport.getAlignment().getSequenceAt(0));
3448     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3449             viewport.getAlignment()));
3450     alignPanel.paintAlignment(true, false);
3451   }
3452
3453   /**
3454    * DOCUMENT ME!
3455    *
3456    * @param e
3457    *          DOCUMENT ME!
3458    */
3459   @Override
3460   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3461   {
3462     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3463     AlignmentSorter.sortByID(viewport.getAlignment());
3464     addHistoryItem(
3465             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3466     alignPanel.paintAlignment(true, false);
3467   }
3468
3469   /**
3470    * DOCUMENT ME!
3471    *
3472    * @param e
3473    *          DOCUMENT ME!
3474    */
3475   @Override
3476   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3477   {
3478     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3479     AlignmentSorter.sortByLength(viewport.getAlignment());
3480     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3481             viewport.getAlignment()));
3482     alignPanel.paintAlignment(true, false);
3483   }
3484
3485   /**
3486    * DOCUMENT ME!
3487    *
3488    * @param e
3489    *          DOCUMENT ME!
3490    */
3491   @Override
3492   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3493   {
3494     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3495     AlignmentSorter.sortByGroup(viewport.getAlignment());
3496     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3497             viewport.getAlignment()));
3498
3499     alignPanel.paintAlignment(true, false);
3500   }
3501
3502   /**
3503    * DOCUMENT ME!
3504    *
3505    * @param e
3506    *          DOCUMENT ME!
3507    */
3508   @Override
3509   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3510   {
3511     new RedundancyPanel(alignPanel, this);
3512   }
3513
3514   /**
3515    * DOCUMENT ME!
3516    *
3517    * @param e
3518    *          DOCUMENT ME!
3519    */
3520   @Override
3521   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3522   {
3523     if ((viewport.getSelectionGroup() == null)
3524             || (viewport.getSelectionGroup().getSize() < 2))
3525     {
3526       JvOptionPane.showInternalMessageDialog(this,
3527               MessageManager.getString(
3528                       "label.you_must_select_least_two_sequences"),
3529               MessageManager.getString("label.invalid_selection"),
3530               JvOptionPane.WARNING_MESSAGE);
3531     }
3532     else
3533     {
3534       JInternalFrame frame = new JInternalFrame();
3535       frame.setContentPane(new PairwiseAlignPanel(viewport));
3536       Desktop.addInternalFrame(frame,
3537               MessageManager.getString("action.pairwise_alignment"), 600,
3538               500);
3539     }
3540   }
3541
3542   @Override
3543   public void autoCalculate_actionPerformed(ActionEvent e)
3544   {
3545     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3546     if (viewport.autoCalculateConsensus)
3547     {
3548       viewport.firePropertyChange("alignment", null,
3549               viewport.getAlignment().getSequences());
3550     }
3551   }
3552
3553   @Override
3554   public void sortByTreeOption_actionPerformed(ActionEvent e)
3555   {
3556     viewport.sortByTree = sortByTree.isSelected();
3557   }
3558
3559   @Override
3560   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3561   {
3562     viewport.followSelection = listenToViewSelections.isSelected();
3563   }
3564
3565   /**
3566    * Constructs a tree panel and adds it to the desktop
3567    *
3568    * @param params
3569    * @param treeAlgo
3570    *
3571    * @param tree
3572    *
3573    *
3574    */
3575   void newTreePanel(TreeModel tree, String treeAlgo,
3576           String substitutionMatrix)
3577   {
3578     String frameTitle = "";
3579     TreePanel tp;
3580
3581     boolean onSelection = false;
3582     if (viewport.getSelectionGroup() != null
3583             && viewport.getSelectionGroup().getSize() > 0)
3584     {
3585       SequenceGroup sg = viewport.getSelectionGroup();
3586
3587       /* Decide if the selection is a column region */
3588       for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
3589       {
3590         if (_s.getLength() < sg.getEndRes())
3591         {
3592           JvOptionPane.showMessageDialog(Desktop.desktop,
3593                   MessageManager.getString(
3594                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3595                   MessageManager.getString(
3596                           "label.sequences_selection_not_aligned"),
3597                   JvOptionPane.WARNING_MESSAGE);
3598
3599           return;
3600         }
3601       }
3602       onSelection = true;
3603     }
3604     else
3605     {
3606       if (viewport.getAlignment().getHeight() < 2)
3607       {
3608         return;
3609       }
3610     }
3611
3612     tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
3613     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3614
3615     frameTitle += " from ";
3616
3617     if (viewport.viewName != null)
3618     {
3619       frameTitle += viewport.viewName + " of ";
3620     }
3621
3622     frameTitle += this.title;
3623
3624     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3625   }
3626
3627   /**
3628    * DOCUMENT ME!
3629    *
3630    * @param title
3631    *          DOCUMENT ME!
3632    * @param order
3633    *          DOCUMENT ME!
3634    */
3635   public void addSortByOrderMenuItem(String title,
3636           final AlignmentOrder order)
3637   {
3638     final JMenuItem item = new JMenuItem(MessageManager
3639             .formatMessage("action.by_title_param", new Object[]
3640             { title }));
3641     sort.add(item);
3642     item.addActionListener(new java.awt.event.ActionListener()
3643     {
3644       @Override
3645       public void actionPerformed(ActionEvent e)
3646       {
3647         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3648
3649         // TODO: JBPNote - have to map order entries to curent SequenceI
3650         // pointers
3651         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3652
3653         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3654                 viewport.getAlignment()));
3655
3656         alignPanel.paintAlignment(true, false);
3657       }
3658     });
3659   }
3660
3661   /**
3662    * Add a new sort by annotation score menu item
3663    *
3664    * @param sort
3665    *          the menu to add the option to
3666    * @param scoreLabel
3667    *          the label used to retrieve scores for each sequence on the
3668    *          alignment
3669    */
3670   public void addSortByAnnotScoreMenuItem(JMenu sort,
3671           final String scoreLabel)
3672   {
3673     final JMenuItem item = new JMenuItem(scoreLabel);
3674     sort.add(item);
3675     item.addActionListener(new java.awt.event.ActionListener()
3676     {
3677       @Override
3678       public void actionPerformed(ActionEvent e)
3679       {
3680         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3681         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3682                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3683         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3684                 viewport.getAlignment()));
3685         alignPanel.paintAlignment(true, false);
3686       }
3687     });
3688   }
3689
3690   /**
3691    * last hash for alignment's annotation array - used to minimise cost of
3692    * rebuild.
3693    */
3694   protected int _annotationScoreVectorHash;
3695
3696   /**
3697    * search the alignment and rebuild the sort by annotation score submenu the
3698    * last alignment annotation vector hash is stored to minimize cost of
3699    * rebuilding in subsequence calls.
3700    *
3701    */
3702   @Override
3703   public void buildSortByAnnotationScoresMenu()
3704   {
3705     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3706     {
3707       return;
3708     }
3709
3710     if (viewport.getAlignment().getAlignmentAnnotation()
3711             .hashCode() != _annotationScoreVectorHash)
3712     {
3713       sortByAnnotScore.removeAll();
3714       // almost certainly a quicker way to do this - but we keep it simple
3715       Hashtable scoreSorts = new Hashtable();
3716       AlignmentAnnotation aann[];
3717       for (SequenceI sqa : viewport.getAlignment().getSequences())
3718       {
3719         aann = sqa.getAnnotation();
3720         for (int i = 0; aann != null && i < aann.length; i++)
3721         {
3722           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3723           {
3724             scoreSorts.put(aann[i].label, aann[i].label);
3725           }
3726         }
3727       }
3728       Enumeration labels = scoreSorts.keys();
3729       while (labels.hasMoreElements())
3730       {
3731         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3732                 (String) labels.nextElement());
3733       }
3734       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3735       scoreSorts.clear();
3736
3737       _annotationScoreVectorHash = viewport.getAlignment()
3738               .getAlignmentAnnotation().hashCode();
3739     }
3740   }
3741
3742   /**
3743    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3744    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3745    * call. Listeners are added to remove the menu item when the treePanel is
3746    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3747    * modified.
3748    */
3749   @Override
3750   public void buildTreeSortMenu()
3751   {
3752     sortByTreeMenu.removeAll();
3753
3754     List<Component> comps = PaintRefresher.components
3755             .get(viewport.getSequenceSetId());
3756     List<TreePanel> treePanels = new ArrayList<>();
3757     for (Component comp : comps)
3758     {
3759       if (comp instanceof TreePanel)
3760       {
3761         treePanels.add((TreePanel) comp);
3762       }
3763     }
3764
3765     if (treePanels.size() < 1)
3766     {
3767       sortByTreeMenu.setVisible(false);
3768       return;
3769     }
3770
3771     sortByTreeMenu.setVisible(true);
3772
3773     for (final TreePanel tp : treePanels)
3774     {
3775       final JMenuItem item = new JMenuItem(tp.getTitle());
3776       item.addActionListener(new java.awt.event.ActionListener()
3777       {
3778         @Override
3779         public void actionPerformed(ActionEvent e)
3780         {
3781           // adapt to Aptx
3782           tp.sortByTree_actionPerformed();
3783           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3784
3785         }
3786       });
3787
3788       sortByTreeMenu.add(item);
3789     }
3790   }
3791
3792   public boolean sortBy(AlignmentOrder alorder, String undoname)
3793   {
3794     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3795     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3796     if (undoname != null)
3797     {
3798       addHistoryItem(new OrderCommand(undoname, oldOrder,
3799               viewport.getAlignment()));
3800     }
3801     alignPanel.paintAlignment(true, false);
3802     return true;
3803   }
3804
3805   /**
3806    * Work out whether the whole set of sequences or just the selected set will
3807    * be submitted for multiple alignment.
3808    *
3809    */
3810   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3811   {
3812     // Now, check we have enough sequences
3813     AlignmentView msa = null;
3814
3815     if ((viewport.getSelectionGroup() != null)
3816             && (viewport.getSelectionGroup().getSize() > 1))
3817     {
3818       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3819       // some common interface!
3820       /*
3821        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3822        * SequenceI[sz = seqs.getSize(false)];
3823        *
3824        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3825        * seqs.getSequenceAt(i); }
3826        */
3827       msa = viewport.getAlignmentView(true);
3828     }
3829     else if (viewport.getSelectionGroup() != null
3830             && viewport.getSelectionGroup().getSize() == 1)
3831     {
3832       int option = JvOptionPane.showConfirmDialog(this,
3833               MessageManager.getString("warn.oneseq_msainput_selection"),
3834               MessageManager.getString("label.invalid_selection"),
3835               JvOptionPane.OK_CANCEL_OPTION);
3836       if (option == JvOptionPane.OK_OPTION)
3837       {
3838         msa = viewport.getAlignmentView(false);
3839       }
3840     }
3841     else
3842     {
3843       msa = viewport.getAlignmentView(false);
3844     }
3845     return msa;
3846   }
3847
3848   /**
3849    * Decides what is submitted to a secondary structure prediction service: the
3850    * first sequence in the alignment, or in the current selection, or, if the
3851    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3852    * region or the whole alignment. (where the first sequence in the set is the
3853    * one that the prediction will be for).
3854    */
3855   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3856   {
3857     AlignmentView seqs = null;
3858
3859     if ((viewport.getSelectionGroup() != null)
3860             && (viewport.getSelectionGroup().getSize() > 0))
3861     {
3862       seqs = viewport.getAlignmentView(true);
3863     }
3864     else
3865     {
3866       seqs = viewport.getAlignmentView(false);
3867     }
3868     // limit sequences - JBPNote in future - could spawn multiple prediction
3869     // jobs
3870     // TODO: viewport.getAlignment().isAligned is a global state - the local
3871     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3872     if (!viewport.getAlignment().isAligned(false))
3873     {
3874       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3875       // TODO: if seqs.getSequences().length>1 then should really have warned
3876       // user!
3877
3878     }
3879     return seqs;
3880   }
3881
3882   /**
3883    * DOCUMENT ME!
3884    *
3885    * @param e
3886    *          DOCUMENT ME!
3887    */
3888   @Override
3889   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3890   {
3891     chooseTreeFile();
3892   }
3893
3894   @Override
3895   protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
3896   {
3897     chooseTreeUrl();
3898   }
3899
3900   @Override
3901   protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
3902   {
3903     chooseTreeDb(0);
3904
3905   }
3906
3907   @Override
3908   protected void loadTreeBase_actionPerformed(ActionEvent e)
3909   {
3910     chooseTreeDb(1);
3911
3912   }
3913   @Override
3914   protected void loadTreePfam_actionPerformed(ActionEvent e)
3915   {
3916     chooseTreeDb(2);
3917
3918   }
3919   @Override
3920   protected void loadTreeFam_actionPerformed(ActionEvent e)
3921   {
3922     chooseTreeDb(3);
3923
3924   }
3925
3926   @Override
3927   protected void loadTreeOfLife_actionPerformed(ActionEvent e)
3928   {
3929     chooseTreeDb(4);
3930
3931   }
3932
3933
3934
3935
3936
3937   public void chooseTreeFile()
3938   {
3939     // Pick the tree file
3940     JalviewFileChooser chooser = new JalviewFileChooser(
3941             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3942     chooser.setFileView(new JalviewFileView());
3943     chooser.setDialogTitle(
3944             MessageManager.getString("label.select_tree_file")); // modify
3945     chooser.setToolTipText(
3946             MessageManager.getString("label.load_tree_for_sequence_set"));
3947     for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
3948             .values())
3949     {
3950       chooser.setFileFilter(treeFormat.getTreeFilter());
3951     }
3952
3953     int value = chooser.showOpenDialog(null);
3954
3955     if (value == JalviewFileChooser.APPROVE_OPTION)
3956     {
3957       String filePath = chooser.getSelectedFile().getPath();
3958       Cache.setProperty("LAST_DIRECTORY", filePath);
3959
3960
3961       TreeParser treeParser = new TreeParser(filePath);
3962       treeParser.loadTree(viewport);
3963
3964     }
3965   }
3966
3967   /**
3968    * Break up and move to TreeParser?
3969    */
3970   public void chooseTreeUrl()
3971   {
3972
3973     JLabel label = new JLabel(
3974             MessageManager.getString("label.tree_url_example"));
3975     // add "example" button
3976     final JComboBox<String> history = new JComboBox<>();
3977
3978     JPanel panel = new JPanel(new GridLayout(2, 1));
3979     panel.add(label);
3980     panel.add(history);
3981     history.setPreferredSize(new Dimension(400, 20));
3982     history.setEditable(true);
3983     history.addItem("http://www.");
3984
3985     String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
3986
3987     StringTokenizer st;
3988
3989     if (historyItems != null)
3990       {
3991       st = new StringTokenizer(historyItems, "\t");
3992
3993       while (st.hasMoreTokens())
3994       {
3995         history.addItem(st.nextToken());
3996       }
3997       }
3998
3999     int reply = JvOptionPane.showInternalConfirmDialog(this, panel,
4000             MessageManager.getString("label.load_tree_url"),
4001             JvOptionPane.OK_CANCEL_OPTION);
4002
4003     if (reply == JvOptionPane.OK_OPTION)
4004     {
4005
4006       String urlString = history.getSelectedItem().toString();
4007       URL treeUrl;
4008
4009       try
4010       {
4011         FileFormatI format = null;
4012
4013         format = new IdentifyFile().identify(urlString, DataSourceType.URL);
4014         // add actual use for the format identification (jalview .jar files)
4015         treeUrl = new URL(urlString);
4016         AptxInit.createInstancesFromUrl(treeUrl, viewport);
4017
4018       } catch (IOException | RuntimeException e)
4019       {
4020         JvOptionPane.showMessageDialog(this, MessageManager.formatMessage(
4021                 "exception.failed_to_read_data_from_source", new String[]
4022                 { urlString }),
4023                 MessageManager.getString("label.url_not_found"),
4024                 JvOptionPane.ERROR_MESSAGE);
4025         e.printStackTrace();
4026       }
4027     }
4028     else
4029     {
4030
4031     }
4032   }
4033
4034   public void chooseTreeDb(int databaseIndex)
4035   {
4036     AptxInit.createInstancesFromDb(databaseIndex, viewport);
4037   }
4038
4039   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4040   {
4041     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4042   }
4043
4044   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4045           int h, int x, int y)
4046   {
4047     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4048   }
4049
4050   /**
4051    * Add a treeviewer for the tree extracted from a Newick file object to the
4052    * current alignment view
4053    *
4054    * @param nf
4055    *          the tree
4056    * @param title
4057    *          tree viewer title
4058    * @param input
4059    *          Associated alignment input data (or null)
4060    * @param w
4061    *          width
4062    * @param h
4063    *          height
4064    * @param x
4065    *          position
4066    * @param y
4067    *          position
4068    * @return TreePanel handle
4069    */
4070   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4071           AlignmentView input, int w, int h, int x, int y)
4072   {
4073     TreePanel tp = null;
4074
4075     try
4076     {
4077       nf.parse();
4078
4079       if (nf.getTree() != null)
4080       {
4081         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4082
4083         tp.setSize(w, h);
4084
4085         if (x > 0 && y > 0)
4086         {
4087           tp.setLocation(x, y);
4088         }
4089
4090         Desktop.addInternalFrame(tp, treeTitle, w, h);
4091       }
4092     } catch (Exception ex)
4093     {
4094       ex.printStackTrace();
4095     }
4096
4097     return tp;
4098   }
4099
4100   private boolean buildingMenu = false;
4101
4102   public void BuildTreeDbMenu()
4103   {
4104
4105   }
4106   /**
4107    * Generates menu items and listener event actions for web service clients
4108    *
4109    */
4110   public void BuildWebServiceMenu()
4111   {
4112     while (buildingMenu)
4113     {
4114       try
4115       {
4116         System.err.println("Waiting for building menu to finish.");
4117         Thread.sleep(10);
4118       } catch (Exception e)
4119       {
4120       }
4121     }
4122     final AlignFrame me = this;
4123     buildingMenu = true;
4124     new Thread(new Runnable()
4125     {
4126       @Override
4127       public void run()
4128       {
4129         final List<JMenuItem> legacyItems = new ArrayList<>();
4130         try
4131         {
4132           // System.err.println("Building ws menu again "
4133           // + Thread.currentThread());
4134           // TODO: add support for context dependent disabling of services based
4135           // on
4136           // alignment and current selection
4137           // TODO: add additional serviceHandle parameter to specify abstract
4138           // handler
4139           // class independently of AbstractName
4140           // TODO: add in rediscovery GUI function to restart discoverer
4141           // TODO: group services by location as well as function and/or
4142           // introduce
4143           // object broker mechanism.
4144           final Vector<JMenu> wsmenu = new Vector<>();
4145           final IProgressIndicator af = me;
4146
4147           /*
4148            * do not i18n these strings - they are hard-coded in class
4149            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4150            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4151            */
4152           final JMenu msawsmenu = new JMenu("Alignment");
4153           final JMenu secstrmenu = new JMenu(
4154                   "Secondary Structure Prediction");
4155           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4156           final JMenu analymenu = new JMenu("Analysis");
4157           final JMenu dismenu = new JMenu("Protein Disorder");
4158           final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
4159
4160           // JAL-940 - only show secondary structure prediction services from
4161           // the legacy server
4162           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4163               // &&
4164           Discoverer.services != null && (Discoverer.services.size() > 0))
4165           {
4166             // TODO: refactor to allow list of AbstractName/Handler bindings to
4167             // be
4168             // stored or retrieved from elsewhere
4169             // No MSAWS used any more:
4170             // Vector msaws = null; // (Vector)
4171             // Discoverer.services.get("MsaWS");
4172             Vector secstrpr = (Vector) Discoverer.services
4173                     .get("SecStrPred");
4174             if (secstrpr != null)
4175             {
4176               // Add any secondary structure prediction services
4177               for (int i = 0, j = secstrpr.size(); i < j; i++)
4178               {
4179                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4180                         .get(i);
4181                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4182                         .getServiceClient(sh);
4183                 int p = secstrmenu.getItemCount();
4184                 impl.attachWSMenuEntry(secstrmenu, me);
4185                 int q = secstrmenu.getItemCount();
4186                 for (int litm = p; litm < q; litm++)
4187                 {
4188                   legacyItems.add(secstrmenu.getItem(litm));
4189                 }
4190               }
4191             }
4192           }
4193
4194           // Add all submenus in the order they should appear on the web
4195           // services menu
4196           wsmenu.add(msawsmenu);
4197           wsmenu.add(secstrmenu);
4198           wsmenu.add(dismenu);
4199           wsmenu.add(analymenu);
4200           wsmenu.add(phylogenmenu);
4201           // No search services yet
4202           // wsmenu.add(seqsrchmenu);
4203
4204           javax.swing.SwingUtilities.invokeLater(new Runnable()
4205           {
4206             @Override
4207             public void run()
4208             {
4209               try
4210               {
4211                 webService.removeAll();
4212                 // first, add discovered services onto the webservices menu
4213                 if (wsmenu.size() > 0)
4214                 {
4215                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4216                   {
4217                     webService.add(wsmenu.get(i));
4218                   }
4219                 }
4220                 else
4221                 {
4222                   webService.add(me.webServiceNoServices);
4223                 }
4224                 // TODO: move into separate menu builder class.
4225                 boolean new_sspred = false;
4226                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4227                 {
4228                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4229                   if (jws2servs != null)
4230                   {
4231                     if (jws2servs.hasServices())
4232                     {
4233                       jws2servs.attachWSMenuEntry(webService, me);
4234                       for (Jws2Instance sv : jws2servs.getServices())
4235                       {
4236                         if (sv.description.toLowerCase().contains("jpred"))
4237                         {
4238                           for (JMenuItem jmi : legacyItems)
4239                           {
4240                             jmi.setVisible(false);
4241                           }
4242                         }
4243                       }
4244
4245                     }
4246                     if (jws2servs.isRunning())
4247                     {
4248                       JMenuItem tm = new JMenuItem(
4249                               "Still discovering JABA Services");
4250                       tm.setEnabled(false);
4251                       webService.add(tm);
4252                     }
4253                   }
4254                 }
4255                 build_urlServiceMenu(me.webService);
4256                 build_fetchdbmenu(webService);
4257                 for (JMenu item : wsmenu)
4258                 {
4259                   if (item.getItemCount() == 0)
4260                   {
4261                     item.setEnabled(false);
4262                   }
4263                   else
4264                   {
4265                     item.setEnabled(true);
4266                   }
4267                 }
4268               } catch (Exception e)
4269               {
4270                 Cache.log.debug(
4271                         "Exception during web service menu building process.",
4272                         e);
4273               }
4274             }
4275           });
4276         } catch (Exception e)
4277         {
4278         }
4279         buildingMenu = false;
4280       }
4281     }, "BuildWebServiceThread").start();
4282
4283   }
4284
4285   /**
4286    * construct any groupURL type service menu entries.
4287    *
4288    * @param webService
4289    */
4290   private void build_urlServiceMenu(JMenu webService)
4291   {
4292     // TODO: remove this code when 2.7 is released
4293     // DEBUG - alignmentView
4294     /*
4295      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4296      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4297      *
4298      * @Override public void actionPerformed(ActionEvent e) {
4299      * jalview.datamodel.AlignmentView
4300      * .testSelectionViews(af.viewport.getAlignment(),
4301      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4302      *
4303      * }); webService.add(testAlView);
4304      */
4305     // TODO: refactor to RestClient discoverer and merge menu entries for
4306     // rest-style services with other types of analysis/calculation service
4307     // SHmmr test client - still being implemented.
4308     // DEBUG - alignmentView
4309
4310     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4311             .getRestClients())
4312     {
4313       client.attachWSMenuEntry(
4314               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4315               this);
4316     }
4317   }
4318
4319   /**
4320    * Searches the alignment sequences for xRefs and builds the Show
4321    * Cross-References menu (formerly called Show Products), with database
4322    * sources for which cross-references are found (protein sources for a
4323    * nucleotide alignment and vice versa)
4324    *
4325    * @return true if Show Cross-references menu should be enabled
4326    */
4327   public boolean canShowProducts()
4328   {
4329     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4330     AlignmentI dataset = viewport.getAlignment().getDataset();
4331
4332     showProducts.removeAll();
4333     final boolean dna = viewport.getAlignment().isNucleotide();
4334
4335     if (seqs == null || seqs.length == 0)
4336     {
4337       // nothing to see here.
4338       return false;
4339     }
4340
4341     boolean showp = false;
4342     try
4343     {
4344       List<String> ptypes = new CrossRef(seqs, dataset)
4345               .findXrefSourcesForSequences(dna);
4346
4347       for (final String source : ptypes)
4348       {
4349         showp = true;
4350         final AlignFrame af = this;
4351         JMenuItem xtype = new JMenuItem(source);
4352         xtype.addActionListener(new ActionListener()
4353         {
4354           @Override
4355           public void actionPerformed(ActionEvent e)
4356           {
4357             showProductsFor(af.viewport.getSequenceSelection(), dna,
4358                     source);
4359           }
4360         });
4361         showProducts.add(xtype);
4362       }
4363       showProducts.setVisible(showp);
4364       showProducts.setEnabled(showp);
4365     } catch (Exception e)
4366     {
4367       Cache.log.warn(
4368               "canShowProducts threw an exception - please report to help@jalview.org",
4369               e);
4370       return false;
4371     }
4372     return showp;
4373   }
4374
4375   /**
4376    * Finds and displays cross-references for the selected sequences (protein
4377    * products for nucleotide sequences, dna coding sequences for peptides).
4378    *
4379    * @param sel
4380    *          the sequences to show cross-references for
4381    * @param dna
4382    *          true if from a nucleotide alignment (so showing proteins)
4383    * @param source
4384    *          the database to show cross-references for
4385    */
4386   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4387           final String source)
4388   {
4389     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
4390             "CrossReferencesThread")
4391             .start();
4392   }
4393
4394   /**
4395    * Construct and display a new frame containing the translation of this
4396    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4397    */
4398   @Override
4399   public void showTranslation_actionPerformed(ActionEvent e)
4400   {
4401     AlignmentI al = null;
4402     try
4403     {
4404       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4405
4406       al = dna.translateCdna();
4407     } catch (Exception ex)
4408     {
4409       jalview.bin.Cache.log.error(
4410               "Exception during translation. Please report this !", ex);
4411       final String msg = MessageManager.getString(
4412               "label.error_when_translating_sequences_submit_bug_report");
4413       final String errorTitle = MessageManager
4414               .getString("label.implementation_error")
4415               + MessageManager.getString("label.translation_failed");
4416       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4417               JvOptionPane.ERROR_MESSAGE);
4418       return;
4419     }
4420     if (al == null || al.getHeight() == 0)
4421     {
4422       final String msg = MessageManager.getString(
4423               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4424       final String errorTitle = MessageManager
4425               .getString("label.translation_failed");
4426       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4427               JvOptionPane.WARNING_MESSAGE);
4428     }
4429     else
4430     {
4431       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4432       af.setFileFormat(this.currentFileFormat);
4433       final String newTitle = MessageManager
4434               .formatMessage("label.translation_of_params", new Object[]
4435               { this.getTitle() });
4436       af.setTitle(newTitle);
4437       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4438       {
4439         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4440         viewport.openSplitFrame(af, new Alignment(seqs));
4441       }
4442       else
4443       {
4444         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4445                 DEFAULT_HEIGHT);
4446       }
4447     }
4448   }
4449
4450   /**
4451    * Set the file format
4452    *
4453    * @param format
4454    */
4455   public void setFileFormat(FileFormatI format)
4456   {
4457     this.currentFileFormat = format;
4458   }
4459
4460   /**
4461    * Try to load a features file onto the alignment.
4462    *
4463    * @param file
4464    *          contents or path to retrieve file
4465    * @param sourceType
4466    *          access mode of file (see jalview.io.AlignFile)
4467    * @return true if features file was parsed correctly.
4468    */
4469   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4470   {
4471     return avc.parseFeaturesFile(file, sourceType,
4472             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4473
4474   }
4475
4476   @Override
4477   public void refreshFeatureUI(boolean enableIfNecessary)
4478   {
4479     // note - currently this is only still here rather than in the controller
4480     // because of the featureSettings hard reference that is yet to be
4481     // abstracted
4482     if (enableIfNecessary)
4483     {
4484       viewport.setShowSequenceFeatures(true);
4485       showSeqFeatures.setSelected(true);
4486     }
4487
4488   }
4489
4490   @Override
4491   public void dragEnter(DropTargetDragEvent evt)
4492   {
4493   }
4494
4495   @Override
4496   public void dragExit(DropTargetEvent evt)
4497   {
4498   }
4499
4500   @Override
4501   public void dragOver(DropTargetDragEvent evt)
4502   {
4503   }
4504
4505   @Override
4506   public void dropActionChanged(DropTargetDragEvent evt)
4507   {
4508   }
4509
4510   @Override
4511   public void drop(DropTargetDropEvent evt)
4512   {
4513     // JAL-1552 - acceptDrop required before getTransferable call for
4514     // Java's Transferable for native dnd
4515     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4516     Transferable t = evt.getTransferable();
4517     final AlignFrame thisaf = this;
4518     final List<String> files = new ArrayList<>();
4519     List<DataSourceType> protocols = new ArrayList<>();
4520
4521     try
4522     {
4523       Desktop.transferFromDropTarget(files, protocols, evt, t);
4524     } catch (Exception e)
4525     {
4526       e.printStackTrace();
4527     }
4528     if (files != null)
4529     {
4530       new Thread(new Runnable()
4531       {
4532         @Override
4533         public void run()
4534         {
4535           try
4536           {
4537             // check to see if any of these files have names matching sequences
4538             // in
4539             // the alignment
4540             SequenceIdMatcher idm = new SequenceIdMatcher(
4541                     viewport.getAlignment().getSequencesArray());
4542             /**
4543              * Object[] { String,SequenceI}
4544              */
4545             ArrayList<Object[]> filesmatched = new ArrayList<>();
4546             ArrayList<String> filesnotmatched = new ArrayList<>();
4547             for (int i = 0; i < files.size(); i++)
4548             {
4549               String file = files.get(i).toString();
4550               String pdbfn = "";
4551               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4552               if (protocol == DataSourceType.FILE)
4553               {
4554                 File fl = new File(file);
4555                 pdbfn = fl.getName();
4556               }
4557               else if (protocol == DataSourceType.URL)
4558               {
4559                 URL url = new URL(file);
4560                 pdbfn = url.getFile();
4561               }
4562               if (pdbfn.length() > 0)
4563               {
4564                 // attempt to find a match in the alignment
4565                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4566                 int l = 0, c = pdbfn.indexOf(".");
4567                 while (mtch == null && c != -1)
4568                 {
4569                   do
4570                   {
4571                     l = c;
4572                   } while ((c = pdbfn.indexOf(".", l)) > l);
4573                   if (l > -1)
4574                   {
4575                     pdbfn = pdbfn.substring(0, l);
4576                   }
4577                   mtch = idm.findAllIdMatches(pdbfn);
4578                 }
4579                 if (mtch != null)
4580                 {
4581                   FileFormatI type = null;
4582                   try
4583                   {
4584                     type = new IdentifyFile().identify(file, protocol);
4585                   } catch (Exception ex)
4586                   {
4587                     type = null;
4588                   }
4589                   if (type != null && type.isStructureFile())
4590                   {
4591                     filesmatched.add(new Object[] { file, protocol, mtch });
4592                     continue;
4593                   }
4594                 }
4595                 // File wasn't named like one of the sequences or wasn't a PDB
4596                 // file.
4597                 filesnotmatched.add(file);
4598               }
4599             }
4600             int assocfiles = 0;
4601             if (filesmatched.size() > 0)
4602             {
4603               if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4604                       || JvOptionPane.showConfirmDialog(thisaf,
4605                               MessageManager.formatMessage(
4606                                       "label.automatically_associate_structure_files_with_sequences_same_name",
4607                                       new Object[]
4608                                       { Integer.valueOf(filesmatched.size())
4609                                               .toString() }),
4610                               MessageManager.getString(
4611                                       "label.automatically_associate_structure_files_by_name"),
4612                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4613
4614               {
4615                 for (Object[] fm : filesmatched)
4616                 {
4617                   // try and associate
4618                   // TODO: may want to set a standard ID naming formalism for
4619                   // associating PDB files which have no IDs.
4620                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4621                   {
4622                     PDBEntry pe = new AssociatePdbFileWithSeq()
4623                             .associatePdbWithSeq((String) fm[0],
4624                                     (DataSourceType) fm[1], toassoc, false,
4625                                     Desktop.instance);
4626                     if (pe != null)
4627                     {
4628                       System.err.println("Associated file : "
4629                               + ((String) fm[0]) + " with "
4630                               + toassoc.getDisplayId(true));
4631                       assocfiles++;
4632                     }
4633                   }
4634                   // TODO: do we need to update overview ? only if features are
4635                   // shown I guess
4636                   alignPanel.paintAlignment(true, false);
4637                 }
4638               }
4639             }
4640             if (filesnotmatched.size() > 0)
4641             {
4642               if (assocfiles > 0 && (Cache.getDefault(
4643                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4644                       || JvOptionPane.showConfirmDialog(thisaf,
4645                               "<html>" + MessageManager.formatMessage(
4646                                       "label.ignore_unmatched_dropped_files_info",
4647                                       new Object[]
4648                                       { Integer.valueOf(
4649                                               filesnotmatched.size())
4650                                               .toString() })
4651                                       + "</html>",
4652                               MessageManager.getString(
4653                                       "label.ignore_unmatched_dropped_files"),
4654                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4655               {
4656                 return;
4657               }
4658               for (String fn : filesnotmatched)
4659               {
4660                 loadJalviewDataFile(fn, null, null, null);
4661               }
4662
4663             }
4664           } catch (Exception ex)
4665           {
4666             ex.printStackTrace();
4667           }
4668         }
4669       }, "DropFileThread").start();
4670     }
4671   }
4672
4673   /**
4674    * Attempt to load a "dropped" file or URL string, by testing in turn for
4675    * <ul>
4676    * <li>an Annotation file</li>
4677    * <li>a JNet file</li>
4678    * <li>a features file</li>
4679    * <li>else try to interpret as an alignment file</li>
4680    * </ul>
4681    *
4682    * @param file
4683    *          either a filename or a URL string.
4684    */
4685   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4686           FileFormatI format, SequenceI assocSeq)
4687   {
4688     try
4689     {
4690       if (sourceType == null)
4691       {
4692         sourceType = FormatAdapter.checkProtocol(file);
4693       }
4694       // if the file isn't identified, or not positively identified as some
4695       // other filetype (PFAM is default unidentified alignment file type) then
4696       // try to parse as annotation.
4697       boolean isAnnotation = (format == null
4698               || FileFormat.Pfam.equals(format))
4699                       ? new AnnotationFile().annotateAlignmentView(viewport,
4700                               file, sourceType)
4701                       : false;
4702
4703       if (!isAnnotation)
4704       {
4705         // first see if its a T-COFFEE score file
4706         TCoffeeScoreFile tcf = null;
4707         try
4708         {
4709           tcf = new TCoffeeScoreFile(file, sourceType);
4710           if (tcf.isValid())
4711           {
4712             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4713             {
4714               buildColourMenu();
4715               changeColour(
4716                       new TCoffeeColourScheme(viewport.getAlignment()));
4717               isAnnotation = true;
4718               statusBar.setText(MessageManager.getString(
4719                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4720             }
4721             else
4722             {
4723               // some problem - if no warning its probable that the ID matching
4724               // process didn't work
4725               JvOptionPane.showMessageDialog(Desktop.desktop,
4726                       tcf.getWarningMessage() == null
4727                               ? MessageManager.getString(
4728                                       "label.check_file_matches_sequence_ids_alignment")
4729                               : tcf.getWarningMessage(),
4730                       MessageManager.getString(
4731                               "label.problem_reading_tcoffee_score_file"),
4732                       JvOptionPane.WARNING_MESSAGE);
4733             }
4734           }
4735           else
4736           {
4737             tcf = null;
4738           }
4739         } catch (Exception x)
4740         {
4741           Cache.log.debug(
4742                   "Exception when processing data source as T-COFFEE score file",
4743                   x);
4744           tcf = null;
4745         }
4746         if (tcf == null)
4747         {
4748           // try to see if its a JNet 'concise' style annotation file *before*
4749           // we
4750           // try to parse it as a features file
4751           if (format == null)
4752           {
4753             format = new IdentifyFile().identify(file, sourceType);
4754           }
4755           if (FileFormat.ScoreMatrix == format)
4756           {
4757             ScoreMatrixFile sm = new ScoreMatrixFile(
4758                     new FileParse(file, sourceType));
4759             sm.parse();
4760             // todo: i18n this message
4761             statusBar.setText(MessageManager.formatMessage(
4762                     "label.successfully_loaded_matrix",
4763                     sm.getMatrixName()));
4764           }
4765           else if (FileFormat.Jnet.equals(format))
4766           {
4767             JPredFile predictions = new JPredFile(file, sourceType);
4768             new JnetAnnotationMaker();
4769             JnetAnnotationMaker.add_annotation(predictions,
4770                     viewport.getAlignment(), 0, false);
4771             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4772             viewport.getAlignment().setSeqrep(repseq);
4773             HiddenColumns cs = new HiddenColumns();
4774             cs.hideInsertionsFor(repseq);
4775             viewport.getAlignment().setHiddenColumns(cs);
4776             isAnnotation = true;
4777           }
4778           // else if (IdentifyFile.FeaturesFile.equals(format))
4779           else if (FileFormat.Features.equals(format))
4780           {
4781             if (parseFeaturesFile(file, sourceType))
4782             {
4783               alignPanel.paintAlignment(true, true);
4784             }
4785           }
4786           else
4787           {
4788             new FileLoader().LoadFile(viewport, file, sourceType, format);
4789           }
4790         }
4791       }
4792       if (isAnnotation)
4793       {
4794
4795         alignPanel.adjustAnnotationHeight();
4796         viewport.updateSequenceIdColours();
4797         buildSortByAnnotationScoresMenu();
4798         alignPanel.paintAlignment(true, true);
4799       }
4800     } catch (Exception ex)
4801     {
4802       ex.printStackTrace();
4803     } catch (OutOfMemoryError oom)
4804     {
4805       try
4806       {
4807         System.gc();
4808       } catch (Exception x)
4809       {
4810       }
4811       new OOMWarning(
4812               "loading data "
4813                       + (sourceType != null
4814                               ? (sourceType == DataSourceType.PASTE
4815                                       ? "from clipboard."
4816                                       : "using " + sourceType + " from "
4817                                               + file)
4818                               : ".")
4819                       + (format != null
4820                               ? "(parsing as '" + format + "' file)"
4821                               : ""),
4822               oom, Desktop.desktop);
4823     }
4824   }
4825
4826   /**
4827    * Method invoked by the ChangeListener on the tabbed pane, in other words
4828    * when a different tabbed pane is selected by the user or programmatically.
4829    */
4830   @Override
4831   public void tabSelectionChanged(int index)
4832   {
4833     if (index > -1)
4834     {
4835       alignPanel = alignPanels.get(index);
4836       viewport = alignPanel.av;
4837       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4838       setMenusFromViewport(viewport);
4839     }
4840
4841     /*
4842      * 'focus' any colour slider that is open to the selected viewport
4843      */
4844     if (viewport.getConservationSelected())
4845     {
4846       SliderPanel.setConservationSlider(alignPanel,
4847               viewport.getResidueShading(), alignPanel.getViewName());
4848     }
4849     else
4850     {
4851       SliderPanel.hideConservationSlider();
4852     }
4853     if (viewport.getAbovePIDThreshold())
4854     {
4855       SliderPanel.setPIDSliderSource(alignPanel,
4856               viewport.getResidueShading(), alignPanel.getViewName());
4857     }
4858     else
4859     {
4860       SliderPanel.hidePIDSlider();
4861     }
4862
4863     /*
4864      * If there is a frame linked to this one in a SplitPane, switch it to the
4865      * same view tab index. No infinite recursion of calls should happen, since
4866      * tabSelectionChanged() should not get invoked on setting the selected
4867      * index to an unchanged value. Guard against setting an invalid index
4868      * before the new view peer tab has been created.
4869      */
4870     final AlignViewportI peer = viewport.getCodingComplement();
4871     if (peer != null)
4872     {
4873       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4874               .getAlignPanel().alignFrame;
4875       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4876       {
4877         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4878       }
4879     }
4880   }
4881
4882   /**
4883    * On right mouse click on view tab, prompt for and set new view name.
4884    */
4885   @Override
4886   public void tabbedPane_mousePressed(MouseEvent e)
4887   {
4888     if (e.isPopupTrigger())
4889     {
4890       String msg = MessageManager.getString("label.enter_view_name");
4891       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4892               JvOptionPane.QUESTION_MESSAGE);
4893
4894       if (reply != null)
4895       {
4896         viewport.viewName = reply;
4897         // TODO warn if reply is in getExistingViewNames()?
4898         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4899       }
4900     }
4901   }
4902
4903   public AlignViewport getCurrentView()
4904   {
4905     return viewport;
4906   }
4907
4908   /**
4909    * Open the dialog for regex description parsing.
4910    */
4911   @Override
4912   protected void extractScores_actionPerformed(ActionEvent e)
4913   {
4914     ParseProperties pp = new jalview.analysis.ParseProperties(
4915             viewport.getAlignment());
4916     // TODO: verify regex and introduce GUI dialog for version 2.5
4917     // if (pp.getScoresFromDescription("col", "score column ",
4918     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4919     // true)>0)
4920     if (pp.getScoresFromDescription("description column",
4921             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4922     {
4923       buildSortByAnnotationScoresMenu();
4924     }
4925   }
4926
4927   /*
4928    * (non-Javadoc)
4929    *
4930    * @see
4931    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4932    * )
4933    */
4934   @Override
4935   protected void showDbRefs_actionPerformed(ActionEvent e)
4936   {
4937     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4938   }
4939
4940   /*
4941    * (non-Javadoc)
4942    *
4943    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4944    * ActionEvent)
4945    */
4946   @Override
4947   protected void showNpFeats_actionPerformed(ActionEvent e)
4948   {
4949     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4950   }
4951
4952   /**
4953    * find the viewport amongst the tabs in this alignment frame and close that
4954    * tab
4955    *
4956    * @param av
4957    */
4958   public boolean closeView(AlignViewportI av)
4959   {
4960     if (viewport == av)
4961     {
4962       this.closeMenuItem_actionPerformed(false);
4963       return true;
4964     }
4965     Component[] comp = tabbedPane.getComponents();
4966     for (int i = 0; comp != null && i < comp.length; i++)
4967     {
4968       if (comp[i] instanceof AlignmentPanel)
4969       {
4970         if (((AlignmentPanel) comp[i]).av == av)
4971         {
4972           // close the view.
4973           closeView((AlignmentPanel) comp[i]);
4974           return true;
4975         }
4976       }
4977     }
4978     return false;
4979   }
4980
4981   protected void build_fetchdbmenu(JMenu webService)
4982   {
4983     // Temporary hack - DBRef Fetcher always top level ws entry.
4984     // TODO We probably want to store a sequence database checklist in
4985     // preferences and have checkboxes.. rather than individual sources selected
4986     // here
4987     final JMenu rfetch = new JMenu(
4988             MessageManager.getString("action.fetch_db_references"));
4989     rfetch.setToolTipText(MessageManager.getString(
4990             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4991     webService.add(rfetch);
4992
4993     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4994             MessageManager.getString("option.trim_retrieved_seqs"));
4995     trimrs.setToolTipText(
4996             MessageManager.getString("label.trim_retrieved_sequences"));
4997     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4998     trimrs.addActionListener(new ActionListener()
4999     {
5000       @Override
5001       public void actionPerformed(ActionEvent e)
5002       {
5003         trimrs.setSelected(trimrs.isSelected());
5004         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5005                 Boolean.valueOf(trimrs.isSelected()).toString());
5006       };
5007     });
5008     rfetch.add(trimrs);
5009     JMenuItem fetchr = new JMenuItem(
5010             MessageManager.getString("label.standard_databases"));
5011     fetchr.setToolTipText(
5012             MessageManager.getString("label.fetch_embl_uniprot"));
5013     fetchr.addActionListener(new ActionListener()
5014     {
5015
5016       @Override
5017       public void actionPerformed(ActionEvent e)
5018       {
5019         new Thread(new Runnable()
5020         {
5021           @Override
5022           public void run()
5023           {
5024             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5025                     .getAlignment().isNucleotide();
5026             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5027                     alignPanel.av.getSequenceSelection(),
5028                     alignPanel.alignFrame, null,
5029                     alignPanel.alignFrame.featureSettings, isNucleotide);
5030             dbRefFetcher.addListener(new FetchFinishedListenerI()
5031             {
5032               @Override
5033               public void finished()
5034               {
5035                 AlignFrame.this.setMenusForViewport();
5036               }
5037             });
5038             dbRefFetcher.fetchDBRefs(false);
5039           }
5040         }, "BuildFetchDBMenuThread").start();
5041
5042       }
5043
5044     });
5045     rfetch.add(fetchr);
5046     final AlignFrame me = this;
5047     new Thread(new Runnable()
5048     {
5049       @Override
5050       public void run()
5051       {
5052         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5053                 .getSequenceFetcherSingleton(me);
5054         javax.swing.SwingUtilities.invokeLater(new Runnable()
5055         {
5056           @Override
5057           public void run()
5058           {
5059             String[] dbclasses = sf.getOrderedSupportedSources();
5060             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5061             // jalview.util.QuickSort.sort(otherdb, otherdb);
5062             List<DbSourceProxy> otherdb;
5063             JMenu dfetch = new JMenu();
5064             JMenu ifetch = new JMenu();
5065             JMenuItem fetchr = null;
5066             int comp = 0, icomp = 0, mcomp = 15;
5067             String mname = null;
5068             int dbi = 0;
5069             for (String dbclass : dbclasses)
5070             {
5071               otherdb = sf.getSourceProxy(dbclass);
5072               // add a single entry for this class, or submenu allowing 'fetch
5073               // all' or pick one
5074               if (otherdb == null || otherdb.size() < 1)
5075               {
5076                 continue;
5077               }
5078               // List<DbSourceProxy> dbs=otherdb;
5079               // otherdb=new ArrayList<DbSourceProxy>();
5080               // for (DbSourceProxy db:dbs)
5081               // {
5082               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5083               // }
5084               if (mname == null)
5085               {
5086                 mname = "From " + dbclass;
5087               }
5088               if (otherdb.size() == 1)
5089               {
5090                 final DbSourceProxy[] dassource = otherdb
5091                         .toArray(new DbSourceProxy[0]);
5092                 DbSourceProxy src = otherdb.get(0);
5093                 fetchr = new JMenuItem(src.getDbSource());
5094                 fetchr.addActionListener(new ActionListener()
5095                 {
5096
5097                   @Override
5098                   public void actionPerformed(ActionEvent e)
5099                   {
5100                     new Thread(new Runnable()
5101                     {
5102
5103                       @Override
5104                       public void run()
5105                       {
5106                         boolean isNucleotide = alignPanel.alignFrame
5107                                 .getViewport().getAlignment()
5108                                 .isNucleotide();
5109                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5110                                 alignPanel.av.getSequenceSelection(),
5111                                 alignPanel.alignFrame, dassource,
5112                                 alignPanel.alignFrame.featureSettings,
5113                                 isNucleotide);
5114                         dbRefFetcher
5115                                 .addListener(new FetchFinishedListenerI()
5116                                 {
5117                                   @Override
5118                                   public void finished()
5119                                   {
5120                                     AlignFrame.this.setMenusForViewport();
5121                                   }
5122                                 });
5123                         dbRefFetcher.fetchDBRefs(false);
5124                       }
5125                     }).start();
5126                   }
5127
5128                 });
5129                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5130                         MessageManager.formatMessage(
5131                                 "label.fetch_retrieve_from", new Object[]
5132                                 { src.getDbName() })));
5133                 dfetch.add(fetchr);
5134                 comp++;
5135               }
5136               else
5137               {
5138                 final DbSourceProxy[] dassource = otherdb
5139                         .toArray(new DbSourceProxy[0]);
5140                 // fetch all entry
5141                 DbSourceProxy src = otherdb.get(0);
5142                 fetchr = new JMenuItem(MessageManager
5143                         .formatMessage("label.fetch_all_param", new Object[]
5144                         { src.getDbSource() }));
5145                 fetchr.addActionListener(new ActionListener()
5146                 {
5147                   @Override
5148                   public void actionPerformed(ActionEvent e)
5149                   {
5150                     new Thread(new Runnable()
5151                     {
5152
5153                       @Override
5154                       public void run()
5155                       {
5156                         boolean isNucleotide = alignPanel.alignFrame
5157                                 .getViewport().getAlignment()
5158                                 .isNucleotide();
5159                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5160                                 alignPanel.av.getSequenceSelection(),
5161                                 alignPanel.alignFrame, dassource,
5162                                 alignPanel.alignFrame.featureSettings,
5163                                 isNucleotide);
5164                         dbRefFetcher
5165                                 .addListener(new FetchFinishedListenerI()
5166                                 {
5167                                   @Override
5168                                   public void finished()
5169                                   {
5170                                     AlignFrame.this.setMenusForViewport();
5171                                   }
5172                                 });
5173                         dbRefFetcher.fetchDBRefs(false);
5174                       }
5175                     }).start();
5176                   }
5177                 });
5178
5179                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5180                         MessageManager.formatMessage(
5181                                 "label.fetch_retrieve_from_all_sources",
5182                                 new Object[]
5183                                 { Integer.valueOf(otherdb.size())
5184                                         .toString(),
5185                                     src.getDbSource(), src.getDbName() })));
5186                 dfetch.add(fetchr);
5187                 comp++;
5188                 // and then build the rest of the individual menus
5189                 ifetch = new JMenu(MessageManager.formatMessage(
5190                         "label.source_from_db_source", new Object[]
5191                         { src.getDbSource() }));
5192                 icomp = 0;
5193                 String imname = null;
5194                 int i = 0;
5195                 for (DbSourceProxy sproxy : otherdb)
5196                 {
5197                   String dbname = sproxy.getDbName();
5198                   String sname = dbname.length() > 5
5199                           ? dbname.substring(0, 5) + "..."
5200                           : dbname;
5201                   String msname = dbname.length() > 10
5202                           ? dbname.substring(0, 10) + "..."
5203                           : dbname;
5204                   if (imname == null)
5205                   {
5206                     imname = MessageManager
5207                             .formatMessage("label.from_msname", new Object[]
5208                             { sname });
5209                   }
5210                   fetchr = new JMenuItem(msname);
5211                   final DbSourceProxy[] dassrc = { sproxy };
5212                   fetchr.addActionListener(new ActionListener()
5213                   {
5214
5215                     @Override
5216                     public void actionPerformed(ActionEvent e)
5217                     {
5218                       new Thread(new Runnable()
5219                       {
5220
5221                         @Override
5222                         public void run()
5223                         {
5224                           boolean isNucleotide = alignPanel.alignFrame
5225                                   .getViewport().getAlignment()
5226                                   .isNucleotide();
5227                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5228                                   alignPanel.av.getSequenceSelection(),
5229                                   alignPanel.alignFrame, dassrc,
5230                                   alignPanel.alignFrame.featureSettings,
5231                                   isNucleotide);
5232                           dbRefFetcher
5233                                   .addListener(new FetchFinishedListenerI()
5234                                   {
5235                                     @Override
5236                                     public void finished()
5237                                     {
5238                                       AlignFrame.this.setMenusForViewport();
5239                                     }
5240                                   });
5241                           dbRefFetcher.fetchDBRefs(false);
5242                         }
5243                       }).start();
5244                     }
5245
5246                   });
5247                   fetchr.setToolTipText(
5248                           "<html>" + MessageManager.formatMessage(
5249                                   "label.fetch_retrieve_from", new Object[]
5250                                   { dbname }));
5251                   ifetch.add(fetchr);
5252                   ++i;
5253                   if (++icomp >= mcomp || i == (otherdb.size()))
5254                   {
5255                     ifetch.setText(MessageManager.formatMessage(
5256                             "label.source_to_target", imname, sname));
5257                     dfetch.add(ifetch);
5258                     ifetch = new JMenu();
5259                     imname = null;
5260                     icomp = 0;
5261                     comp++;
5262                   }
5263                 }
5264               }
5265               ++dbi;
5266               if (comp >= mcomp || dbi >= (dbclasses.length))
5267               {
5268                 dfetch.setText(MessageManager.formatMessage(
5269                         "label.source_to_target", mname, dbclass));
5270                 rfetch.add(dfetch);
5271                 dfetch = new JMenu();
5272                 mname = null;
5273                 comp = 0;
5274               }
5275             }
5276           }
5277         });
5278       }
5279     }).start();
5280
5281   }
5282
5283   /**
5284    * Left justify the whole alignment.
5285    */
5286   @Override
5287   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5288   {
5289     AlignmentI al = viewport.getAlignment();
5290     al.justify(false);
5291     viewport.firePropertyChange("alignment", null, al);
5292   }
5293
5294   /**
5295    * Right justify the whole alignment.
5296    */
5297   @Override
5298   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5299   {
5300     AlignmentI al = viewport.getAlignment();
5301     al.justify(true);
5302     viewport.firePropertyChange("alignment", null, al);
5303   }
5304
5305   @Override
5306   public void setShowSeqFeatures(boolean b)
5307   {
5308     showSeqFeatures.setSelected(b);
5309     viewport.setShowSequenceFeatures(b);
5310   }
5311
5312   /*
5313    * (non-Javadoc)
5314    *
5315    * @see
5316    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5317    * awt.event.ActionEvent)
5318    */
5319   @Override
5320   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5321   {
5322     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5323     alignPanel.paintAlignment(false, false);
5324   }
5325
5326   /*
5327    * (non-Javadoc)
5328    *
5329    * @see
5330    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5331    * .ActionEvent)
5332    */
5333   @Override
5334   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5335   {
5336     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5337     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5338
5339   }
5340
5341   /*
5342    * (non-Javadoc)
5343    *
5344    * @see
5345    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5346    * .event.ActionEvent)
5347    */
5348   @Override
5349   protected void showGroupConservation_actionPerformed(ActionEvent e)
5350   {
5351     viewport.setShowGroupConservation(showGroupConservation.getState());
5352     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5353   }
5354
5355   /*
5356    * (non-Javadoc)
5357    *
5358    * @see
5359    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5360    * .event.ActionEvent)
5361    */
5362   @Override
5363   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5364   {
5365     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5366     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5367   }
5368
5369   /*
5370    * (non-Javadoc)
5371    *
5372    * @see
5373    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5374    * .event.ActionEvent)
5375    */
5376   @Override
5377   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5378   {
5379     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5380     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5381   }
5382
5383   @Override
5384   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5385   {
5386     showSequenceLogo.setState(true);
5387     viewport.setShowSequenceLogo(true);
5388     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5389     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5390   }
5391
5392   @Override
5393   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5394   {
5395     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5396   }
5397
5398   /*
5399    * (non-Javadoc)
5400    *
5401    * @see
5402    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5403    * .event.ActionEvent)
5404    */
5405   @Override
5406   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5407   {
5408     if (avc.makeGroupsFromSelection())
5409     {
5410       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5411       alignPanel.updateAnnotation();
5412       alignPanel.paintAlignment(true, true);
5413     }
5414   }
5415
5416   public void clearAlignmentSeqRep()
5417   {
5418     // TODO refactor alignmentseqrep to controller
5419     if (viewport.getAlignment().hasSeqrep())
5420     {
5421       viewport.getAlignment().setSeqrep(null);
5422       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5423       alignPanel.updateAnnotation();
5424       alignPanel.paintAlignment(true, true);
5425     }
5426   }
5427
5428   @Override
5429   protected void createGroup_actionPerformed(ActionEvent e)
5430   {
5431     if (avc.createGroup())
5432     {
5433       alignPanel.alignmentChanged();
5434     }
5435   }
5436
5437   @Override
5438   protected void unGroup_actionPerformed(ActionEvent e)
5439   {
5440     if (avc.unGroup())
5441     {
5442       alignPanel.alignmentChanged();
5443     }
5444   }
5445
5446   /**
5447    * make the given alignmentPanel the currently selected tab
5448    *
5449    * @param alignmentPanel
5450    */
5451   public void setDisplayedView(AlignmentPanel alignmentPanel)
5452   {
5453     if (!viewport.getSequenceSetId()
5454             .equals(alignmentPanel.av.getSequenceSetId()))
5455     {
5456       throw new Error(MessageManager.getString(
5457               "error.implementation_error_cannot_show_view_alignment_frame"));
5458     }
5459     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5460             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5461     {
5462       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5463     }
5464   }
5465
5466   /**
5467    * Action on selection of menu options to Show or Hide annotations.
5468    *
5469    * @param visible
5470    * @param forSequences
5471    *          update sequence-related annotations
5472    * @param forAlignment
5473    *          update non-sequence-related annotations
5474    */
5475   @Override
5476   protected void setAnnotationsVisibility(boolean visible,
5477           boolean forSequences, boolean forAlignment)
5478   {
5479     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5480             .getAlignmentAnnotation();
5481     if (anns == null)
5482     {
5483       return;
5484     }
5485     for (AlignmentAnnotation aa : anns)
5486     {
5487       /*
5488        * don't display non-positional annotations on an alignment
5489        */
5490       if (aa.annotations == null)
5491       {
5492         continue;
5493       }
5494       boolean apply = (aa.sequenceRef == null && forAlignment)
5495               || (aa.sequenceRef != null && forSequences);
5496       if (apply)
5497       {
5498         aa.visible = visible;
5499       }
5500     }
5501     alignPanel.validateAnnotationDimensions(true);
5502     alignPanel.alignmentChanged();
5503   }
5504
5505   /**
5506    * Store selected annotation sort order for the view and repaint.
5507    */
5508   @Override
5509   protected void sortAnnotations_actionPerformed()
5510   {
5511     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5512     this.alignPanel.av
5513             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5514     alignPanel.paintAlignment(false, false);
5515   }
5516
5517   /**
5518    *
5519    * @return alignment panels in this alignment frame
5520    */
5521   public List<? extends AlignmentViewPanel> getAlignPanels()
5522   {
5523     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5524   }
5525
5526   /**
5527    * Open a new alignment window, with the cDNA associated with this (protein)
5528    * alignment, aligned as is the protein.
5529    */
5530   protected void viewAsCdna_actionPerformed()
5531   {
5532     // TODO no longer a menu action - refactor as required
5533     final AlignmentI alignment = getViewport().getAlignment();
5534     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5535     if (mappings == null)
5536     {
5537       return;
5538     }
5539     List<SequenceI> cdnaSeqs = new ArrayList<>();
5540     for (SequenceI aaSeq : alignment.getSequences())
5541     {
5542       for (AlignedCodonFrame acf : mappings)
5543       {
5544         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5545         if (dnaSeq != null)
5546         {
5547           /*
5548            * There is a cDNA mapping for this protein sequence - add to new
5549            * alignment. It will share the same dataset sequence as other mapped
5550            * cDNA (no new mappings need to be created).
5551            */
5552           final Sequence newSeq = new Sequence(dnaSeq);
5553           newSeq.setDatasetSequence(dnaSeq);
5554           cdnaSeqs.add(newSeq);
5555         }
5556       }
5557     }
5558     if (cdnaSeqs.size() == 0)
5559     {
5560       // show a warning dialog no mapped cDNA
5561       return;
5562     }
5563     AlignmentI cdna = new Alignment(
5564             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5565     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5566             AlignFrame.DEFAULT_HEIGHT);
5567     cdna.alignAs(alignment);
5568     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5569             + this.title;
5570     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5571             AlignFrame.DEFAULT_HEIGHT);
5572   }
5573
5574   /**
5575    * Set visibility of dna/protein complement view (available when shown in a
5576    * split frame).
5577    *
5578    * @param show
5579    */
5580   @Override
5581   protected void showComplement_actionPerformed(boolean show)
5582   {
5583     SplitContainerI sf = getSplitViewContainer();
5584     if (sf != null)
5585     {
5586       sf.setComplementVisible(this, show);
5587     }
5588   }
5589
5590   /**
5591    * Generate the reverse (optionally complemented) of the selected sequences,
5592    * and add them to the alignment
5593    */
5594   @Override
5595   protected void showReverse_actionPerformed(boolean complement)
5596   {
5597     AlignmentI al = null;
5598     try
5599     {
5600       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5601       al = dna.reverseCdna(complement);
5602       viewport.addAlignment(al, "");
5603       addHistoryItem(new EditCommand(
5604               MessageManager.getString("label.add_sequences"), Action.PASTE,
5605               al.getSequencesArray(), 0, al.getWidth(),
5606               viewport.getAlignment()));
5607     } catch (Exception ex)
5608     {
5609       System.err.println(ex.getMessage());
5610       return;
5611     }
5612   }
5613
5614   /**
5615    * Try to run a script in the Groovy console, having first ensured that this
5616    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5617    * be targeted at this alignment.
5618    */
5619   @Override
5620   protected void runGroovy_actionPerformed()
5621   {
5622     Jalview.setCurrentAlignFrame(this);
5623     groovy.ui.Console console = Desktop.getGroovyConsole();
5624     if (console != null)
5625     {
5626       try
5627       {
5628         console.runScript();
5629       } catch (Exception ex)
5630       {
5631         System.err.println((ex.toString()));
5632         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5633                 MessageManager.getString("label.couldnt_run_groovy_script"),
5634                 MessageManager.getString("label.groovy_support_failed"),
5635                 JvOptionPane.ERROR_MESSAGE);
5636       }
5637     }
5638     else
5639     {
5640       System.err.println("Can't run Groovy script as console not found");
5641     }
5642   }
5643
5644   /**
5645    * Hides columns containing (or not containing) a specified feature, provided
5646    * that would not leave all columns hidden
5647    *
5648    * @param featureType
5649    * @param columnsContaining
5650    * @return
5651    */
5652   public boolean hideFeatureColumns(String featureType,
5653           boolean columnsContaining)
5654   {
5655     boolean notForHiding = avc.markColumnsContainingFeatures(
5656             columnsContaining, false, false, featureType);
5657     if (notForHiding)
5658     {
5659       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5660               false, featureType))
5661       {
5662         getViewport().hideSelectedColumns();
5663         return true;
5664       }
5665     }
5666     return false;
5667   }
5668
5669   @Override
5670   protected void selectHighlightedColumns_actionPerformed(
5671           ActionEvent actionEvent)
5672   {
5673     // include key modifier check in case user selects from menu
5674     avc.markHighlightedColumns(
5675             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5676             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5677                     | ActionEvent.CTRL_MASK)) != 0);
5678   }
5679
5680   /**
5681    * Rebuilds the Colour menu, including any user-defined colours which have
5682    * been loaded either on startup or during the session
5683    */
5684   public void buildColourMenu()
5685   {
5686     colourMenu.removeAll();
5687
5688     colourMenu.add(applyToAllGroups);
5689     colourMenu.add(textColour);
5690     colourMenu.addSeparator();
5691
5692     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5693             false);
5694
5695     colourMenu.addSeparator();
5696     colourMenu.add(conservationMenuItem);
5697     colourMenu.add(modifyConservation);
5698     colourMenu.add(abovePIDThreshold);
5699     colourMenu.add(modifyPID);
5700     colourMenu.add(annotationColour);
5701
5702     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5703     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5704   }
5705
5706   /**
5707    * Open a dialog (if not already open) that allows the user to select and
5708    * calculate PCA or Tree analysis
5709    */
5710   protected void openTreePcaDialog()
5711   {
5712     if (alignPanel.getCalculationDialog() == null)
5713     {
5714       new CalculationChooser(AlignFrame.this);
5715     }
5716   }
5717 }
5718
5719 class PrintThread extends Thread
5720 {
5721   AlignmentPanel ap;
5722
5723   public PrintThread(AlignmentPanel ap)
5724   {
5725     this.ap = ap;
5726   }
5727
5728   static PageFormat pf;
5729
5730   @Override
5731   public void run()
5732   {
5733     PrinterJob printJob = PrinterJob.getPrinterJob();
5734
5735     if (pf != null)
5736     {
5737       printJob.setPrintable(ap, pf);
5738     }
5739     else
5740     {
5741       printJob.setPrintable(ap);
5742     }
5743
5744     if (printJob.printDialog())
5745     {
5746       try
5747       {
5748         printJob.print();
5749       } catch (Exception PrintException)
5750       {
5751         PrintException.printStackTrace();
5752       }
5753     }
5754   }
5755 }