src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  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.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.io.vcf.VCFLoader;
  85 import jalview.jbgui.GAlignFrame;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemes;
  88 import jalview.schemes.ResidueColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.util.MessageManager;
  91 import jalview.viewmodel.AlignmentViewport;
  92 import jalview.viewmodel.ViewportRanges;
  93 import jalview.ws.DBRefFetcher;
  94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  95 import jalview.ws.jws1.Discoverer;
  96 import jalview.ws.jws2.Jws2Discoverer;
  97 import jalview.ws.jws2.jabaws2.Jws2Instance;
  98 import jalview.ws.seqfetcher.DbSourceProxy;
  99
 100 import java.awt.BorderLayout;
 101 import java.awt.Component;
 102 import java.awt.Rectangle;
 103 import java.awt.Toolkit;
 104 import java.awt.datatransfer.Clipboard;
 105 import java.awt.datatransfer.DataFlavor;
 106 import java.awt.datatransfer.StringSelection;
 107 import java.awt.datatransfer.Transferable;
 108 import java.awt.dnd.DnDConstants;
 109 import java.awt.dnd.DropTargetDragEvent;
 110 import java.awt.dnd.DropTargetDropEvent;
 111 import java.awt.dnd.DropTargetEvent;
 112 import java.awt.dnd.DropTargetListener;
 113 import java.awt.event.ActionEvent;
 114 import java.awt.event.ActionListener;
 115 import java.awt.event.FocusAdapter;
 116 import java.awt.event.FocusEvent;
 117 import java.awt.event.ItemEvent;
 118 import java.awt.event.ItemListener;
 119 import java.awt.event.KeyAdapter;
 120 import java.awt.event.KeyEvent;
 121 import java.awt.event.MouseEvent;
 122 import java.awt.print.PageFormat;
 123 import java.awt.print.PrinterJob;
 124 import java.beans.PropertyChangeEvent;
 125 import java.beans.PropertyChangeListener;
 126 import java.io.File;
 127 import java.io.FileWriter;
 128 import java.io.PrintWriter;
 129 import java.net.URL;
 130 import java.util.ArrayList;
 131 import java.util.Arrays;
 132 import java.util.Deque;
 133 import java.util.Enumeration;
 134 import java.util.Hashtable;
 135 import java.util.List;
 136 import java.util.Vector;
 137
 138 import javax.swing.JCheckBoxMenuItem;
 139 import javax.swing.JEditorPane;
 140 import javax.swing.JFileChooser;
 141 import javax.swing.JInternalFrame;
 142 import javax.swing.JLayeredPane;
 143 import javax.swing.JMenu;
 144 import javax.swing.JMenuItem;
 145 import javax.swing.JScrollPane;
 146 import javax.swing.SwingUtilities;
 147
 148 /**
 149  * DOCUMENT ME!
 150  *
 151  * @author $author$
 152  * @version $Revision$
 153  */
 154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 155         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener,
 156         PropertyChangeListener
 157 {
 158
 159   public static final int DEFAULT_WIDTH = 700;
 160
 161   public static final int DEFAULT_HEIGHT = 500;
 162
 163   /*
 164    * The currently displayed panel (selected tabbed view if more than one)
 165    */
 166   public AlignmentPanel alignPanel;
 167
 168   AlignViewport viewport;
 169
 170   public AlignViewControllerI avc;
 171
 172   List<AlignmentPanel> alignPanels = new ArrayList<>();
 173
 174   /**
 175    * Last format used to load or save alignments in this window
 176    */
 177   FileFormatI currentFileFormat = null;
 178
 179   /**
 180    * Current filename for this alignment
 181    */
 182   String fileName = null;
 183
 184   /**
 185    * Creates a new AlignFrame object with specific width and height.
 186    *
 187    * @param al
 188    * @param width
 189    * @param height
 190    */
 191   public AlignFrame(AlignmentI al, int width, int height)
 192   {
 193     this(al, null, width, height);
 194   }
 195
 196   /**
 197    * Creates a new AlignFrame object with specific width, height and
 198    * sequenceSetId
 199    *
 200    * @param al
 201    * @param width
 202    * @param height
 203    * @param sequenceSetId
 204    */
 205   public AlignFrame(AlignmentI al, int width, int height,
 206           String sequenceSetId)
 207   {
 208     this(al, null, width, height, sequenceSetId);
 209   }
 210
 211   /**
 212    * Creates a new AlignFrame object with specific width, height and
 213    * sequenceSetId
 214    *
 215    * @param al
 216    * @param width
 217    * @param height
 218    * @param sequenceSetId
 219    * @param viewId
 220    */
 221   public AlignFrame(AlignmentI al, int width, int height,
 222           String sequenceSetId, String viewId)
 223   {
 224     this(al, null, width, height, sequenceSetId, viewId);
 225   }
 226
 227   /**
 228    * new alignment window with hidden columns
 229    *
 230    * @param al
 231    *          AlignmentI
 232    * @param hiddenColumns
 233    *          ColumnSelection or null
 234    * @param width
 235    *          Width of alignment frame
 236    * @param height
 237    *          height of frame.
 238    */
 239   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 240           int height)
 241   {
 242     this(al, hiddenColumns, width, height, null);
 243   }
 244
 245   /**
 246    * Create alignment frame for al with hiddenColumns, a specific width and
 247    * height, and specific sequenceId
 248    *
 249    * @param al
 250    * @param hiddenColumns
 251    * @param width
 252    * @param height
 253    * @param sequenceSetId
 254    *          (may be null)
 255    */
 256   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 257           int height, String sequenceSetId)
 258   {
 259     this(al, hiddenColumns, width, height, sequenceSetId, null);
 260   }
 261
 262   /**
 263    * Create alignment frame for al with hiddenColumns, a specific width and
 264    * height, and specific sequenceId
 265    *
 266    * @param al
 267    * @param hiddenColumns
 268    * @param width
 269    * @param height
 270    * @param sequenceSetId
 271    *          (may be null)
 272    * @param viewId
 273    *          (may be null)
 274    */
 275   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 276           int height, String sequenceSetId, String viewId)
 277   {
 278     setSize(width, height);
 279
 280     if (al.getDataset() == null)
 281     {
 282       al.setDataset(null);
 283     }
 284
 285     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 286
 287     alignPanel = new AlignmentPanel(this, viewport);
 288
 289     addAlignmentPanel(alignPanel, true);
 290     init();
 291   }
 292
 293   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 294           HiddenColumns hiddenColumns, int width, int height)
 295   {
 296     setSize(width, height);
 297
 298     if (al.getDataset() == null)
 299     {
 300       al.setDataset(null);
 301     }
 302
 303     viewport = new AlignViewport(al, hiddenColumns);
 304
 305     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 306     {
 307       viewport.hideSequence(hiddenSeqs);
 308     }
 309     alignPanel = new AlignmentPanel(this, viewport);
 310     addAlignmentPanel(alignPanel, true);
 311     init();
 312   }
 313
 314   /**
 315    * Make a new AlignFrame from existing alignmentPanels
 316    *
 317    * @param ap
 318    *          AlignmentPanel
 319    * @param av
 320    *          AlignViewport
 321    */
 322   public AlignFrame(AlignmentPanel ap)
 323   {
 324     viewport = ap.av;
 325     alignPanel = ap;
 326     addAlignmentPanel(ap, false);
 327     init();
 328   }
 329
 330   @Override
 331   public void propertyChange(PropertyChangeEvent evt)
 332   {
 333     Desktop.getDesktop().propertyChange(evt);
 334   }
 335
 336
 337   /**
 338    *  BH 2018
 339    *
 340    * @return true if we have any features
 341    */
 342   @Override
 343   protected boolean haveAlignmentFeatures() {
 344     AlignmentI alignment = getViewport().getAlignment();
 345
 346     for (int i = 0; i < alignment.getHeight(); i++)
 347     {
 348       SequenceI seq = alignment.getSequenceAt(i);
 349       for (String group : seq.getFeatures().getFeatureGroups(true))
 350       {
 351         if (group != null)return true;
 352       }
 353     }
 354     return  false;
 355   }
 356
 357   /**
 358    * initalise the alignframe from the underlying viewport data and the
 359    * configurations
 360    */
 361   void init()
 362   {
 363     if (!Jalview.isHeadlessMode())
 364     {
 365       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 366     }
 367
 368     avc = new jalview.controller.AlignViewController(this, viewport,
 369             alignPanel);
 370     if (viewport.getAlignmentConservationAnnotation() == null)
 371     {
 372       // BLOSUM62Colour.setEnabled(false);
 373       conservationMenuItem.setEnabled(false);
 374       modifyConservation.setEnabled(false);
 375       // PIDColour.setEnabled(false);
 376       // abovePIDThreshold.setEnabled(false);
 377       // modifyPID.setEnabled(false);
 378     }
 379
 380     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 381             "No sort");
 382
 383     if (sortby.equals("Id"))
 384     {
 385       sortIDMenuItem_actionPerformed(null);
 386     }
 387     else if (sortby.equals("Pairwise Identity"))
 388     {
 389       sortPairwiseMenuItem_actionPerformed(null);
 390     }
 391
 392     this.alignPanel.av
 393             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 394
 395     setMenusFromViewport(viewport);
 396     buildSortByAnnotationScoresMenu();
 397     calculateTree.addActionListener(new ActionListener()
 398     {
 399
 400       @Override
 401       public void actionPerformed(ActionEvent e)
 402       {
 403         openTreePcaDialog();
 404       }
 405     });
 406     buildColourMenu();
 407
 408     if (Desktop.desktop != null)
 409     {
 410       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 411       /**
 412        * BH 2018 ignore service listeners
 413        *
 414        * @j2sNative
 415        *
 416        */
 417       {
 418       addServiceListeners();
 419       }
 420       setGUINucleotide();
 421     }
 422
 423     if (viewport.getWrapAlignment())
 424     {
 425       wrapMenuItem_actionPerformed(null);
 426     }
 427
 428     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 429     {
 430       this.overviewMenuItem_actionPerformed(null);
 431     }
 432
 433     addKeyListener();
 434
 435     final List<AlignmentPanel> selviews = new ArrayList<>();
 436     final List<AlignmentPanel> origview = new ArrayList<>();
 437     final String menuLabel = MessageManager
 438             .getString("label.copy_format_from");
 439     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 440             new ViewSetProvider()
 441             {
 442
 443               @Override
 444               public AlignmentPanel[] getAllAlignmentPanels()
 445               {
 446                 origview.clear();
 447                 origview.add(alignPanel);
 448                 // make an array of all alignment panels except for this one
 449                 List<AlignmentPanel> aps = new ArrayList<>(
 450                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 451                 aps.remove(AlignFrame.this.alignPanel);
 452                 return aps.toArray(new AlignmentPanel[aps.size()]);
 453               }
 454             }, selviews, new ItemListener()
 455             {
 456
 457               @Override
 458               public void itemStateChanged(ItemEvent e)
 459               {
 460                 if (origview.size() > 0)
 461                 {
 462                   final AlignmentPanel ap = origview.get(0);
 463
 464                   /*
 465                    * Copy the ViewStyle of the selected panel to 'this one'.
 466                    * Don't change value of 'scaleProteinAsCdna' unless copying
 467                    * from a SplitFrame.
 468                    */
 469                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 470                           .getViewStyle();
 471                   boolean fromSplitFrame = selviews.get(0)
 472                           .getAlignViewport().getCodingComplement() != null;
 473                   if (!fromSplitFrame)
 474                   {
 475                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 476                             .getViewStyle().isScaleProteinAsCdna());
 477                   }
 478                   ap.getAlignViewport().setViewStyle(vs);
 479
 480                   /*
 481                    * Also rescale ViewStyle of SplitFrame complement if there is
 482                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 483                    * the whole ViewStyle (allow cDNA protein to have different
 484                    * fonts)
 485                    */
 486                   AlignViewportI complement = ap.getAlignViewport()
 487                           .getCodingComplement();
 488                   if (complement != null && vs.isScaleProteinAsCdna())
 489                   {
 490                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 491                     ((SplitFrame) af.getSplitViewContainer())
 492                             .adjustLayout();
 493                     af.setMenusForViewport();
 494                   }
 495
 496                   ap.updateLayout();
 497                   ap.setSelected(true);
 498                   ap.alignFrame.setMenusForViewport();
 499
 500                 }
 501               }
 502             });
 503     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 504             .indexOf("devel") > -1
 505             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 506                     .indexOf("test") > -1)
 507     {
 508       formatMenu.add(vsel);
 509     }
 510     addFocusListener(new FocusAdapter()
 511     {
 512       @Override
 513       public void focusGained(FocusEvent e)
 514       {
 515         Jalview.setCurrentAlignFrame(AlignFrame.this);
 516       }
 517     });
 518
 519   }
 520
 521   /**
 522    * Change the filename and format for the alignment, and enable the 'reload'
 523    * button functionality.
 524    *
 525    * @param file
 526    *          valid filename
 527    * @param format
 528    *          format of file
 529    */
 530   public void setFileName(String file, FileFormatI format)
 531   {
 532     fileName = file;
 533     setFileFormat(format);
 534     reload.setEnabled(true);
 535   }
 536
 537   /**
 538    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 539    * events
 540    */
 541   void addKeyListener()
 542   {
 543     addKeyListener(new KeyAdapter()
 544     {
 545       @Override
 546       public void keyPressed(KeyEvent evt)
 547       {
 548         if (viewport.cursorMode
 549                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 550                         && evt.getKeyCode() <= KeyEvent.VK_9)
 551                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 552                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 553                 && Character.isDigit(evt.getKeyChar()))
 554         {
 555           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 556         }
 557
 558         switch (evt.getKeyCode())
 559         {
 560
 561         case 27: // escape key
 562           deselectAllSequenceMenuItem_actionPerformed(null);
 563
 564           break;
 565
 566         case KeyEvent.VK_DOWN:
 567           if (evt.isAltDown() || !viewport.cursorMode)
 568           {
 569             moveSelectedSequences(false);
 570           }
 571           if (viewport.cursorMode)
 572           {
 573             alignPanel.getSeqPanel().moveCursor(0, 1);
 574           }
 575           break;
 576
 577         case KeyEvent.VK_UP:
 578           if (evt.isAltDown() || !viewport.cursorMode)
 579           {
 580             moveSelectedSequences(true);
 581           }
 582           if (viewport.cursorMode)
 583           {
 584             alignPanel.getSeqPanel().moveCursor(0, -1);
 585           }
 586
 587           break;
 588
 589         case KeyEvent.VK_LEFT:
 590           if (evt.isAltDown() || !viewport.cursorMode)
 591           {
 592             slideSequences(false,
 593                     alignPanel.getSeqPanel().getKeyboardNo1());
 594           }
 595           else
 596           {
 597             alignPanel.getSeqPanel().moveCursor(-1, 0);
 598           }
 599
 600           break;
 601
 602         case KeyEvent.VK_RIGHT:
 603           if (evt.isAltDown() || !viewport.cursorMode)
 604           {
 605             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 606           }
 607           else
 608           {
 609             alignPanel.getSeqPanel().moveCursor(1, 0);
 610           }
 611           break;
 612
 613         case KeyEvent.VK_SPACE:
 614           if (viewport.cursorMode)
 615           {
 616             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 617                     || evt.isShiftDown() || evt.isAltDown());
 618           }
 619           break;
 620
 621         // case KeyEvent.VK_A:
 622         // if (viewport.cursorMode)
 623         // {
 624         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 625         // //System.out.println("A");
 626         // }
 627         // break;
 628         /*
 629          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 630          * System.out.println("closing bracket"); } break;
 631          */
 632         case KeyEvent.VK_DELETE:
 633         case KeyEvent.VK_BACK_SPACE:
 634           if (!viewport.cursorMode)
 635           {
 636             cut_actionPerformed(null);
 637           }
 638           else
 639           {
 640             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 641                     || evt.isShiftDown() || evt.isAltDown());
 642           }
 643
 644           break;
 645
 646         case KeyEvent.VK_S:
 647           if (viewport.cursorMode)
 648           {
 649             alignPanel.getSeqPanel().setCursorRow();
 650           }
 651           break;
 652         case KeyEvent.VK_C:
 653           if (viewport.cursorMode && !evt.isControlDown())
 654           {
 655             alignPanel.getSeqPanel().setCursorColumn();
 656           }
 657           break;
 658         case KeyEvent.VK_P:
 659           if (viewport.cursorMode)
 660           {
 661             alignPanel.getSeqPanel().setCursorPosition();
 662           }
 663           break;
 664
 665         case KeyEvent.VK_ENTER:
 666         case KeyEvent.VK_COMMA:
 667           if (viewport.cursorMode)
 668           {
 669             alignPanel.getSeqPanel().setCursorRowAndColumn();
 670           }
 671           break;
 672
 673         case KeyEvent.VK_Q:
 674           if (viewport.cursorMode)
 675           {
 676             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 677           }
 678           break;
 679         case KeyEvent.VK_M:
 680           if (viewport.cursorMode)
 681           {
 682             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 683           }
 684           break;
 685
 686         case KeyEvent.VK_F2:
 687           viewport.cursorMode = !viewport.cursorMode;
 688           statusBar.setText(MessageManager
 689                   .formatMessage("label.keyboard_editing_mode", new String[]
 690                   { (viewport.cursorMode ? "on" : "off") }));
 691           if (viewport.cursorMode)
 692           {
 693             ViewportRanges ranges = viewport.getRanges();
 694             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 695                     .getStartRes();
 696             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 697                     .getStartSeq();
 698           }
 699           alignPanel.getSeqPanel().seqCanvas.repaint();
 700           break;
 701
 702         case KeyEvent.VK_F1:
 703           try
 704           {
 705             Help.showHelpWindow();
 706           } catch (Exception ex)
 707           {
 708             ex.printStackTrace();
 709           }
 710           break;
 711         case KeyEvent.VK_H:
 712         {
 713           boolean toggleSeqs = !evt.isControlDown();
 714           boolean toggleCols = !evt.isShiftDown();
 715           toggleHiddenRegions(toggleSeqs, toggleCols);
 716           break;
 717         }
 718         case KeyEvent.VK_B:
 719         {
 720           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 721           boolean modifyExisting = true; // always modify, don't clear
 722                                          // evt.isShiftDown();
 723           boolean invertHighlighted = evt.isAltDown();
 724           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 725                   toggleSel);
 726           break;
 727         }
 728         case KeyEvent.VK_PAGE_UP:
 729           viewport.getRanges().pageUp();
 730           break;
 731         case KeyEvent.VK_PAGE_DOWN:
 732           viewport.getRanges().pageDown();
 733           break;
 734         }
 735       }
 736
 737       @Override
 738       public void keyReleased(KeyEvent evt)
 739       {
 740         switch (evt.getKeyCode())
 741         {
 742         case KeyEvent.VK_LEFT:
 743           if (evt.isAltDown() || !viewport.cursorMode)
 744           {
 745             viewport.firePropertyChange("alignment", null,
 746                     viewport.getAlignment().getSequences());
 747           }
 748           break;
 749
 750         case KeyEvent.VK_RIGHT:
 751           if (evt.isAltDown() || !viewport.cursorMode)
 752           {
 753             viewport.firePropertyChange("alignment", null,
 754                     viewport.getAlignment().getSequences());
 755           }
 756           break;
 757         }
 758       }
 759     });
 760   }
 761
 762   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 763   {
 764     ap.alignFrame = this;
 765     avc = new jalview.controller.AlignViewController(this, viewport,
 766             alignPanel);
 767
 768     alignPanels.add(ap);
 769
 770     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 771
 772     int aSize = alignPanels.size();
 773
 774     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 775
 776     if (aSize == 1 && ap.av.viewName == null)
 777     {
 778       this.getContentPane().add(ap, BorderLayout.CENTER);
 779     }
 780     else
 781     {
 782       if (aSize == 2)
 783       {
 784         setInitialTabVisible();
 785       }
 786
 787       expandViews.setEnabled(true);
 788       gatherViews.setEnabled(true);
 789       tabbedPane.addTab(ap.av.viewName, ap);
 790
 791       ap.setVisible(false);
 792     }
 793
 794     if (newPanel)
 795     {
 796       if (ap.av.isPadGaps())
 797       {
 798         ap.av.getAlignment().padGaps();
 799       }
 800       ap.av.updateConservation(ap);
 801       ap.av.updateConsensus(ap);
 802       ap.av.updateStrucConsensus(ap);
 803     }
 804   }
 805
 806   public void setInitialTabVisible()
 807   {
 808     expandViews.setEnabled(true);
 809     gatherViews.setEnabled(true);
 810     tabbedPane.setVisible(true);
 811     AlignmentPanel first = alignPanels.get(0);
 812     tabbedPane.addTab(first.av.viewName, first);
 813     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 814   }
 815
 816   public AlignViewport getViewport()
 817   {
 818     return viewport;
 819   }
 820
 821   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 822   private void addServiceListeners()
 823   {
 824     final java.beans.PropertyChangeListener thisListener;
 825     Desktop.instance.addJalviewPropertyChangeListener("services",
 826             thisListener = new java.beans.PropertyChangeListener()
 827             {
 828               @Override
 829               public void propertyChange(PropertyChangeEvent evt)
 830               {
 831                 // // System.out.println("Discoverer property change.");
 832                 // if (evt.getPropertyName().equals("services"))
 833                 {
 834                   SwingUtilities.invokeLater(new Runnable()
 835                   {
 836
 837                     @Override
 838                     public void run()
 839                     {
 840                       System.err.println(
 841                               "Rebuild WS Menu for service change");
 842                       BuildWebServiceMenu();
 843                     }
 844
 845                   });
 846                 }
 847               }
 848             });
 849     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 850     {
 851       @Override
 852       public void internalFrameClosed(
 853               javax.swing.event.InternalFrameEvent evt)
 854       {
 855         // System.out.println("deregistering discoverer listener");
 856         Desktop.instance.removeJalviewPropertyChangeListener("services",
 857                 thisListener);
 858         closeMenuItem_actionPerformed(true);
 859       };
 860     });
 861     // Finally, build the menu once to get current service state
 862     new Thread(new Runnable()
 863     {
 864       @Override
 865       public void run()
 866       {
 867         BuildWebServiceMenu();
 868       }
 869     }).start();
 870   }
 871
 872   /**
 873    * Configure menu items that vary according to whether the alignment is
 874    * nucleotide or protein
 875    */
 876   public void setGUINucleotide()
 877   {
 878     AlignmentI al = getViewport().getAlignment();
 879     boolean nucleotide = al.isNucleotide();
 880
 881     loadVcf.setVisible(nucleotide);
 882     showTranslation.setVisible(nucleotide);
 883     showReverse.setVisible(nucleotide);
 884     showReverseComplement.setVisible(nucleotide);
 885     conservationMenuItem.setEnabled(!nucleotide);
 886     modifyConservation
 887             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 888     showGroupConservation.setEnabled(!nucleotide);
 889
 890     showComplementMenuItem
 891             .setText(nucleotide ? MessageManager.getString("label.protein")
 892                     : MessageManager.getString("label.nucleotide"));
 893   }
 894
 895   /**
 896    * set up menus for the current viewport. This may be called after any
 897    * operation that affects the data in the current view (selection changed,
 898    * etc) to update the menus to reflect the new state.
 899    */
 900   @Override
 901   public void setMenusForViewport()
 902   {
 903     setMenusFromViewport(viewport);
 904   }
 905
 906   /**
 907    * Need to call this method when tabs are selected for multiple views, or when
 908    * loading from Jalview2XML.java
 909    *
 910    * @param av
 911    *          AlignViewport
 912    */
 913   void setMenusFromViewport(AlignViewport av)
 914   {
 915     padGapsMenuitem.setSelected(av.isPadGaps());
 916     colourTextMenuItem.setSelected(av.isShowColourText());
 917     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 918     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 919     conservationMenuItem.setSelected(av.getConservationSelected());
 920     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 921     seqLimits.setSelected(av.getShowJVSuffix());
 922     idRightAlign.setSelected(av.isRightAlignIds());
 923     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 924     renderGapsMenuItem.setSelected(av.isRenderGaps());
 925     wrapMenuItem.setSelected(av.getWrapAlignment());
 926     scaleAbove.setVisible(av.getWrapAlignment());
 927     scaleLeft.setVisible(av.getWrapAlignment());
 928     scaleRight.setVisible(av.getWrapAlignment());
 929     annotationPanelMenuItem.setState(av.isShowAnnotation());
 930     /*
 931      * Show/hide annotations only enabled if annotation panel is shown
 932      */
 933     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 934     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 935     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 936     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 937     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 938     viewTextMenuItem.setSelected(av.getShowText());
 939     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 940     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 941     showGroupConservation.setSelected(av.isShowGroupConservation());
 942     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 943     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 944     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 945
 946     ColourMenuHelper.setColourSelected(colourMenu,
 947             av.getGlobalColourScheme());
 948
 949     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 950     hiddenMarkers.setState(av.getShowHiddenMarkers());
 951     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 952     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 953     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 954     autoCalculate.setSelected(av.autoCalculateConsensus);
 955     sortByTree.setSelected(av.sortByTree);
 956     listenToViewSelections.setSelected(av.followSelection);
 957
 958     showProducts.setEnabled(canShowProducts());
 959     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 960
 961     updateEditMenuBar();
 962   }
 963
 964   /**
 965    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 966    *
 967    * @param b
 968    */
 969   public void setGroovyEnabled(boolean b)
 970   {
 971     runGroovy.setEnabled(b);
 972   }
 973
 974   private IProgressIndicator progressBar;
 975
 976   /*
 977    * (non-Javadoc)
 978    *
 979    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 980    */
 981   @Override
 982   public void setProgressBar(String message, long id)
 983   {
 984     progressBar.setProgressBar(message, id);
 985   }
 986
 987   @Override
 988   public void registerHandler(final long id,
 989           final IProgressIndicatorHandler handler)
 990   {
 991     progressBar.registerHandler(id, handler);
 992   }
 993
 994   /**
 995    *
 996    * @return true if any progress bars are still active
 997    */
 998   @Override
 999   public boolean operationInProgress()
1000   {
1001     return progressBar.operationInProgress();
1002   }
1003
1004   @Override
1005   public void setStatus(String text)
1006   {
1007     statusBar.setText(text);
1008   }
1009
1010   /*
1011    * Added so Castor Mapping file can obtain Jalview Version
1012    */
1013   public String getVersion()
1014   {
1015     return jalview.bin.Cache.getProperty("VERSION");
1016   }
1017
1018   public FeatureRenderer getFeatureRenderer()
1019   {
1020     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1021   }
1022
1023   @Override
1024   public void fetchSequence_actionPerformed(ActionEvent e)
1025   {
1026     new jalview.gui.SequenceFetcher(this);
1027   }
1028
1029   @Override
1030   public void addFromFile_actionPerformed(ActionEvent e)
1031   {
1032     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1033   }
1034
1035   @Override
1036   public void reload_actionPerformed(ActionEvent e)
1037   {
1038     if (fileName != null)
1039     {
1040       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1041       // originating file's format
1042       // TODO: work out how to recover feature settings for correct view(s) when
1043       // file is reloaded.
1044       if (FileFormat.Jalview.equals(currentFileFormat))
1045       {
1046         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1047         for (int i = 0; i < frames.length; i++)
1048         {
1049           if (frames[i] instanceof AlignFrame && frames[i] != this
1050                   && ((AlignFrame) frames[i]).fileName != null
1051                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1052           {
1053             try
1054             {
1055               frames[i].setSelected(true);
1056               Desktop.instance.closeAssociatedWindows();
1057             } catch (java.beans.PropertyVetoException ex)
1058             {
1059             }
1060           }
1061
1062         }
1063         Desktop.instance.closeAssociatedWindows();
1064
1065         FileLoader loader = new FileLoader();
1066         DataSourceType protocol = fileName.startsWith("http:")
1067                 ? DataSourceType.URL
1068                 : DataSourceType.FILE;
1069         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1070       }
1071       else
1072       {
1073         Rectangle bounds = this.getBounds();
1074
1075         FileLoader loader = new FileLoader();
1076         DataSourceType protocol = fileName.startsWith("http:")
1077                 ? DataSourceType.URL
1078                 : DataSourceType.FILE;
1079         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1080                 protocol, currentFileFormat);
1081
1082         newframe.setBounds(bounds);
1083         if (featureSettings != null && featureSettings.isShowing())
1084         {
1085           final Rectangle fspos = featureSettings.frame.getBounds();
1086           // TODO: need a 'show feature settings' function that takes bounds -
1087           // need to refactor Desktop.addFrame
1088           newframe.featureSettings_actionPerformed(null);
1089           final FeatureSettings nfs = newframe.featureSettings;
1090           SwingUtilities.invokeLater(new Runnable()
1091           {
1092             @Override
1093             public void run()
1094             {
1095               nfs.frame.setBounds(fspos);
1096             }
1097           });
1098           this.featureSettings.close();
1099           this.featureSettings = null;
1100         }
1101         this.closeMenuItem_actionPerformed(true);
1102       }
1103     }
1104   }
1105
1106   @Override
1107   public void addFromText_actionPerformed(ActionEvent e)
1108   {
1109     Desktop.instance
1110             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1111   }
1112
1113   @Override
1114   public void addFromURL_actionPerformed(ActionEvent e)
1115   {
1116     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1117   }
1118
1119   @Override
1120   public void save_actionPerformed(ActionEvent e)
1121   {
1122     if (fileName == null || (currentFileFormat == null)
1123             || fileName.startsWith("http"))
1124     {
1125       saveAs_actionPerformed(null);
1126     }
1127     else
1128     {
1129       saveAlignment(fileName, currentFileFormat);
1130     }
1131   }
1132
1133   /**
1134    * DOCUMENT ME!
1135    *
1136    * @param e
1137    *          DOCUMENT ME!
1138    */
1139   @Override
1140   public void saveAs_actionPerformed(ActionEvent e)
1141   {
1142     // TODO: JAL-3048 JalviewFileChooser - Save option
1143
1144     String format = currentFileFormat == null ? null
1145             : currentFileFormat.getName();
1146     JalviewFileChooser chooser = JalviewFileChooser
1147             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1148
1149     chooser.setFileView(new JalviewFileView());
1150     chooser.setDialogTitle(
1151             MessageManager.getString("label.save_alignment_to_file"));
1152     chooser.setToolTipText(MessageManager.getString("action.save"));
1153
1154     int value = chooser.showSaveDialog(this);
1155
1156
1157     if (value == JalviewFileChooser.APPROVE_OPTION)
1158     {
1159       currentFileFormat = chooser.getSelectedFormat();
1160       while (currentFileFormat == null)
1161       {
1162         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1163                 MessageManager.getString(
1164                         "label.select_file_format_before_saving"),
1165                 MessageManager.getString("label.file_format_not_specified"),
1166                 JvOptionPane.WARNING_MESSAGE);
1167         currentFileFormat = chooser.getSelectedFormat();
1168         value = chooser.showSaveDialog(this);
1169         if (value != JalviewFileChooser.APPROVE_OPTION)
1170         {
1171           return;
1172         }
1173       }
1174
1175       fileName = chooser.getSelectedFile().getPath();
1176
1177       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1178
1179       Cache.setProperty("LAST_DIRECTORY", fileName);
1180       saveAlignment(fileName, currentFileFormat);
1181     }
1182   }
1183
1184   public boolean saveAlignment(String file, FileFormatI format)
1185   {
1186     boolean success = true;
1187
1188     if (FileFormat.Jalview.equals(format))
1189     {
1190       String shortName = title;
1191
1192       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1193       {
1194         shortName = shortName.substring(
1195                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1196       }
1197
1198       success = new Jalview2XML().saveAlignment(this, file, shortName);
1199
1200       statusBar.setText(MessageManager.formatMessage(
1201               "label.successfully_saved_to_file_in_format", new Object[]
1202               { fileName, format }));
1203
1204     }
1205     else
1206     {
1207       AlignmentExportData exportData = getAlignmentForExport(format,
1208               viewport, null);
1209       if (exportData.getSettings().isCancelled())
1210       {
1211         return false;
1212       }
1213       FormatAdapter f = new FormatAdapter(alignPanel,
1214               exportData.getSettings());
1215       String output = f.formatSequences(format, exportData.getAlignment(), // class
1216                                                                            // cast
1217                                                                            // exceptions
1218                                                                            // will
1219               // occur in the distant future
1220               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1221               f.getCacheSuffixDefault(format),
1222               viewport.getAlignment().getHiddenColumns());
1223
1224       if (output == null)
1225       {
1226         success = false;
1227       }
1228       else
1229       {
1230         try
1231         {
1232           PrintWriter out = new PrintWriter(new FileWriter(file));
1233
1234           out.print(output);
1235           out.close();
1236           this.setTitle(file);
1237           statusBar.setText(MessageManager.formatMessage(
1238                   "label.successfully_saved_to_file_in_format", new Object[]
1239                   { fileName, format.getName() }));
1240         } catch (Exception ex)
1241         {
1242           success = false;
1243           ex.printStackTrace();
1244         }
1245       }
1246     }
1247
1248     if (!success)
1249     {
1250       JvOptionPane.showInternalMessageDialog(this, MessageManager
1251               .formatMessage("label.couldnt_save_file", new Object[]
1252               { fileName }),
1253               MessageManager.getString("label.error_saving_file"),
1254               JvOptionPane.WARNING_MESSAGE);
1255     }
1256
1257     return success;
1258   }
1259
1260   private void warningMessage(String warning, String title)
1261   {
1262     if (new jalview.util.Platform().isHeadless())
1263     {
1264       System.err.println("Warning: " + title + "\nWarning: " + warning);
1265
1266     }
1267     else
1268     {
1269       JvOptionPane.showInternalMessageDialog(this, warning, title,
1270               JvOptionPane.WARNING_MESSAGE);
1271     }
1272     return;
1273   }
1274
1275   /**
1276    * DOCUMENT ME!
1277    *
1278    * @param e
1279    *          DOCUMENT ME!
1280    */
1281   @Override
1282   protected void outputText_actionPerformed(ActionEvent e)
1283   {
1284     FileFormatI fileFormat = FileFormats.getInstance()
1285             .forName(e.getActionCommand());
1286     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1287             viewport, null);
1288     if (exportData.getSettings().isCancelled())
1289     {
1290       return;
1291     }
1292     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1293     cap.setForInput(null);
1294     try
1295     {
1296       FileFormatI format = fileFormat;
1297       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1298               .formatSequences(format, exportData.getAlignment(),
1299                       exportData.getOmitHidden(),
1300                       exportData.getStartEndPostions(),
1301                       viewport.getAlignment().getHiddenColumns()));
1302       Desktop.addInternalFrame(cap, MessageManager
1303               .formatMessage("label.alignment_output_command", new Object[]
1304               { e.getActionCommand() }), 600, 500);
1305     } catch (OutOfMemoryError oom)
1306     {
1307       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1308               oom);
1309       cap.dispose();
1310     }
1311
1312   }
1313
1314   public static AlignmentExportData getAlignmentForExport(
1315           FileFormatI format, AlignViewportI viewport,
1316           AlignExportSettingI exportSettings)
1317   {
1318     AlignmentI alignmentToExport = null;
1319     AlignExportSettingI settings = exportSettings;
1320     String[] omitHidden = null;
1321
1322     HiddenSequences hiddenSeqs = viewport.getAlignment()
1323             .getHiddenSequences();
1324
1325     alignmentToExport = viewport.getAlignment();
1326
1327     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1328     if (settings == null)
1329     {
1330       settings = new AlignExportSettings(hasHiddenSeqs,
1331               viewport.hasHiddenColumns(), format);
1332     }
1333     // settings.isExportAnnotations();
1334
1335     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1336     {
1337       omitHidden = viewport.getViewAsString(false,
1338               settings.isExportHiddenSequences());
1339     }
1340
1341     int[] alignmentStartEnd = new int[2];
1342     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1343     {
1344       alignmentToExport = hiddenSeqs.getFullAlignment();
1345     }
1346     else
1347     {
1348       alignmentToExport = viewport.getAlignment();
1349     }
1350     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1351             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1352     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1353             omitHidden, alignmentStartEnd, settings);
1354     return ed;
1355   }
1356
1357   /**
1358    * DOCUMENT ME!
1359    *
1360    * @param e
1361    *          DOCUMENT ME!
1362    */
1363   @Override
1364   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1365   {
1366     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1367     htmlSVG.exportHTML(null);
1368   }
1369
1370   @Override
1371   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1372   {
1373     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1374     bjs.exportHTML(null);
1375   }
1376
1377   public void createImageMap(File file, String image)
1378   {
1379     alignPanel.makePNGImageMap(file, image);
1380   }
1381
1382   /**
1383    * DOCUMENT ME!
1384    *
1385    * @param e
1386    *          DOCUMENT ME!
1387    */
1388   @Override
1389   public void createPNG(File f)
1390   {
1391     alignPanel.makePNG(f);
1392   }
1393
1394   /**
1395    * DOCUMENT ME!
1396    *
1397    * @param e
1398    *          DOCUMENT ME!
1399    */
1400   @Override
1401   public void createEPS(File f)
1402   {
1403     alignPanel.makeEPS(f);
1404   }
1405
1406   @Override
1407   public void createSVG(File f)
1408   {
1409     alignPanel.makeSVG(f);
1410   }
1411
1412   @Override
1413   public void pageSetup_actionPerformed(ActionEvent e)
1414   {
1415     PrinterJob printJob = PrinterJob.getPrinterJob();
1416     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1417   }
1418
1419   /**
1420    * DOCUMENT ME!
1421    *
1422    * @param e
1423    *          DOCUMENT ME!
1424    */
1425   @Override
1426   public void printMenuItem_actionPerformed(ActionEvent e)
1427   {
1428     // Putting in a thread avoids Swing painting problems
1429     PrintThread thread = new PrintThread(alignPanel);
1430     thread.start();
1431   }
1432
1433   @Override
1434   public void exportFeatures_actionPerformed(ActionEvent e)
1435   {
1436     new AnnotationExporter(alignPanel).exportFeatures();
1437   }
1438
1439   @Override
1440   public void exportAnnotations_actionPerformed(ActionEvent e)
1441   {
1442     new AnnotationExporter(alignPanel).exportAnnotations();
1443   }
1444
1445   @Override
1446   public void associatedData_actionPerformed(ActionEvent e)
1447   {
1448     JalviewFileChooser chooser = new JalviewFileChooser(
1449             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1450     chooser.setFileView(new JalviewFileView());
1451     chooser.setDialogTitle(
1452             MessageManager.getString("label.load_jalview_annotations"));
1453     chooser.setToolTipText(
1454             MessageManager.getString("label.load_jalview_annotations"));
1455
1456     Desktop.getDesktop().dialogData = new Object[] { "SelectedFile",
1457         new Runnable()
1458         {
1459
1460           @Override
1461           public void run()
1462           {
1463             Object[] data = Desktop.getDesktop().dialogData;
1464             int value = ((Integer) data[0]).intValue();
1465
1466             if (value == JFileChooser.APPROVE_OPTION)
1467             {
1468               JalviewFileChooser chooser = (JalviewFileChooser) data[2];
1469               String choice = chooser.getSelectedFile().getPath();
1470               jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1471               loadJalviewDataFile(choice, null, null, null);
1472             }
1473           }
1474
1475         }, chooser };
1476
1477     chooser.showOpenDialog(null);
1478
1479
1480
1481   }
1482
1483   /**
1484    * Close the current view or all views in the alignment frame. If the frame
1485    * only contains one view then the alignment will be removed from memory.
1486    *
1487    * @param closeAllTabs
1488    */
1489   @Override
1490   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1491   {
1492     if (alignPanels != null && alignPanels.size() < 2)
1493     {
1494       closeAllTabs = true;
1495     }
1496
1497     try
1498     {
1499       if (alignPanels != null)
1500       {
1501         if (closeAllTabs)
1502         {
1503           if (this.isClosed())
1504           {
1505             // really close all the windows - otherwise wait till
1506             // setClosed(true) is called
1507             for (int i = 0; i < alignPanels.size(); i++)
1508             {
1509               AlignmentPanel ap = alignPanels.get(i);
1510               ap.closePanel();
1511             }
1512           }
1513         }
1514         else
1515         {
1516           closeView(alignPanel);
1517         }
1518       }
1519
1520       if (closeAllTabs)
1521       {
1522         /*
1523          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1524          * be called recursively, with the frame now in 'closed' state
1525          */
1526         this.setClosed(true);
1527       }
1528     } catch (Exception ex)
1529     {
1530       ex.printStackTrace();
1531     }
1532   }
1533
1534   /**
1535    * Close the specified panel and close up tabs appropriately.
1536    *
1537    * @param panelToClose
1538    */
1539   public void closeView(AlignmentPanel panelToClose)
1540   {
1541     int index = tabbedPane.getSelectedIndex();
1542     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1543     alignPanels.remove(panelToClose);
1544     panelToClose.closePanel();
1545     panelToClose = null;
1546
1547     tabbedPane.removeTabAt(closedindex);
1548     tabbedPane.validate();
1549
1550     if (index > closedindex || index == tabbedPane.getTabCount())
1551     {
1552       // modify currently selected tab index if necessary.
1553       index--;
1554     }
1555
1556     this.tabSelectionChanged(index);
1557   }
1558
1559   /**
1560    * DOCUMENT ME!
1561    */
1562   void updateEditMenuBar()
1563   {
1564
1565     if (viewport.getHistoryList().size() > 0)
1566     {
1567       undoMenuItem.setEnabled(true);
1568       CommandI command = viewport.getHistoryList().peek();
1569       undoMenuItem.setText(MessageManager
1570               .formatMessage("label.undo_command", new Object[]
1571               { command.getDescription() }));
1572     }
1573     else
1574     {
1575       undoMenuItem.setEnabled(false);
1576       undoMenuItem.setText(MessageManager.getString("action.undo"));
1577     }
1578
1579     if (viewport.getRedoList().size() > 0)
1580     {
1581       redoMenuItem.setEnabled(true);
1582
1583       CommandI command = viewport.getRedoList().peek();
1584       redoMenuItem.setText(MessageManager
1585               .formatMessage("label.redo_command", new Object[]
1586               { command.getDescription() }));
1587     }
1588     else
1589     {
1590       redoMenuItem.setEnabled(false);
1591       redoMenuItem.setText(MessageManager.getString("action.redo"));
1592     }
1593   }
1594
1595   @Override
1596   public void addHistoryItem(CommandI command)
1597   {
1598     if (command.getSize() > 0)
1599     {
1600       viewport.addToHistoryList(command);
1601       viewport.clearRedoList();
1602       updateEditMenuBar();
1603       viewport.updateHiddenColumns();
1604       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1605       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1606       // viewport.getColumnSelection()
1607       // .getHiddenColumns().size() > 0);
1608     }
1609   }
1610
1611   /**
1612    *
1613    * @return alignment objects for all views
1614    */
1615   AlignmentI[] getViewAlignments()
1616   {
1617     if (alignPanels != null)
1618     {
1619       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1620       int i = 0;
1621       for (AlignmentPanel ap : alignPanels)
1622       {
1623         als[i++] = ap.av.getAlignment();
1624       }
1625       return als;
1626     }
1627     if (viewport != null)
1628     {
1629       return new AlignmentI[] { viewport.getAlignment() };
1630     }
1631     return null;
1632   }
1633
1634   /**
1635    * DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   @Override
1641   protected void undoMenuItem_actionPerformed(ActionEvent e)
1642   {
1643     if (viewport.getHistoryList().isEmpty())
1644     {
1645       return;
1646     }
1647     CommandI command = viewport.getHistoryList().pop();
1648     viewport.addToRedoList(command);
1649     command.undoCommand(getViewAlignments());
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     updateEditMenuBar();
1653
1654     if (originalSource != null)
1655     {
1656       if (originalSource != viewport)
1657       {
1658         Cache.log.warn(
1659                 "Implementation worry: mismatch of viewport origin for undo");
1660       }
1661       originalSource.updateHiddenColumns();
1662       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1663       // null
1664       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1665       // viewport.getColumnSelection()
1666       // .getHiddenColumns().size() > 0);
1667       originalSource.firePropertyChange("alignment", null,
1668               originalSource.getAlignment().getSequences());
1669     }
1670   }
1671
1672   /**
1673    * DOCUMENT ME!
1674    *
1675    * @param e
1676    *          DOCUMENT ME!
1677    */
1678   @Override
1679   protected void redoMenuItem_actionPerformed(ActionEvent e)
1680   {
1681     if (viewport.getRedoList().size() < 1)
1682     {
1683       return;
1684     }
1685
1686     CommandI command = viewport.getRedoList().pop();
1687     viewport.addToHistoryList(command);
1688     command.doCommand(getViewAlignments());
1689
1690     AlignmentViewport originalSource = getOriginatingSource(command);
1691     updateEditMenuBar();
1692
1693     if (originalSource != null)
1694     {
1695
1696       if (originalSource != viewport)
1697       {
1698         Cache.log.warn(
1699                 "Implementation worry: mismatch of viewport origin for redo");
1700       }
1701       originalSource.updateHiddenColumns();
1702       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1703       // null
1704       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1705       // viewport.getColumnSelection()
1706       // .getHiddenColumns().size() > 0);
1707       originalSource.firePropertyChange("alignment", null,
1708               originalSource.getAlignment().getSequences());
1709     }
1710   }
1711
1712   AlignmentViewport getOriginatingSource(CommandI command)
1713   {
1714     AlignmentViewport originalSource = null;
1715     // For sequence removal and addition, we need to fire
1716     // the property change event FROM the viewport where the
1717     // original alignment was altered
1718     AlignmentI al = null;
1719     if (command instanceof EditCommand)
1720     {
1721       EditCommand editCommand = (EditCommand) command;
1722       al = editCommand.getAlignment();
1723       List<Component> comps = PaintRefresher.components
1724               .get(viewport.getSequenceSetId());
1725
1726       for (Component comp : comps)
1727       {
1728         if (comp instanceof AlignmentPanel)
1729         {
1730           if (al == ((AlignmentPanel) comp).av.getAlignment())
1731           {
1732             originalSource = ((AlignmentPanel) comp).av;
1733             break;
1734           }
1735         }
1736       }
1737     }
1738
1739     if (originalSource == null)
1740     {
1741       // The original view is closed, we must validate
1742       // the current view against the closed view first
1743       if (al != null)
1744       {
1745         PaintRefresher.validateSequences(al, viewport.getAlignment());
1746       }
1747
1748       originalSource = viewport;
1749     }
1750
1751     return originalSource;
1752   }
1753
1754   /**
1755    * DOCUMENT ME!
1756    *
1757    * @param up
1758    *          DOCUMENT ME!
1759    */
1760   public void moveSelectedSequences(boolean up)
1761   {
1762     SequenceGroup sg = viewport.getSelectionGroup();
1763
1764     if (sg == null)
1765     {
1766       return;
1767     }
1768     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1769             viewport.getHiddenRepSequences(), up);
1770     alignPanel.paintAlignment(true, false);
1771   }
1772
1773   synchronized void slideSequences(boolean right, int size)
1774   {
1775     List<SequenceI> sg = new ArrayList<>();
1776     if (viewport.cursorMode)
1777     {
1778       sg.add(viewport.getAlignment()
1779               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1780     }
1781     else if (viewport.getSelectionGroup() != null
1782             && viewport.getSelectionGroup().getSize() != viewport
1783                     .getAlignment().getHeight())
1784     {
1785       sg = viewport.getSelectionGroup()
1786               .getSequences(viewport.getHiddenRepSequences());
1787     }
1788
1789     if (sg.size() < 1)
1790     {
1791       return;
1792     }
1793
1794     List<SequenceI> invertGroup = new ArrayList<>();
1795
1796     for (SequenceI seq : viewport.getAlignment().getSequences())
1797     {
1798       if (!sg.contains(seq))
1799       {
1800         invertGroup.add(seq);
1801       }
1802     }
1803
1804     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1805
1806     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1807     for (int i = 0; i < invertGroup.size(); i++)
1808     {
1809       seqs2[i] = invertGroup.get(i);
1810     }
1811
1812     SlideSequencesCommand ssc;
1813     if (right)
1814     {
1815       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1816               viewport.getGapCharacter());
1817     }
1818     else
1819     {
1820       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1821               viewport.getGapCharacter());
1822     }
1823
1824     int groupAdjustment = 0;
1825     if (ssc.getGapsInsertedBegin() && right)
1826     {
1827       if (viewport.cursorMode)
1828       {
1829         alignPanel.getSeqPanel().moveCursor(size, 0);
1830       }
1831       else
1832       {
1833         groupAdjustment = size;
1834       }
1835     }
1836     else if (!ssc.getGapsInsertedBegin() && !right)
1837     {
1838       if (viewport.cursorMode)
1839       {
1840         alignPanel.getSeqPanel().moveCursor(-size, 0);
1841       }
1842       else
1843       {
1844         groupAdjustment = -size;
1845       }
1846     }
1847
1848     if (groupAdjustment != 0)
1849     {
1850       viewport.getSelectionGroup().setStartRes(
1851               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1852       viewport.getSelectionGroup().setEndRes(
1853               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1854     }
1855
1856     /*
1857      * just extend the last slide command if compatible; but not if in
1858      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1859      */
1860     boolean appendHistoryItem = false;
1861     Deque<CommandI> historyList = viewport.getHistoryList();
1862     boolean inSplitFrame = getSplitViewContainer() != null;
1863     if (!inSplitFrame && historyList != null && historyList.size() > 0
1864             && historyList.peek() instanceof SlideSequencesCommand)
1865     {
1866       appendHistoryItem = ssc.appendSlideCommand(
1867               (SlideSequencesCommand) historyList.peek());
1868     }
1869
1870     if (!appendHistoryItem)
1871     {
1872       addHistoryItem(ssc);
1873     }
1874
1875     repaint();
1876   }
1877
1878   /**
1879    * DOCUMENT ME!
1880    *
1881    * @param e
1882    *          DOCUMENT ME!
1883    */
1884   @Override
1885   protected void copy_actionPerformed(ActionEvent e)
1886   {
1887     if (viewport.getSelectionGroup() == null)
1888     {
1889       return;
1890     }
1891     // TODO: preserve the ordering of displayed alignment annotation in any
1892     // internal paste (particularly sequence associated annotation)
1893     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1894     String[] omitHidden = null;
1895
1896     if (viewport.hasHiddenColumns())
1897     {
1898       omitHidden = viewport.getViewAsString(true);
1899     }
1900
1901     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1902             seqs, omitHidden, null);
1903
1904     StringSelection ss = new StringSelection(output);
1905
1906     try
1907     {
1908       jalview.gui.Desktop.internalCopy = true;
1909       // Its really worth setting the clipboard contents
1910       // to empty before setting the large StringSelection!!
1911       Toolkit.getDefaultToolkit().getSystemClipboard()
1912               .setContents(new StringSelection(""), null);
1913
1914       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1915               Desktop.instance);
1916     } catch (OutOfMemoryError er)
1917     {
1918       new OOMWarning("copying region", er);
1919       return;
1920     }
1921
1922     HiddenColumns hiddenColumns = null;
1923     if (viewport.hasHiddenColumns())
1924     {
1925       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1926       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1927
1928       // create new HiddenColumns object with copy of hidden regions
1929       // between startRes and endRes, offset by startRes
1930       hiddenColumns = new HiddenColumns(
1931               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1932               hiddenCutoff, hiddenOffset);
1933     }
1934
1935     Desktop.jalviewClipboard = new Object[] { seqs,
1936         viewport.getAlignment().getDataset(), hiddenColumns };
1937     statusBar.setText(MessageManager.formatMessage(
1938             "label.copied_sequences_to_clipboard", new Object[]
1939             { Integer.valueOf(seqs.length).toString() }));
1940   }
1941
1942   /**
1943    * DOCUMENT ME!
1944    *
1945    * @param e
1946    *          DOCUMENT ME!
1947    */
1948   @Override
1949   protected void pasteNew_actionPerformed(ActionEvent e)
1950   {
1951     paste(true);
1952   }
1953
1954   /**
1955    * DOCUMENT ME!
1956    *
1957    * @param e
1958    *          DOCUMENT ME!
1959    */
1960   @Override
1961   protected void pasteThis_actionPerformed(ActionEvent e)
1962   {
1963     paste(false);
1964   }
1965
1966   /**
1967    * Paste contents of Jalview clipboard
1968    *
1969    * @param newAlignment
1970    *          true to paste to a new alignment, otherwise add to this.
1971    */
1972   void paste(boolean newAlignment)
1973   {
1974     boolean externalPaste = true;
1975     try
1976     {
1977       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1978       Transferable contents = c.getContents(this);
1979
1980       if (contents == null)
1981       {
1982         return;
1983       }
1984
1985       String str;
1986       FileFormatI format;
1987       try
1988       {
1989         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1990         if (str.length() < 1)
1991         {
1992           return;
1993         }
1994
1995         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1996
1997       } catch (OutOfMemoryError er)
1998       {
1999         new OOMWarning("Out of memory pasting sequences!!", er);
2000         return;
2001       }
2002
2003       SequenceI[] sequences;
2004       boolean annotationAdded = false;
2005       AlignmentI alignment = null;
2006
2007       if (Desktop.jalviewClipboard != null)
2008       {
2009         // The clipboard was filled from within Jalview, we must use the
2010         // sequences
2011         // And dataset from the copied alignment
2012         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2013         // be doubly sure that we create *new* sequence objects.
2014         sequences = new SequenceI[newseq.length];
2015         for (int i = 0; i < newseq.length; i++)
2016         {
2017           sequences[i] = new Sequence(newseq[i]);
2018         }
2019         alignment = new Alignment(sequences);
2020         externalPaste = false;
2021       }
2022       else
2023       {
2024         // parse the clipboard as an alignment.
2025         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2026                 format);
2027         sequences = alignment.getSequencesArray();
2028       }
2029
2030       int alwidth = 0;
2031       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2032       int fgroup = -1;
2033
2034       if (newAlignment)
2035       {
2036
2037         if (Desktop.jalviewClipboard != null)
2038         {
2039           // dataset is inherited
2040           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2041         }
2042         else
2043         {
2044           // new dataset is constructed
2045           alignment.setDataset(null);
2046         }
2047         alwidth = alignment.getWidth() + 1;
2048       }
2049       else
2050       {
2051         AlignmentI pastedal = alignment; // preserve pasted alignment object
2052         // Add pasted sequences and dataset into existing alignment.
2053         alignment = viewport.getAlignment();
2054         alwidth = alignment.getWidth() + 1;
2055         // decide if we need to import sequences from an existing dataset
2056         boolean importDs = Desktop.jalviewClipboard != null
2057                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2058         // importDs==true instructs us to copy over new dataset sequences from
2059         // an existing alignment
2060         Vector newDs = (importDs) ? new Vector() : null; // used to create
2061         // minimum dataset set
2062
2063         for (int i = 0; i < sequences.length; i++)
2064         {
2065           if (importDs)
2066           {
2067             newDs.addElement(null);
2068           }
2069           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2070           // paste
2071           if (importDs && ds != null)
2072           {
2073             if (!newDs.contains(ds))
2074             {
2075               newDs.setElementAt(ds, i);
2076               ds = new Sequence(ds);
2077               // update with new dataset sequence
2078               sequences[i].setDatasetSequence(ds);
2079             }
2080             else
2081             {
2082               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2083             }
2084           }
2085           else
2086           {
2087             // copy and derive new dataset sequence
2088             sequences[i] = sequences[i].deriveSequence();
2089             alignment.getDataset()
2090                     .addSequence(sequences[i].getDatasetSequence());
2091             // TODO: avoid creation of duplicate dataset sequences with a
2092             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2093           }
2094           alignment.addSequence(sequences[i]); // merges dataset
2095         }
2096         if (newDs != null)
2097         {
2098           newDs.clear(); // tidy up
2099         }
2100         if (alignment.getAlignmentAnnotation() != null)
2101         {
2102           for (AlignmentAnnotation alan : alignment
2103                   .getAlignmentAnnotation())
2104           {
2105             if (alan.graphGroup > fgroup)
2106             {
2107               fgroup = alan.graphGroup;
2108             }
2109           }
2110         }
2111         if (pastedal.getAlignmentAnnotation() != null)
2112         {
2113           // Add any annotation attached to alignment.
2114           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2115           for (int i = 0; i < alann.length; i++)
2116           {
2117             annotationAdded = true;
2118             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2119             {
2120               AlignmentAnnotation newann = new AlignmentAnnotation(
2121                       alann[i]);
2122               if (newann.graphGroup > -1)
2123               {
2124                 if (newGraphGroups.size() <= newann.graphGroup
2125                         || newGraphGroups.get(newann.graphGroup) == null)
2126                 {
2127                   for (int q = newGraphGroups
2128                           .size(); q <= newann.graphGroup; q++)
2129                   {
2130                     newGraphGroups.add(q, null);
2131                   }
2132                   newGraphGroups.set(newann.graphGroup,
2133                           new Integer(++fgroup));
2134                 }
2135                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2136                         .intValue();
2137               }
2138
2139               newann.padAnnotation(alwidth);
2140               alignment.addAnnotation(newann);
2141             }
2142           }
2143         }
2144       }
2145       if (!newAlignment)
2146       {
2147         // /////
2148         // ADD HISTORY ITEM
2149         //
2150         addHistoryItem(new EditCommand(
2151                 MessageManager.getString("label.add_sequences"),
2152                 Action.PASTE, sequences, 0, alignment.getWidth(),
2153                 alignment));
2154       }
2155       // Add any annotations attached to sequences
2156       for (int i = 0; i < sequences.length; i++)
2157       {
2158         if (sequences[i].getAnnotation() != null)
2159         {
2160           AlignmentAnnotation newann;
2161           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2162           {
2163             annotationAdded = true;
2164             newann = sequences[i].getAnnotation()[a];
2165             newann.adjustForAlignment();
2166             newann.padAnnotation(alwidth);
2167             if (newann.graphGroup > -1)
2168             {
2169               if (newann.graphGroup > -1)
2170               {
2171                 if (newGraphGroups.size() <= newann.graphGroup
2172                         || newGraphGroups.get(newann.graphGroup) == null)
2173                 {
2174                   for (int q = newGraphGroups
2175                           .size(); q <= newann.graphGroup; q++)
2176                   {
2177                     newGraphGroups.add(q, null);
2178                   }
2179                   newGraphGroups.set(newann.graphGroup,
2180                           new Integer(++fgroup));
2181                 }
2182                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2183                         .intValue();
2184               }
2185             }
2186             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2187             // was
2188             // duplicated
2189             // earlier
2190             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2191                     a);
2192           }
2193         }
2194       }
2195       if (!newAlignment)
2196       {
2197
2198         // propagate alignment changed.
2199         viewport.getRanges().setEndSeq(alignment.getHeight());
2200         if (annotationAdded)
2201         {
2202           // Duplicate sequence annotation in all views.
2203           AlignmentI[] alview = this.getViewAlignments();
2204           for (int i = 0; i < sequences.length; i++)
2205           {
2206             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2207             if (sann == null)
2208             {
2209               continue;
2210             }
2211             for (int avnum = 0; avnum < alview.length; avnum++)
2212             {
2213               if (alview[avnum] != alignment)
2214               {
2215                 // duplicate in a view other than the one with input focus
2216                 int avwidth = alview[avnum].getWidth() + 1;
2217                 // this relies on sann being preserved after we
2218                 // modify the sequence's annotation array for each duplication
2219                 for (int a = 0; a < sann.length; a++)
2220                 {
2221                   AlignmentAnnotation newann = new AlignmentAnnotation(
2222                           sann[a]);
2223                   sequences[i].addAlignmentAnnotation(newann);
2224                   newann.padAnnotation(avwidth);
2225                   alview[avnum].addAnnotation(newann); // annotation was
2226                   // duplicated earlier
2227                   // TODO JAL-1145 graphGroups are not updated for sequence
2228                   // annotation added to several views. This may cause
2229                   // strangeness
2230                   alview[avnum].setAnnotationIndex(newann, a);
2231                 }
2232               }
2233             }
2234           }
2235           buildSortByAnnotationScoresMenu();
2236         }
2237         viewport.firePropertyChange("alignment", null,
2238                 alignment.getSequences());
2239         if (alignPanels != null)
2240         {
2241           for (AlignmentPanel ap : alignPanels)
2242           {
2243             ap.validateAnnotationDimensions(false);
2244           }
2245         }
2246         else
2247         {
2248           alignPanel.validateAnnotationDimensions(false);
2249         }
2250
2251       }
2252       else
2253       {
2254         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2255                 DEFAULT_HEIGHT);
2256         String newtitle = new String("Copied sequences");
2257
2258         if (Desktop.jalviewClipboard != null
2259                 && Desktop.jalviewClipboard[2] != null)
2260         {
2261           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2262           af.viewport.setHiddenColumns(hc);
2263         }
2264
2265         // >>>This is a fix for the moment, until a better solution is
2266         // found!!<<<
2267         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2268                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2269                         .getFeatureRenderer());
2270
2271         // TODO: maintain provenance of an alignment, rather than just make the
2272         // title a concatenation of operations.
2273         if (!externalPaste)
2274         {
2275           if (title.startsWith("Copied sequences"))
2276           {
2277             newtitle = title;
2278           }
2279           else
2280           {
2281             newtitle = newtitle.concat("- from " + title);
2282           }
2283         }
2284         else
2285         {
2286           newtitle = new String("Pasted sequences");
2287         }
2288
2289         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2290                 DEFAULT_HEIGHT);
2291
2292       }
2293
2294     } catch (Exception ex)
2295     {
2296       ex.printStackTrace();
2297       System.out.println("Exception whilst pasting: " + ex);
2298       // could be anything being pasted in here
2299     }
2300
2301   }
2302
2303   @Override
2304   protected void expand_newalign(ActionEvent e)
2305   {
2306     try
2307     {
2308       AlignmentI alignment = AlignmentUtils
2309               .expandContext(getViewport().getAlignment(), -1);
2310       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2311               DEFAULT_HEIGHT);
2312       String newtitle = new String("Flanking alignment");
2313
2314       if (Desktop.jalviewClipboard != null
2315               && Desktop.jalviewClipboard[2] != null)
2316       {
2317         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2318         af.viewport.setHiddenColumns(hc);
2319       }
2320
2321       // >>>This is a fix for the moment, until a better solution is
2322       // found!!<<<
2323       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2324               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2325                       .getFeatureRenderer());
2326
2327       // TODO: maintain provenance of an alignment, rather than just make the
2328       // title a concatenation of operations.
2329       {
2330         if (title.startsWith("Copied sequences"))
2331         {
2332           newtitle = title;
2333         }
2334         else
2335         {
2336           newtitle = newtitle.concat("- from " + title);
2337         }
2338       }
2339
2340       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2341
2342     } catch (Exception ex)
2343     {
2344       ex.printStackTrace();
2345       System.out.println("Exception whilst pasting: " + ex);
2346       // could be anything being pasted in here
2347     } catch (OutOfMemoryError oom)
2348     {
2349       new OOMWarning("Viewing flanking region of alignment", oom);
2350     }
2351   }
2352
2353   /**
2354    * DOCUMENT ME!
2355    *
2356    * @param e
2357    *          DOCUMENT ME!
2358    */
2359   @Override
2360   protected void cut_actionPerformed(ActionEvent e)
2361   {
2362     copy_actionPerformed(null);
2363     delete_actionPerformed(null);
2364   }
2365
2366   /**
2367    * DOCUMENT ME!
2368    *
2369    * @param e
2370    *          DOCUMENT ME!
2371    */
2372   @Override
2373   protected void delete_actionPerformed(ActionEvent evt)
2374   {
2375
2376     SequenceGroup sg = viewport.getSelectionGroup();
2377     if (sg == null)
2378     {
2379       return;
2380     }
2381
2382     /*
2383      * If the cut affects all sequences, warn, remove highlighted columns
2384      */
2385     if (sg.getSize() == viewport.getAlignment().getHeight())
2386     {
2387       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2388               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2389       if (isEntireAlignWidth)
2390       {
2391         int confirm = JvOptionPane.showConfirmDialog(this,
2392                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2393                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2394                 JvOptionPane.OK_CANCEL_OPTION);
2395
2396         if (confirm == JvOptionPane.CANCEL_OPTION
2397                 || confirm == JvOptionPane.CLOSED_OPTION)
2398         {
2399           return;
2400         }
2401       }
2402       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2403               sg.getEndRes() + 1);
2404     }
2405     SequenceI[] cut = sg.getSequences()
2406             .toArray(new SequenceI[sg.getSize()]);
2407
2408     addHistoryItem(new EditCommand(
2409             MessageManager.getString("label.cut_sequences"), Action.CUT,
2410             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2411             viewport.getAlignment()));
2412
2413     viewport.setSelectionGroup(null);
2414     viewport.sendSelection();
2415     viewport.getAlignment().deleteGroup(sg);
2416
2417     viewport.firePropertyChange("alignment", null,
2418             viewport.getAlignment().getSequences());
2419     if (viewport.getAlignment().getHeight() < 1)
2420     {
2421       try
2422       {
2423         this.setClosed(true);
2424       } catch (Exception ex)
2425       {
2426       }
2427     }
2428   }
2429
2430   /**
2431    * DOCUMENT ME!
2432    *
2433    * @param e
2434    *          DOCUMENT ME!
2435    */
2436   @Override
2437   protected void deleteGroups_actionPerformed(ActionEvent e)
2438   {
2439     if (avc.deleteGroups())
2440     {
2441       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2442       alignPanel.updateAnnotation();
2443       alignPanel.paintAlignment(true, true);
2444     }
2445   }
2446
2447   /**
2448    * DOCUMENT ME!
2449    *
2450    * @param e
2451    *          DOCUMENT ME!
2452    */
2453   @Override
2454   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2455   {
2456     SequenceGroup sg = new SequenceGroup();
2457
2458     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2459     {
2460       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2461     }
2462
2463     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2464     viewport.setSelectionGroup(sg);
2465     viewport.sendSelection();
2466     // JAL-2034 - should delegate to
2467     // alignPanel to decide if overview needs
2468     // updating.
2469     alignPanel.paintAlignment(false, false);
2470     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2471   }
2472
2473   /**
2474    * DOCUMENT ME!
2475    *
2476    * @param e
2477    *          DOCUMENT ME!
2478    */
2479   @Override
2480   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2481   {
2482     if (viewport.cursorMode)
2483     {
2484       alignPanel.getSeqPanel().keyboardNo1 = null;
2485       alignPanel.getSeqPanel().keyboardNo2 = null;
2486     }
2487     viewport.setSelectionGroup(null);
2488     viewport.getColumnSelection().clear();
2489     viewport.setSelectionGroup(null);
2490     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2491     // JAL-2034 - should delegate to
2492     // alignPanel to decide if overview needs
2493     // updating.
2494     alignPanel.paintAlignment(false, false);
2495     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496     viewport.sendSelection();
2497   }
2498
2499   /**
2500    * DOCUMENT ME!
2501    *
2502    * @param e
2503    *          DOCUMENT ME!
2504    */
2505   @Override
2506   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2507   {
2508     SequenceGroup sg = viewport.getSelectionGroup();
2509
2510     if (sg == null)
2511     {
2512       selectAllSequenceMenuItem_actionPerformed(null);
2513
2514       return;
2515     }
2516
2517     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2518     {
2519       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2520     }
2521     // JAL-2034 - should delegate to
2522     // alignPanel to decide if overview needs
2523     // updating.
2524
2525     alignPanel.paintAlignment(true, false);
2526     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2527     viewport.sendSelection();
2528   }
2529
2530   @Override
2531   public void invertColSel_actionPerformed(ActionEvent e)
2532   {
2533     viewport.invertColumnSelection();
2534     alignPanel.paintAlignment(true, false);
2535     viewport.sendSelection();
2536   }
2537
2538   /**
2539    * DOCUMENT ME!
2540    *
2541    * @param e
2542    *          DOCUMENT ME!
2543    */
2544   @Override
2545   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2546   {
2547     trimAlignment(true);
2548   }
2549
2550   /**
2551    * DOCUMENT ME!
2552    *
2553    * @param e
2554    *          DOCUMENT ME!
2555    */
2556   @Override
2557   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2558   {
2559     trimAlignment(false);
2560   }
2561
2562   void trimAlignment(boolean trimLeft)
2563   {
2564     ColumnSelection colSel = viewport.getColumnSelection();
2565     int column;
2566
2567     if (!colSel.isEmpty())
2568     {
2569       if (trimLeft)
2570       {
2571         column = colSel.getMin();
2572       }
2573       else
2574       {
2575         column = colSel.getMax();
2576       }
2577
2578       SequenceI[] seqs;
2579       if (viewport.getSelectionGroup() != null)
2580       {
2581         seqs = viewport.getSelectionGroup()
2582                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2583       }
2584       else
2585       {
2586         seqs = viewport.getAlignment().getSequencesArray();
2587       }
2588
2589       TrimRegionCommand trimRegion;
2590       if (trimLeft)
2591       {
2592         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2593                 column, viewport.getAlignment());
2594         viewport.getRanges().setStartRes(0);
2595       }
2596       else
2597       {
2598         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2599                 column, viewport.getAlignment());
2600       }
2601
2602       statusBar.setText(MessageManager
2603               .formatMessage("label.removed_columns", new String[]
2604               { Integer.valueOf(trimRegion.getSize()).toString() }));
2605
2606       addHistoryItem(trimRegion);
2607
2608       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2609       {
2610         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2611                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2612         {
2613           viewport.getAlignment().deleteGroup(sg);
2614         }
2615       }
2616
2617       viewport.firePropertyChange("alignment", null,
2618               viewport.getAlignment().getSequences());
2619     }
2620   }
2621
2622   /**
2623    * DOCUMENT ME!
2624    *
2625    * @param e
2626    *          DOCUMENT ME!
2627    */
2628   @Override
2629   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2630   {
2631     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2632
2633     SequenceI[] seqs;
2634     if (viewport.getSelectionGroup() != null)
2635     {
2636       seqs = viewport.getSelectionGroup()
2637               .getSequencesAsArray(viewport.getHiddenRepSequences());
2638       start = viewport.getSelectionGroup().getStartRes();
2639       end = viewport.getSelectionGroup().getEndRes();
2640     }
2641     else
2642     {
2643       seqs = viewport.getAlignment().getSequencesArray();
2644     }
2645
2646     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2647             "Remove Gapped Columns", seqs, start, end,
2648             viewport.getAlignment());
2649
2650     addHistoryItem(removeGapCols);
2651
2652     statusBar.setText(MessageManager
2653             .formatMessage("label.removed_empty_columns", new Object[]
2654             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2655
2656     // This is to maintain viewport position on first residue
2657     // of first sequence
2658     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2659     ViewportRanges ranges = viewport.getRanges();
2660     int startRes = seq.findPosition(ranges.getStartRes());
2661     // ShiftList shifts;
2662     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2663     // edit.alColumnChanges=shifts.getInverse();
2664     // if (viewport.hasHiddenColumns)
2665     // viewport.getColumnSelection().compensateForEdits(shifts);
2666     ranges.setStartRes(seq.findIndex(startRes) - 1);
2667     viewport.firePropertyChange("alignment", null,
2668             viewport.getAlignment().getSequences());
2669
2670   }
2671
2672   /**
2673    * DOCUMENT ME!
2674    *
2675    * @param e
2676    *          DOCUMENT ME!
2677    */
2678   @Override
2679   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2680   {
2681     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2682
2683     SequenceI[] seqs;
2684     if (viewport.getSelectionGroup() != null)
2685     {
2686       seqs = viewport.getSelectionGroup()
2687               .getSequencesAsArray(viewport.getHiddenRepSequences());
2688       start = viewport.getSelectionGroup().getStartRes();
2689       end = viewport.getSelectionGroup().getEndRes();
2690     }
2691     else
2692     {
2693       seqs = viewport.getAlignment().getSequencesArray();
2694     }
2695
2696     // This is to maintain viewport position on first residue
2697     // of first sequence
2698     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2699     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2700
2701     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2702             viewport.getAlignment()));
2703
2704     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2705
2706     viewport.firePropertyChange("alignment", null,
2707             viewport.getAlignment().getSequences());
2708
2709   }
2710
2711   /**
2712    * DOCUMENT ME!
2713    *
2714    * @param e
2715    *          DOCUMENT ME!
2716    */
2717   @Override
2718   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2719   {
2720     viewport.setPadGaps(padGapsMenuitem.isSelected());
2721     viewport.firePropertyChange("alignment", null,
2722             viewport.getAlignment().getSequences());
2723   }
2724
2725   /**
2726    * DOCUMENT ME!
2727    *
2728    * @param e
2729    *          DOCUMENT ME!
2730    */
2731   @Override
2732   public void findMenuItem_actionPerformed(ActionEvent e)
2733   {
2734     new Finder();
2735   }
2736
2737   /**
2738    * Create a new view of the current alignment.
2739    */
2740   @Override
2741   public void newView_actionPerformed(ActionEvent e)
2742   {
2743     newView(null, true);
2744   }
2745
2746   /**
2747    * Creates and shows a new view of the current alignment.
2748    *
2749    * @param viewTitle
2750    *          title of newly created view; if null, one will be generated
2751    * @param copyAnnotation
2752    *          if true then duplicate all annnotation, groups and settings
2753    * @return new alignment panel, already displayed.
2754    */
2755   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2756   {
2757     /*
2758      * Create a new AlignmentPanel (with its own, new Viewport)
2759      */
2760     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2761     if (!copyAnnotation)
2762     {
2763       /*
2764        * remove all groups and annotation except for the automatic stuff
2765        */
2766       newap.av.getAlignment().deleteAllGroups();
2767       newap.av.getAlignment().deleteAllAnnotations(false);
2768     }
2769
2770     newap.av.setGatherViewsHere(false);
2771
2772     if (viewport.viewName == null)
2773     {
2774       viewport.viewName = MessageManager
2775               .getString("label.view_name_original");
2776     }
2777
2778     /*
2779      * Views share the same edits undo and redo stacks
2780      */
2781     newap.av.setHistoryList(viewport.getHistoryList());
2782     newap.av.setRedoList(viewport.getRedoList());
2783
2784     /*
2785      * Views share the same mappings; need to deregister any new mappings
2786      * created by copyAlignPanel, and register the new reference to the shared
2787      * mappings
2788      */
2789     newap.av.replaceMappings(viewport.getAlignment());
2790
2791     /*
2792      * start up cDNA consensus (if applicable) now mappings are in place
2793      */
2794     if (newap.av.initComplementConsensus())
2795     {
2796       newap.refresh(true); // adjust layout of annotations
2797     }
2798
2799     newap.av.viewName = getNewViewName(viewTitle);
2800
2801     addAlignmentPanel(newap, true);
2802     newap.alignmentChanged();
2803
2804     if (alignPanels.size() == 2)
2805     {
2806       viewport.setGatherViewsHere(true);
2807     }
2808     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2809     return newap;
2810   }
2811
2812   /**
2813    * Make a new name for the view, ensuring it is unique within the current
2814    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2815    * these now use viewId. Unique view names are still desirable for usability.)
2816    *
2817    * @param viewTitle
2818    * @return
2819    */
2820   protected String getNewViewName(String viewTitle)
2821   {
2822     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2823     boolean addFirstIndex = false;
2824     if (viewTitle == null || viewTitle.trim().length() == 0)
2825     {
2826       viewTitle = MessageManager.getString("action.view");
2827       addFirstIndex = true;
2828     }
2829     else
2830     {
2831       index = 1;// we count from 1 if given a specific name
2832     }
2833     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2834
2835     List<Component> comps = PaintRefresher.components
2836             .get(viewport.getSequenceSetId());
2837
2838     List<String> existingNames = getExistingViewNames(comps);
2839
2840     while (existingNames.contains(newViewName))
2841     {
2842       newViewName = viewTitle + " " + (++index);
2843     }
2844     return newViewName;
2845   }
2846
2847   /**
2848    * Returns a list of distinct view names found in the given list of
2849    * components. View names are held on the viewport of an AlignmentPanel.
2850    *
2851    * @param comps
2852    * @return
2853    */
2854   protected List<String> getExistingViewNames(List<Component> comps)
2855   {
2856     List<String> existingNames = new ArrayList<>();
2857     for (Component comp : comps)
2858     {
2859       if (comp instanceof AlignmentPanel)
2860       {
2861         AlignmentPanel ap = (AlignmentPanel) comp;
2862         if (!existingNames.contains(ap.av.viewName))
2863         {
2864           existingNames.add(ap.av.viewName);
2865         }
2866       }
2867     }
2868     return existingNames;
2869   }
2870
2871   /**
2872    * Explode tabbed views into separate windows.
2873    */
2874   @Override
2875   public void expandViews_actionPerformed(ActionEvent e)
2876   {
2877     Desktop.explodeViews(this);
2878   }
2879
2880   /**
2881    * Gather views in separate windows back into a tabbed presentation.
2882    */
2883   @Override
2884   public void gatherViews_actionPerformed(ActionEvent e)
2885   {
2886     Desktop.instance.gatherViews(this);
2887   }
2888
2889   /**
2890    * DOCUMENT ME!
2891    *
2892    * @param e
2893    *          DOCUMENT ME!
2894    */
2895   @Override
2896   public void font_actionPerformed(ActionEvent e)
2897   {
2898     new FontChooser(alignPanel);
2899   }
2900
2901   /**
2902    * DOCUMENT ME!
2903    *
2904    * @param e
2905    *          DOCUMENT ME!
2906    */
2907   @Override
2908   protected void seqLimit_actionPerformed(ActionEvent e)
2909   {
2910     viewport.setShowJVSuffix(seqLimits.isSelected());
2911
2912     alignPanel.getIdPanel().getIdCanvas()
2913             .setPreferredSize(alignPanel.calculateIdWidth());
2914     alignPanel.paintAlignment(true, false);
2915   }
2916
2917   @Override
2918   public void idRightAlign_actionPerformed(ActionEvent e)
2919   {
2920     viewport.setRightAlignIds(idRightAlign.isSelected());
2921     alignPanel.paintAlignment(false, false);
2922   }
2923
2924   @Override
2925   public void centreColumnLabels_actionPerformed(ActionEvent e)
2926   {
2927     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2928     alignPanel.paintAlignment(false, false);
2929   }
2930
2931   /*
2932    * (non-Javadoc)
2933    *
2934    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2935    */
2936   @Override
2937   protected void followHighlight_actionPerformed()
2938   {
2939     /*
2940      * Set the 'follow' flag on the Viewport (and scroll to position if now
2941      * true).
2942      */
2943     final boolean state = this.followHighlightMenuItem.getState();
2944     viewport.setFollowHighlight(state);
2945     if (state)
2946     {
2947       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2948     }
2949   }
2950
2951   /**
2952    * DOCUMENT ME!
2953    *
2954    * @param e
2955    *          DOCUMENT ME!
2956    */
2957   @Override
2958   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2959   {
2960     viewport.setColourText(colourTextMenuItem.isSelected());
2961     alignPanel.paintAlignment(false, false);
2962   }
2963
2964   /**
2965    * DOCUMENT ME!
2966    *
2967    * @param e
2968    *          DOCUMENT ME!
2969    */
2970   @Override
2971   public void wrapMenuItem_actionPerformed(ActionEvent e)
2972   {
2973     scaleAbove.setVisible(wrapMenuItem.isSelected());
2974     scaleLeft.setVisible(wrapMenuItem.isSelected());
2975     scaleRight.setVisible(wrapMenuItem.isSelected());
2976     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2977     alignPanel.updateLayout();
2978   }
2979
2980   @Override
2981   public void showAllSeqs_actionPerformed(ActionEvent e)
2982   {
2983     viewport.showAllHiddenSeqs();
2984   }
2985
2986   @Override
2987   public void showAllColumns_actionPerformed(ActionEvent e)
2988   {
2989     viewport.showAllHiddenColumns();
2990     alignPanel.paintAlignment(true, true);
2991     viewport.sendSelection();
2992   }
2993
2994   @Override
2995   public void hideSelSequences_actionPerformed(ActionEvent e)
2996   {
2997     viewport.hideAllSelectedSeqs();
2998   }
2999
3000   /**
3001    * called by key handler and the hide all/show all menu items
3002    *
3003    * @param toggleSeqs
3004    * @param toggleCols
3005    */
3006   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3007   {
3008
3009     boolean hide = false;
3010     SequenceGroup sg = viewport.getSelectionGroup();
3011     if (!toggleSeqs && !toggleCols)
3012     {
3013       // Hide everything by the current selection - this is a hack - we do the
3014       // invert and then hide
3015       // first check that there will be visible columns after the invert.
3016       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3017               && sg.getStartRes() <= sg.getEndRes()))
3018       {
3019         // now invert the sequence set, if required - empty selection implies
3020         // that no hiding is required.
3021         if (sg != null)
3022         {
3023           invertSequenceMenuItem_actionPerformed(null);
3024           sg = viewport.getSelectionGroup();
3025           toggleSeqs = true;
3026
3027         }
3028         viewport.expandColSelection(sg, true);
3029         // finally invert the column selection and get the new sequence
3030         // selection.
3031         invertColSel_actionPerformed(null);
3032         toggleCols = true;
3033       }
3034     }
3035
3036     if (toggleSeqs)
3037     {
3038       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3039       {
3040         hideSelSequences_actionPerformed(null);
3041         hide = true;
3042       }
3043       else if (!(toggleCols && viewport.hasSelectedColumns()))
3044       {
3045         showAllSeqs_actionPerformed(null);
3046       }
3047     }
3048
3049     if (toggleCols)
3050     {
3051       if (viewport.hasSelectedColumns())
3052       {
3053         hideSelColumns_actionPerformed(null);
3054         if (!toggleSeqs)
3055         {
3056           viewport.setSelectionGroup(sg);
3057         }
3058       }
3059       else if (!hide)
3060       {
3061         showAllColumns_actionPerformed(null);
3062       }
3063     }
3064   }
3065
3066   /*
3067    * (non-Javadoc)
3068    *
3069    * @see
3070    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3071    * event.ActionEvent)
3072    */
3073   @Override
3074   public void hideAllButSelection_actionPerformed(ActionEvent e)
3075   {
3076     toggleHiddenRegions(false, false);
3077     viewport.sendSelection();
3078   }
3079
3080   /*
3081    * (non-Javadoc)
3082    *
3083    * @see
3084    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3085    * .ActionEvent)
3086    */
3087   @Override
3088   public void hideAllSelection_actionPerformed(ActionEvent e)
3089   {
3090     SequenceGroup sg = viewport.getSelectionGroup();
3091     viewport.expandColSelection(sg, false);
3092     viewport.hideAllSelectedSeqs();
3093     viewport.hideSelectedColumns();
3094     alignPanel.paintAlignment(true, true);
3095     viewport.sendSelection();
3096   }
3097
3098   /*
3099    * (non-Javadoc)
3100    *
3101    * @see
3102    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3103    * ActionEvent)
3104    */
3105   @Override
3106   public void showAllhidden_actionPerformed(ActionEvent e)
3107   {
3108     viewport.showAllHiddenColumns();
3109     viewport.showAllHiddenSeqs();
3110     alignPanel.paintAlignment(true, true);
3111     viewport.sendSelection();
3112   }
3113
3114   @Override
3115   public void hideSelColumns_actionPerformed(ActionEvent e)
3116   {
3117     viewport.hideSelectedColumns();
3118     alignPanel.paintAlignment(true, true);
3119     viewport.sendSelection();
3120   }
3121
3122   @Override
3123   public void hiddenMarkers_actionPerformed(ActionEvent e)
3124   {
3125     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3126     repaint();
3127   }
3128
3129   /**
3130    * DOCUMENT ME!
3131    *
3132    * @param e
3133    *          DOCUMENT ME!
3134    */
3135   @Override
3136   protected void scaleAbove_actionPerformed(ActionEvent e)
3137   {
3138     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3139     // TODO: do we actually need to update overview for scale above change ?
3140     alignPanel.paintAlignment(true, false);
3141   }
3142
3143   /**
3144    * DOCUMENT ME!
3145    *
3146    * @param e
3147    *          DOCUMENT ME!
3148    */
3149   @Override
3150   protected void scaleLeft_actionPerformed(ActionEvent e)
3151   {
3152     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3153     alignPanel.paintAlignment(true, false);
3154   }
3155
3156   /**
3157    * DOCUMENT ME!
3158    *
3159    * @param e
3160    *          DOCUMENT ME!
3161    */
3162   @Override
3163   protected void scaleRight_actionPerformed(ActionEvent e)
3164   {
3165     viewport.setScaleRightWrapped(scaleRight.isSelected());
3166     alignPanel.paintAlignment(true, false);
3167   }
3168
3169   /**
3170    * DOCUMENT ME!
3171    *
3172    * @param e
3173    *          DOCUMENT ME!
3174    */
3175   @Override
3176   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3177   {
3178     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3179     alignPanel.paintAlignment(false, false);
3180   }
3181
3182   /**
3183    * DOCUMENT ME!
3184    *
3185    * @param e
3186    *          DOCUMENT ME!
3187    */
3188   @Override
3189   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3190   {
3191     viewport.setShowText(viewTextMenuItem.isSelected());
3192     alignPanel.paintAlignment(false, false);
3193   }
3194
3195   /**
3196    * DOCUMENT ME!
3197    *
3198    * @param e
3199    *          DOCUMENT ME!
3200    */
3201   @Override
3202   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3203   {
3204     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3205     alignPanel.paintAlignment(false, false);
3206   }
3207
3208   public FeatureSettings featureSettings;
3209
3210   @Override
3211   public FeatureSettingsControllerI getFeatureSettingsUI()
3212   {
3213     return featureSettings;
3214   }
3215
3216   @Override
3217   public void featureSettings_actionPerformed(ActionEvent e)
3218   {
3219     if (featureSettings != null)
3220     {
3221       featureSettings.close();
3222       featureSettings = null;
3223     }
3224     if (!showSeqFeatures.isSelected())
3225     {
3226       // make sure features are actually displayed
3227       showSeqFeatures.setSelected(true);
3228       showSeqFeatures_actionPerformed(null);
3229     }
3230     featureSettings = new FeatureSettings(this);
3231   }
3232
3233   /**
3234    * Set or clear 'Show Sequence Features'
3235    *
3236    * @param evt
3237    *          DOCUMENT ME!
3238    */
3239   @Override
3240   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3241   {
3242     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3243     alignPanel.paintAlignment(true, true);
3244   }
3245
3246   /**
3247    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3248    * the annotations panel as a whole.
3249    *
3250    * The options to show/hide all annotations should be enabled when the panel
3251    * is shown, and disabled when the panel is hidden.
3252    *
3253    * @param e
3254    */
3255   @Override
3256   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3257   {
3258     final boolean setVisible = annotationPanelMenuItem.isSelected();
3259     viewport.setShowAnnotation(setVisible);
3260     this.showAllSeqAnnotations.setEnabled(setVisible);
3261     this.hideAllSeqAnnotations.setEnabled(setVisible);
3262     this.showAllAlAnnotations.setEnabled(setVisible);
3263     this.hideAllAlAnnotations.setEnabled(setVisible);
3264     alignPanel.updateLayout();
3265   }
3266
3267   @Override
3268   public void alignmentProperties()
3269   {
3270     JEditorPane editPane = new JEditorPane("text/html", "");
3271     editPane.setEditable(false);
3272     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3273             .formatAsHtml();
3274     editPane.setText(
3275             MessageManager.formatMessage("label.html_content", new Object[]
3276             { contents.toString() }));
3277     JInternalFrame frame = new JInternalFrame();
3278     frame.getContentPane().add(new JScrollPane(editPane));
3279
3280     Desktop.addInternalFrame(frame, MessageManager
3281             .formatMessage("label.alignment_properties", new Object[]
3282             { getTitle() }), 500, 400);
3283   }
3284
3285   /**
3286    * DOCUMENT ME!
3287    *
3288    * @param e
3289    *          DOCUMENT ME!
3290    */
3291   @Override
3292   public void overviewMenuItem_actionPerformed(ActionEvent e)
3293   {
3294     if (alignPanel.overviewPanel != null)
3295     {
3296       return;
3297     }
3298
3299     JInternalFrame frame = new JInternalFrame();
3300     final OverviewPanel overview = new OverviewPanel(alignPanel);
3301     frame.setContentPane(overview);
3302     Desktop.addInternalFrame(frame, MessageManager
3303             .formatMessage("label.overview_params", new Object[]
3304             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3305             true, true);
3306     frame.pack();
3307     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3308     frame.addInternalFrameListener(
3309             new javax.swing.event.InternalFrameAdapter()
3310             {
3311               @Override
3312               public void internalFrameClosed(
3313                       javax.swing.event.InternalFrameEvent evt)
3314               {
3315                 overview.dispose();
3316                 alignPanel.setOverviewPanel(null);
3317               };
3318             });
3319     if (getKeyListeners().length > 0)
3320     {
3321       frame.addKeyListener(getKeyListeners()[0]);
3322     }
3323
3324     alignPanel.setOverviewPanel(overview);
3325   }
3326
3327   @Override
3328   public void textColour_actionPerformed()
3329   {
3330     new TextColourChooser().chooseColour(alignPanel, null);
3331   }
3332
3333   /*
3334    * public void covariationColour_actionPerformed() {
3335    * changeColour(new
3336    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3337    * ()[0])); }
3338    */
3339   @Override
3340   public void annotationColour_actionPerformed()
3341   {
3342     new AnnotationColourChooser(viewport, alignPanel);
3343   }
3344
3345   @Override
3346   public void annotationColumn_actionPerformed(ActionEvent e)
3347   {
3348     new AnnotationColumnChooser(viewport, alignPanel);
3349   }
3350
3351   /**
3352    * Action on the user checking or unchecking the option to apply the selected
3353    * colour scheme to all groups. If unchecked, groups may have their own
3354    * independent colour schemes.
3355    *
3356    * @param selected
3357    */
3358   @Override
3359   public void applyToAllGroups_actionPerformed(boolean selected)
3360   {
3361     viewport.setColourAppliesToAllGroups(selected);
3362   }
3363
3364   /**
3365    * Action on user selecting a colour from the colour menu
3366    *
3367    * @param name
3368    *          the name (not the menu item label!) of the colour scheme
3369    */
3370   @Override
3371   public void changeColour_actionPerformed(String name)
3372   {
3373     /*
3374      * 'User Defined' opens a panel to configure or load a
3375      * user-defined colour scheme
3376      */
3377     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3378     {
3379       new UserDefinedColours(alignPanel);
3380       return;
3381     }
3382
3383     /*
3384      * otherwise set the chosen colour scheme (or null for 'None')
3385      */
3386     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3387             viewport.getAlignment(), viewport.getHiddenRepSequences());
3388     changeColour(cs);
3389   }
3390
3391   /**
3392    * Actions on setting or changing the alignment colour scheme
3393    *
3394    * @param cs
3395    */
3396   @Override
3397   public void changeColour(ColourSchemeI cs)
3398   {
3399     // TODO: pull up to controller method
3400     ColourMenuHelper.setColourSelected(colourMenu, cs);
3401
3402     viewport.setGlobalColourScheme(cs);
3403
3404     alignPanel.paintAlignment(true, true);
3405   }
3406
3407   /**
3408    * Show the PID threshold slider panel
3409    */
3410   @Override
3411   protected void modifyPID_actionPerformed()
3412   {
3413     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3414             alignPanel.getViewName());
3415     SliderPanel.showPIDSlider();
3416   }
3417
3418   /**
3419    * Show the Conservation slider panel
3420    */
3421   @Override
3422   protected void modifyConservation_actionPerformed()
3423   {
3424     SliderPanel.setConservationSlider(alignPanel,
3425             viewport.getResidueShading(), alignPanel.getViewName());
3426     SliderPanel.showConservationSlider();
3427   }
3428
3429   /**
3430    * Action on selecting or deselecting (Colour) By Conservation
3431    */
3432   @Override
3433   public void conservationMenuItem_actionPerformed(boolean selected)
3434   {
3435     modifyConservation.setEnabled(selected);
3436     viewport.setConservationSelected(selected);
3437     viewport.getResidueShading().setConservationApplied(selected);
3438
3439     changeColour(viewport.getGlobalColourScheme());
3440     if (selected)
3441     {
3442       modifyConservation_actionPerformed();
3443     }
3444     else
3445     {
3446       SliderPanel.hideConservationSlider();
3447     }
3448   }
3449
3450   /**
3451    * Action on selecting or deselecting (Colour) Above PID Threshold
3452    */
3453   @Override
3454   public void abovePIDThreshold_actionPerformed(boolean selected)
3455   {
3456     modifyPID.setEnabled(selected);
3457     viewport.setAbovePIDThreshold(selected);
3458     if (!selected)
3459     {
3460       viewport.getResidueShading().setThreshold(0,
3461               viewport.isIgnoreGapsConsensus());
3462     }
3463
3464     changeColour(viewport.getGlobalColourScheme());
3465     if (selected)
3466     {
3467       modifyPID_actionPerformed();
3468     }
3469     else
3470     {
3471       SliderPanel.hidePIDSlider();
3472     }
3473   }
3474
3475   /**
3476    * DOCUMENT ME!
3477    *
3478    * @param e
3479    *          DOCUMENT ME!
3480    */
3481   @Override
3482   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3483   {
3484     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3485     AlignmentSorter.sortByPID(viewport.getAlignment(),
3486             viewport.getAlignment().getSequenceAt(0));
3487     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3488             viewport.getAlignment()));
3489     alignPanel.paintAlignment(true, false);
3490   }
3491
3492   /**
3493    * DOCUMENT ME!
3494    *
3495    * @param e
3496    *          DOCUMENT ME!
3497    */
3498   @Override
3499   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3500   {
3501     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3502     AlignmentSorter.sortByID(viewport.getAlignment());
3503     addHistoryItem(
3504             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3505     alignPanel.paintAlignment(true, false);
3506   }
3507
3508   /**
3509    * DOCUMENT ME!
3510    *
3511    * @param e
3512    *          DOCUMENT ME!
3513    */
3514   @Override
3515   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3516   {
3517     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3518     AlignmentSorter.sortByLength(viewport.getAlignment());
3519     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3520             viewport.getAlignment()));
3521     alignPanel.paintAlignment(true, false);
3522   }
3523
3524   /**
3525    * DOCUMENT ME!
3526    *
3527    * @param e
3528    *          DOCUMENT ME!
3529    */
3530   @Override
3531   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3532   {
3533     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3534     AlignmentSorter.sortByGroup(viewport.getAlignment());
3535     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3536             viewport.getAlignment()));
3537
3538     alignPanel.paintAlignment(true, false);
3539   }
3540
3541   /**
3542    * DOCUMENT ME!
3543    *
3544    * @param e
3545    *          DOCUMENT ME!
3546    */
3547   @Override
3548   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3549   {
3550     new RedundancyPanel(alignPanel, this);
3551   }
3552
3553   /**
3554    * DOCUMENT ME!
3555    *
3556    * @param e
3557    *          DOCUMENT ME!
3558    */
3559   @Override
3560   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3561   {
3562     if ((viewport.getSelectionGroup() == null)
3563             || (viewport.getSelectionGroup().getSize() < 2))
3564     {
3565       JvOptionPane.showInternalMessageDialog(this,
3566               MessageManager.getString(
3567                       "label.you_must_select_least_two_sequences"),
3568               MessageManager.getString("label.invalid_selection"),
3569               JvOptionPane.WARNING_MESSAGE);
3570     }
3571     else
3572     {
3573       JInternalFrame frame = new JInternalFrame();
3574       frame.setContentPane(new PairwiseAlignPanel(viewport));
3575       Desktop.addInternalFrame(frame,
3576               MessageManager.getString("action.pairwise_alignment"), 600,
3577               500);
3578     }
3579   }
3580
3581   @Override
3582   public void autoCalculate_actionPerformed(ActionEvent e)
3583   {
3584     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3585     if (viewport.autoCalculateConsensus)
3586     {
3587       viewport.firePropertyChange("alignment", null,
3588               viewport.getAlignment().getSequences());
3589     }
3590   }
3591
3592   @Override
3593   public void sortByTreeOption_actionPerformed(ActionEvent e)
3594   {
3595     viewport.sortByTree = sortByTree.isSelected();
3596   }
3597
3598   @Override
3599   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3600   {
3601     viewport.followSelection = listenToViewSelections.isSelected();
3602   }
3603
3604   /**
3605    * Constructs a tree panel and adds it to the desktop
3606    *
3607    * @param type
3608    *          tree type (NJ or AV)
3609    * @param modelName
3610    *          name of score model used to compute the tree
3611    * @param options
3612    *          parameters for the distance or similarity calculation
3613    */
3614   void newTreePanel(String type, String modelName,
3615           SimilarityParamsI options)
3616   {
3617     String frameTitle = "";
3618     TreePanel tp;
3619
3620     boolean onSelection = false;
3621     if (viewport.getSelectionGroup() != null
3622             && viewport.getSelectionGroup().getSize() > 0)
3623     {
3624       SequenceGroup sg = viewport.getSelectionGroup();
3625
3626       /* Decide if the selection is a column region */
3627       for (SequenceI _s : sg.getSequences())
3628       {
3629         if (_s.getLength() < sg.getEndRes())
3630         {
3631           JvOptionPane.showMessageDialog(Desktop.desktop,
3632                   MessageManager.getString(
3633                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3634                   MessageManager.getString(
3635                           "label.sequences_selection_not_aligned"),
3636                   JvOptionPane.WARNING_MESSAGE);
3637
3638           return;
3639         }
3640       }
3641       onSelection = true;
3642     }
3643     else
3644     {
3645       if (viewport.getAlignment().getHeight() < 2)
3646       {
3647         return;
3648       }
3649     }
3650
3651     tp = new TreePanel(alignPanel, type, modelName, options);
3652     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3653
3654     frameTitle += " from ";
3655
3656     if (viewport.viewName != null)
3657     {
3658       frameTitle += viewport.viewName + " of ";
3659     }
3660
3661     frameTitle += this.title;
3662
3663     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3664   }
3665
3666   /**
3667    * DOCUMENT ME!
3668    *
3669    * @param title
3670    *          DOCUMENT ME!
3671    * @param order
3672    *          DOCUMENT ME!
3673    */
3674   public void addSortByOrderMenuItem(String title,
3675           final AlignmentOrder order)
3676   {
3677     final JMenuItem item = new JMenuItem(MessageManager
3678             .formatMessage("action.by_title_param", new Object[]
3679             { title }));
3680     sort.add(item);
3681     item.addActionListener(new java.awt.event.ActionListener()
3682     {
3683       @Override
3684       public void actionPerformed(ActionEvent e)
3685       {
3686         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3687
3688         // TODO: JBPNote - have to map order entries to curent SequenceI
3689         // pointers
3690         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3691
3692         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3693                 viewport.getAlignment()));
3694
3695         alignPanel.paintAlignment(true, false);
3696       }
3697     });
3698   }
3699
3700   /**
3701    * Add a new sort by annotation score menu item
3702    *
3703    * @param sort
3704    *          the menu to add the option to
3705    * @param scoreLabel
3706    *          the label used to retrieve scores for each sequence on the
3707    *          alignment
3708    */
3709   public void addSortByAnnotScoreMenuItem(JMenu sort,
3710           final String scoreLabel)
3711   {
3712     final JMenuItem item = new JMenuItem(scoreLabel);
3713     sort.add(item);
3714     item.addActionListener(new java.awt.event.ActionListener()
3715     {
3716       @Override
3717       public void actionPerformed(ActionEvent e)
3718       {
3719         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3720         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3721                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3722         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3723                 viewport.getAlignment()));
3724         alignPanel.paintAlignment(true, false);
3725       }
3726     });
3727   }
3728
3729   /**
3730    * last hash for alignment's annotation array - used to minimise cost of
3731    * rebuild.
3732    */
3733   protected int _annotationScoreVectorHash;
3734
3735   /**
3736    * search the alignment and rebuild the sort by annotation score submenu the
3737    * last alignment annotation vector hash is stored to minimize cost of
3738    * rebuilding in subsequence calls.
3739    *
3740    */
3741   @Override
3742   public void buildSortByAnnotationScoresMenu()
3743   {
3744     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3745     {
3746       return;
3747     }
3748
3749     if (viewport.getAlignment().getAlignmentAnnotation()
3750             .hashCode() != _annotationScoreVectorHash)
3751     {
3752       sortByAnnotScore.removeAll();
3753       // almost certainly a quicker way to do this - but we keep it simple
3754       Hashtable scoreSorts = new Hashtable();
3755       AlignmentAnnotation aann[];
3756       for (SequenceI sqa : viewport.getAlignment().getSequences())
3757       {
3758         aann = sqa.getAnnotation();
3759         for (int i = 0; aann != null && i < aann.length; i++)
3760         {
3761           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3762           {
3763             scoreSorts.put(aann[i].label, aann[i].label);
3764           }
3765         }
3766       }
3767       Enumeration labels = scoreSorts.keys();
3768       while (labels.hasMoreElements())
3769       {
3770         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3771                 (String) labels.nextElement());
3772       }
3773       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3774       scoreSorts.clear();
3775
3776       _annotationScoreVectorHash = viewport.getAlignment()
3777               .getAlignmentAnnotation().hashCode();
3778     }
3779   }
3780
3781   /**
3782    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3783    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3784    * call. Listeners are added to remove the menu item when the treePanel is
3785    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3786    * modified.
3787    */
3788   @Override
3789   public void buildTreeSortMenu()
3790   {
3791     sortByTreeMenu.removeAll();
3792
3793     List<Component> comps = PaintRefresher.components
3794             .get(viewport.getSequenceSetId());
3795     List<TreePanel> treePanels = new ArrayList<>();
3796     for (Component comp : comps)
3797     {
3798       if (comp instanceof TreePanel)
3799       {
3800         treePanels.add((TreePanel) comp);
3801       }
3802     }
3803
3804     if (treePanels.size() < 1)
3805     {
3806       sortByTreeMenu.setVisible(false);
3807       return;
3808     }
3809
3810     sortByTreeMenu.setVisible(true);
3811
3812     for (final TreePanel tp : treePanels)
3813     {
3814       final JMenuItem item = new JMenuItem(tp.getTitle());
3815       item.addActionListener(new java.awt.event.ActionListener()
3816       {
3817         @Override
3818         public void actionPerformed(ActionEvent e)
3819         {
3820           tp.sortByTree_actionPerformed();
3821           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3822
3823         }
3824       });
3825
3826       sortByTreeMenu.add(item);
3827     }
3828   }
3829
3830   public boolean sortBy(AlignmentOrder alorder, String undoname)
3831   {
3832     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3833     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3834     if (undoname != null)
3835     {
3836       addHistoryItem(new OrderCommand(undoname, oldOrder,
3837               viewport.getAlignment()));
3838     }
3839     alignPanel.paintAlignment(true, false);
3840     return true;
3841   }
3842
3843   /**
3844    * Work out whether the whole set of sequences or just the selected set will
3845    * be submitted for multiple alignment.
3846    *
3847    */
3848   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3849   {
3850     // Now, check we have enough sequences
3851     AlignmentView msa = null;
3852
3853     if ((viewport.getSelectionGroup() != null)
3854             && (viewport.getSelectionGroup().getSize() > 1))
3855     {
3856       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3857       // some common interface!
3858       /*
3859        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3860        * SequenceI[sz = seqs.getSize(false)];
3861        *
3862        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3863        * seqs.getSequenceAt(i); }
3864        */
3865       msa = viewport.getAlignmentView(true);
3866     }
3867     else if (viewport.getSelectionGroup() != null
3868             && viewport.getSelectionGroup().getSize() == 1)
3869     {
3870       int option = JvOptionPane.showConfirmDialog(this,
3871               MessageManager.getString("warn.oneseq_msainput_selection"),
3872               MessageManager.getString("label.invalid_selection"),
3873               JvOptionPane.OK_CANCEL_OPTION);
3874       if (option == JvOptionPane.OK_OPTION)
3875       {
3876         msa = viewport.getAlignmentView(false);
3877       }
3878     }
3879     else
3880     {
3881       msa = viewport.getAlignmentView(false);
3882     }
3883     return msa;
3884   }
3885
3886   /**
3887    * Decides what is submitted to a secondary structure prediction service: the
3888    * first sequence in the alignment, or in the current selection, or, if the
3889    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3890    * region or the whole alignment. (where the first sequence in the set is the
3891    * one that the prediction will be for).
3892    */
3893   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3894   {
3895     AlignmentView seqs = null;
3896
3897     if ((viewport.getSelectionGroup() != null)
3898             && (viewport.getSelectionGroup().getSize() > 0))
3899     {
3900       seqs = viewport.getAlignmentView(true);
3901     }
3902     else
3903     {
3904       seqs = viewport.getAlignmentView(false);
3905     }
3906     // limit sequences - JBPNote in future - could spawn multiple prediction
3907     // jobs
3908     // TODO: viewport.getAlignment().isAligned is a global state - the local
3909     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3910     if (!viewport.getAlignment().isAligned(false))
3911     {
3912       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3913       // TODO: if seqs.getSequences().length>1 then should really have warned
3914       // user!
3915
3916     }
3917     return seqs;
3918   }
3919
3920   /**
3921    * DOCUMENT ME!
3922    *
3923    * @param e
3924    *          DOCUMENT ME!
3925    */
3926   @Override
3927   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3928   {
3929     // TODO: JAL-3048 JalviewFileChooser
3930     // Pick the tree file
3931     JalviewFileChooser chooser = new JalviewFileChooser(
3932             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3933     chooser.setFileView(new JalviewFileView());
3934     chooser.setDialogTitle(
3935             MessageManager.getString("label.select_newick_like_tree_file"));
3936     chooser.setToolTipText(
3937             MessageManager.getString("label.load_tree_file"));
3938
3939     int value = chooser.showOpenDialog(null);
3940
3941     if (value == JalviewFileChooser.APPROVE_OPTION)
3942     {
3943       String filePath = chooser.getSelectedFile().getPath();
3944       Cache.setProperty("LAST_DIRECTORY", filePath);
3945       NewickFile fin = null;
3946       try
3947       {
3948         fin = new NewickFile(filePath, DataSourceType.FILE);
3949         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3950       } catch (Exception ex)
3951       {
3952         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3953                 MessageManager.getString("label.problem_reading_tree_file"),
3954                 JvOptionPane.WARNING_MESSAGE);
3955         ex.printStackTrace();
3956       }
3957       if (fin != null && fin.hasWarningMessage())
3958       {
3959         JvOptionPane.showMessageDialog(Desktop.desktop,
3960                 fin.getWarningMessage(),
3961                 MessageManager
3962                         .getString("label.possible_problem_with_tree_file"),
3963                 JvOptionPane.WARNING_MESSAGE);
3964       }
3965     }
3966   }
3967
3968   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3969   {
3970     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3971   }
3972
3973   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3974           int h, int x, int y)
3975   {
3976     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3977   }
3978
3979   /**
3980    * Add a treeviewer for the tree extracted from a Newick file object to the
3981    * current alignment view
3982    *
3983    * @param nf
3984    *          the tree
3985    * @param title
3986    *          tree viewer title
3987    * @param input
3988    *          Associated alignment input data (or null)
3989    * @param w
3990    *          width
3991    * @param h
3992    *          height
3993    * @param x
3994    *          position
3995    * @param y
3996    *          position
3997    * @return TreePanel handle
3998    */
3999   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4000           AlignmentView input, int w, int h, int x, int y)
4001   {
4002     TreePanel tp = null;
4003
4004     try
4005     {
4006       nf.parse();
4007
4008       if (nf.getTree() != null)
4009       {
4010         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4011
4012         tp.setSize(w, h);
4013
4014         if (x > 0 && y > 0)
4015         {
4016           tp.setLocation(x, y);
4017         }
4018
4019         Desktop.addInternalFrame(tp, treeTitle, w, h);
4020       }
4021     } catch (Exception ex)
4022     {
4023       ex.printStackTrace();
4024     }
4025
4026     return tp;
4027   }
4028
4029   private boolean buildingMenu = false;
4030
4031   /**
4032    * Generates menu items and listener event actions for web service clients
4033    *
4034    */
4035   public void BuildWebServiceMenu()
4036   {
4037     while (buildingMenu)
4038     {
4039       try
4040       {
4041         System.err.println("Waiting for building menu to finish.");
4042         Thread.sleep(10);
4043       } catch (Exception e)
4044       {
4045       }
4046     }
4047     final AlignFrame me = this;
4048     buildingMenu = true;
4049     new Thread(new Runnable()
4050     {
4051       @Override
4052       public void run()
4053       {
4054         final List<JMenuItem> legacyItems = new ArrayList<>();
4055         try
4056         {
4057           // System.err.println("Building ws menu again "
4058           // + Thread.currentThread());
4059           // TODO: add support for context dependent disabling of services based
4060           // on
4061           // alignment and current selection
4062           // TODO: add additional serviceHandle parameter to specify abstract
4063           // handler
4064           // class independently of AbstractName
4065           // TODO: add in rediscovery GUI function to restart discoverer
4066           // TODO: group services by location as well as function and/or
4067           // introduce
4068           // object broker mechanism.
4069           final Vector<JMenu> wsmenu = new Vector<>();
4070           final IProgressIndicator af = me;
4071
4072           /*
4073            * do not i18n these strings - they are hard-coded in class
4074            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4075            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4076            */
4077           final JMenu msawsmenu = new JMenu("Alignment");
4078           final JMenu secstrmenu = new JMenu(
4079                   "Secondary Structure Prediction");
4080           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4081           final JMenu analymenu = new JMenu("Analysis");
4082           final JMenu dismenu = new JMenu("Protein Disorder");
4083           // JAL-940 - only show secondary structure prediction services from
4084           // the legacy server
4085           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4086               // &&
4087           Discoverer.services != null && (Discoverer.services.size() > 0))
4088           {
4089             // TODO: refactor to allow list of AbstractName/Handler bindings to
4090             // be
4091             // stored or retrieved from elsewhere
4092             // No MSAWS used any more:
4093             // Vector msaws = null; // (Vector)
4094             // Discoverer.services.get("MsaWS");
4095             Vector secstrpr = (Vector) Discoverer.services
4096                     .get("SecStrPred");
4097             if (secstrpr != null)
4098             {
4099               // Add any secondary structure prediction services
4100               for (int i = 0, j = secstrpr.size(); i < j; i++)
4101               {
4102                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4103                         .get(i);
4104                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4105                         .getServiceClient(sh);
4106                 int p = secstrmenu.getItemCount();
4107                 impl.attachWSMenuEntry(secstrmenu, me);
4108                 int q = secstrmenu.getItemCount();
4109                 for (int litm = p; litm < q; litm++)
4110                 {
4111                   legacyItems.add(secstrmenu.getItem(litm));
4112                 }
4113               }
4114             }
4115           }
4116
4117           // Add all submenus in the order they should appear on the web
4118           // services menu
4119           wsmenu.add(msawsmenu);
4120           wsmenu.add(secstrmenu);
4121           wsmenu.add(dismenu);
4122           wsmenu.add(analymenu);
4123           // No search services yet
4124           // wsmenu.add(seqsrchmenu);
4125
4126           javax.swing.SwingUtilities.invokeLater(new Runnable()
4127           {
4128             @Override
4129             public void run()
4130             {
4131               try
4132               {
4133                 webService.removeAll();
4134                 // first, add discovered services onto the webservices menu
4135                 if (wsmenu.size() > 0)
4136                 {
4137                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4138                   {
4139                     webService.add(wsmenu.get(i));
4140                   }
4141                 }
4142                 else
4143                 {
4144                   webService.add(me.webServiceNoServices);
4145                 }
4146                 // TODO: move into separate menu builder class.
4147                 boolean new_sspred = false;
4148                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4149                 {
4150                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4151                   if (jws2servs != null)
4152                   {
4153                     if (jws2servs.hasServices())
4154                     {
4155                       jws2servs.attachWSMenuEntry(webService, me);
4156                       for (Jws2Instance sv : jws2servs.getServices())
4157                       {
4158                         if (sv.description.toLowerCase().contains("jpred"))
4159                         {
4160                           for (JMenuItem jmi : legacyItems)
4161                           {
4162                             jmi.setVisible(false);
4163                           }
4164                         }
4165                       }
4166
4167                     }
4168                     if (jws2servs.isRunning())
4169                     {
4170                       JMenuItem tm = new JMenuItem(
4171                               "Still discovering JABA Services");
4172                       tm.setEnabled(false);
4173                       webService.add(tm);
4174                     }
4175                   }
4176                 }
4177                 build_urlServiceMenu(me.webService);
4178                 build_fetchdbmenu(webService);
4179                 for (JMenu item : wsmenu)
4180                 {
4181                   if (item.getItemCount() == 0)
4182                   {
4183                     item.setEnabled(false);
4184                   }
4185                   else
4186                   {
4187                     item.setEnabled(true);
4188                   }
4189                 }
4190               } catch (Exception e)
4191               {
4192                 Cache.log.debug(
4193                         "Exception during web service menu building process.",
4194                         e);
4195               }
4196             }
4197           });
4198         } catch (Exception e)
4199         {
4200         }
4201         buildingMenu = false;
4202       }
4203     }).start();
4204
4205   }
4206
4207   /**
4208    * construct any groupURL type service menu entries.
4209    *
4210    * @param webService
4211    */
4212   private void build_urlServiceMenu(JMenu webService)
4213   {
4214     // TODO: remove this code when 2.7 is released
4215     // DEBUG - alignmentView
4216     /*
4217      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4218      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4219      *
4220      * @Override public void actionPerformed(ActionEvent e) {
4221      * jalview.datamodel.AlignmentView
4222      * .testSelectionViews(af.viewport.getAlignment(),
4223      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4224      *
4225      * }); webService.add(testAlView);
4226      */
4227     // TODO: refactor to RestClient discoverer and merge menu entries for
4228     // rest-style services with other types of analysis/calculation service
4229     // SHmmr test client - still being implemented.
4230     // DEBUG - alignmentView
4231
4232     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4233             .getRestClients())
4234     {
4235       client.attachWSMenuEntry(
4236               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4237               this);
4238     }
4239   }
4240
4241   /**
4242    * Searches the alignment sequences for xRefs and builds the Show
4243    * Cross-References menu (formerly called Show Products), with database
4244    * sources for which cross-references are found (protein sources for a
4245    * nucleotide alignment and vice versa)
4246    *
4247    * @return true if Show Cross-references menu should be enabled
4248    */
4249   public boolean canShowProducts()
4250   {
4251     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4252     AlignmentI dataset = viewport.getAlignment().getDataset();
4253
4254     showProducts.removeAll();
4255     final boolean dna = viewport.getAlignment().isNucleotide();
4256
4257     if (seqs == null || seqs.length == 0)
4258     {
4259       // nothing to see here.
4260       return false;
4261     }
4262
4263     boolean showp = false;
4264     try
4265     {
4266       List<String> ptypes = new CrossRef(seqs, dataset)
4267               .findXrefSourcesForSequences(dna);
4268
4269       for (final String source : ptypes)
4270       {
4271         showp = true;
4272         final AlignFrame af = this;
4273         JMenuItem xtype = new JMenuItem(source);
4274         xtype.addActionListener(new ActionListener()
4275         {
4276           @Override
4277           public void actionPerformed(ActionEvent e)
4278           {
4279             showProductsFor(af.viewport.getSequenceSelection(), dna,
4280                     source);
4281           }
4282         });
4283         showProducts.add(xtype);
4284       }
4285       showProducts.setVisible(showp);
4286       showProducts.setEnabled(showp);
4287     } catch (Exception e)
4288     {
4289       Cache.log.warn(
4290               "canShowProducts threw an exception - please report to help@jalview.org",
4291               e);
4292       return false;
4293     }
4294     return showp;
4295   }
4296
4297   /**
4298    * Finds and displays cross-references for the selected sequences (protein
4299    * products for nucleotide sequences, dna coding sequences for peptides).
4300    *
4301    * @param sel
4302    *          the sequences to show cross-references for
4303    * @param dna
4304    *          true if from a nucleotide alignment (so showing proteins)
4305    * @param source
4306    *          the database to show cross-references for
4307    */
4308   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4309           final String source)
4310   {
4311     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4312             .start();
4313   }
4314
4315   /**
4316    * Construct and display a new frame containing the translation of this
4317    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4318    */
4319   @Override
4320   public void showTranslation_actionPerformed(ActionEvent e)
4321   {
4322     AlignmentI al = null;
4323     try
4324     {
4325       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4326
4327       al = dna.translateCdna();
4328     } catch (Exception ex)
4329     {
4330       jalview.bin.Cache.log.error(
4331               "Exception during translation. Please report this !", ex);
4332       final String msg = MessageManager.getString(
4333               "label.error_when_translating_sequences_submit_bug_report");
4334       final String errorTitle = MessageManager
4335               .getString("label.implementation_error")
4336               + MessageManager.getString("label.translation_failed");
4337       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4338               JvOptionPane.ERROR_MESSAGE);
4339       return;
4340     }
4341     if (al == null || al.getHeight() == 0)
4342     {
4343       final String msg = MessageManager.getString(
4344               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4345       final String errorTitle = MessageManager
4346               .getString("label.translation_failed");
4347       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4348               JvOptionPane.WARNING_MESSAGE);
4349     }
4350     else
4351     {
4352       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4353       af.setFileFormat(this.currentFileFormat);
4354       final String newTitle = MessageManager
4355               .formatMessage("label.translation_of_params", new Object[]
4356               { this.getTitle() });
4357       af.setTitle(newTitle);
4358       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4359       {
4360         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4361         viewport.openSplitFrame(af, new Alignment(seqs));
4362       }
4363       else
4364       {
4365         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4366                 DEFAULT_HEIGHT);
4367       }
4368     }
4369   }
4370
4371   /**
4372    * Set the file format
4373    *
4374    * @param format
4375    */
4376   public void setFileFormat(FileFormatI format)
4377   {
4378     this.currentFileFormat = format;
4379   }
4380
4381   /**
4382    * Try to load a features file onto the alignment.
4383    *
4384    * @param file
4385    *          contents or path to retrieve file or a File object
4386    * @param sourceType
4387    *          access mode of file (see jalview.io.AlignFile)
4388    * @return true if features file was parsed correctly.
4389    */
4390   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4391   {
4392     // BH 2018
4393     return avc.parseFeaturesFile(file, sourceType,
4394             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4395
4396   }
4397
4398   @Override
4399   public void refreshFeatureUI(boolean enableIfNecessary)
4400   {
4401     // note - currently this is only still here rather than in the controller
4402     // because of the featureSettings hard reference that is yet to be
4403     // abstracted
4404     if (enableIfNecessary)
4405     {
4406       viewport.setShowSequenceFeatures(true);
4407       showSeqFeatures.setSelected(true);
4408     }
4409
4410   }
4411
4412   @Override
4413   public void dragEnter(DropTargetDragEvent evt)
4414   {
4415   }
4416
4417   @Override
4418   public void dragExit(DropTargetEvent evt)
4419   {
4420   }
4421
4422   @Override
4423   public void dragOver(DropTargetDragEvent evt)
4424   {
4425   }
4426
4427   @Override
4428   public void dropActionChanged(DropTargetDragEvent evt)
4429   {
4430   }
4431
4432   @Override
4433   public void drop(DropTargetDropEvent evt)
4434   {
4435     // JAL-1552 - acceptDrop required before getTransferable call for
4436     // Java's Transferable for native dnd
4437     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4438     Transferable t = evt.getTransferable();
4439
4440
4441     final AlignFrame thisaf = this;
4442     final List<Object> files = new ArrayList<>();
4443     List<DataSourceType> protocols = new ArrayList<>();
4444
4445     try
4446     {
4447       Desktop.transferFromDropTarget(files, protocols, evt, t);
4448     } catch (Exception e)
4449     {
4450       e.printStackTrace();
4451     }
4452     if (files != null)
4453     {
4454       new Thread(new Runnable()
4455       {
4456         @Override
4457         public void run()
4458         {
4459           try
4460           {
4461             // check to see if any of these files have names matching sequences
4462             // in
4463             // the alignment
4464             SequenceIdMatcher idm = new SequenceIdMatcher(
4465                     viewport.getAlignment().getSequencesArray());
4466             /**
4467              * Object[] { String,SequenceI}
4468              */
4469             ArrayList<Object[]> filesmatched = new ArrayList<>();
4470             ArrayList<Object> filesnotmatched = new ArrayList<>();
4471             for (int i = 0; i < files.size(); i++)
4472             {
4473               // BH 2018
4474               Object file = files.get(i);
4475               String fileName = file.toString();
4476               String pdbfn = "";
4477               DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
4478               if (protocol == DataSourceType.FILE)
4479               {
4480                 File fl = (file instanceof File ? (File) file : new File(fileName));
4481                 pdbfn = fl.getName();
4482               }
4483               else if (protocol == DataSourceType.URL)
4484               {
4485                 URL url = new URL(fileName);
4486                 pdbfn = url.getFile();
4487               }
4488               if (pdbfn.length() > 0)
4489               {
4490                 // attempt to find a match in the alignment
4491                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4492                 int l = 0, c = pdbfn.indexOf(".");
4493                 while (mtch == null && c != -1)
4494                 {
4495                   do
4496                   {
4497                     l = c;
4498                   } while ((c = pdbfn.indexOf(".", l)) > l);
4499                   if (l > -1)
4500                   {
4501                     pdbfn = pdbfn.substring(0, l);
4502                   }
4503                   mtch = idm.findAllIdMatches(pdbfn);
4504                 }
4505                 if (mtch != null)
4506                 {
4507                   FileFormatI type;
4508                   try
4509                   {
4510                     type = new IdentifyFile().identify(file, protocol);
4511                   } catch (Exception ex)
4512                   {
4513                     type = null;
4514                   }
4515                   if (type != null && type.isStructureFile())
4516                   {
4517                     filesmatched.add(new Object[] { file, protocol, mtch });
4518                     continue;
4519                   }
4520                 }
4521                 // File wasn't named like one of the sequences or wasn't a PDB
4522                 // file.
4523                 filesnotmatched.add(file);
4524               }
4525             }
4526             int assocfiles = 0;
4527             if (filesmatched.size() > 0)
4528             {
4529               boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4530               if (!autoAssociate)
4531               {
4532                 String msg = MessageManager.formatMessage(
4533                         "label.automatically_associate_structure_files_with_sequences_same_name",
4534                         new Object[]
4535                         { Integer.valueOf(filesmatched.size())
4536                                 .toString() });
4537                 String ttl = MessageManager.getString(
4538                         "label.automatically_associate_structure_files_by_name");
4539                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4540                         ttl, JvOptionPane.YES_NO_OPTION);
4541                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4542               }
4543               if (autoAssociate)
4544               {
4545                 for (Object[] fm : filesmatched)
4546                 {
4547                   // try and associate
4548                   // TODO: may want to set a standard ID naming formalism for
4549                   // associating PDB files which have no IDs.
4550                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4551                   {
4552                     PDBEntry pe = new AssociatePdbFileWithSeq()
4553                             .associatePdbWithSeq((String) fm[0],
4554                                     (DataSourceType) fm[1], toassoc, false,
4555                                     Desktop.instance);
4556                     if (pe != null)
4557                     {
4558                       System.err.println("Associated file : "
4559                               + ((String) fm[0]) + " with "
4560                               + toassoc.getDisplayId(true));
4561                       assocfiles++;
4562                     }
4563                   }
4564                   // TODO: do we need to update overview ? only if features are
4565                   // shown I guess
4566                   alignPanel.paintAlignment(true, false);
4567                 }
4568               }
4569               else
4570               {
4571                 /*
4572                  * add declined structures as sequences
4573                  */
4574                 for (Object[] o : filesmatched)
4575                 {
4576                   filesnotmatched.add(o[0]);
4577                 }
4578               }
4579             }
4580             if (filesnotmatched.size() > 0)
4581             {
4582               if (assocfiles > 0 && (Cache.getDefault(
4583                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4584                       || JvOptionPane.showConfirmDialog(thisaf,
4585                               "<html>" + MessageManager.formatMessage(
4586                                       "label.ignore_unmatched_dropped_files_info",
4587                                       new Object[]
4588                                       { Integer.valueOf(
4589                                               filesnotmatched.size())
4590                                               .toString() })
4591                                       + "</html>",
4592                               MessageManager.getString(
4593                                       "label.ignore_unmatched_dropped_files"),
4594                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4595               {
4596                 return;
4597               }
4598               for (Object fn : filesnotmatched)
4599               {
4600                 loadJalviewDataFile(fn, null, null, null);
4601               }
4602
4603             }
4604           } catch (Exception ex)
4605           {
4606             ex.printStackTrace();
4607           }
4608         }
4609       }).start();
4610     }
4611   }
4612
4613   /**
4614    * Attempt to load a "dropped" file or URL string, by testing in turn for
4615    * <ul>
4616    * <li>an Annotation file</li>
4617    * <li>a JNet file</li>
4618    * <li>a features file</li>
4619    * <li>else try to interpret as an alignment file</li>
4620    * </ul>
4621    *
4622    * @param file
4623    *          either a filename or a URL string.
4624    */
4625   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4626           FileFormatI format, SequenceI assocSeq)
4627   {
4628     // BH 2018 was String file
4629     try
4630     {
4631       if (sourceType == null)
4632       {
4633         sourceType = FormatAdapter.checkProtocol(file);
4634       }
4635       // if the file isn't identified, or not positively identified as some
4636       // other filetype (PFAM is default unidentified alignment file type) then
4637       // try to parse as annotation.
4638       boolean isAnnotation = (format == null
4639               || FileFormat.Pfam.equals(format))
4640                       ? new AnnotationFile().annotateAlignmentView(viewport,
4641                               file, sourceType)
4642                       : false;
4643
4644       if (!isAnnotation)
4645       {
4646         // first see if its a T-COFFEE score file
4647         TCoffeeScoreFile tcf = null;
4648         try
4649         {
4650           tcf = new TCoffeeScoreFile(file, sourceType);
4651           if (tcf.isValid())
4652           {
4653             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4654             {
4655               buildColourMenu();
4656               changeColour(
4657                       new TCoffeeColourScheme(viewport.getAlignment()));
4658               isAnnotation = true;
4659               statusBar.setText(MessageManager.getString(
4660                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4661             }
4662             else
4663             {
4664               // some problem - if no warning its probable that the ID matching
4665               // process didn't work
4666               JvOptionPane.showMessageDialog(Desktop.desktop,
4667                       tcf.getWarningMessage() == null
4668                               ? MessageManager.getString(
4669                                       "label.check_file_matches_sequence_ids_alignment")
4670                               : tcf.getWarningMessage(),
4671                       MessageManager.getString(
4672                               "label.problem_reading_tcoffee_score_file"),
4673                       JvOptionPane.WARNING_MESSAGE);
4674             }
4675           }
4676           else
4677           {
4678             tcf = null;
4679           }
4680         } catch (Exception x)
4681         {
4682           Cache.log.debug(
4683                   "Exception when processing data source as T-COFFEE score file",
4684                   x);
4685           tcf = null;
4686         }
4687         if (tcf == null)
4688         {
4689           // try to see if its a JNet 'concise' style annotation file *before*
4690           // we
4691           // try to parse it as a features file
4692           if (format == null)
4693           {
4694             format = new IdentifyFile().identify(file, sourceType);
4695           }
4696           if (FileFormat.ScoreMatrix == format)
4697           {
4698             ScoreMatrixFile sm = new ScoreMatrixFile(
4699                     new FileParse(file, sourceType));
4700             sm.parse();
4701             // todo: i18n this message
4702             statusBar.setText(MessageManager.formatMessage(
4703                     "label.successfully_loaded_matrix",
4704                     sm.getMatrixName()));
4705           }
4706           else if (FileFormat.Jnet.equals(format))
4707           {
4708             JPredFile predictions = new JPredFile(file, sourceType);
4709             new JnetAnnotationMaker();
4710             JnetAnnotationMaker.add_annotation(predictions,
4711                     viewport.getAlignment(), 0, false);
4712             viewport.getAlignment().setupJPredAlignment();
4713             isAnnotation = true;
4714           }
4715           // else if (IdentifyFile.FeaturesFile.equals(format))
4716           else if (FileFormat.Features.equals(format))
4717           {
4718             if (parseFeaturesFile(file, sourceType))
4719             {
4720               alignPanel.paintAlignment(true, true);
4721             }
4722           }
4723           else
4724           {
4725             new FileLoader().LoadFile(viewport, file, sourceType, format);
4726           }
4727         }
4728       }
4729       if (isAnnotation)
4730       {
4731
4732         alignPanel.adjustAnnotationHeight();
4733         viewport.updateSequenceIdColours();
4734         buildSortByAnnotationScoresMenu();
4735         alignPanel.paintAlignment(true, true);
4736       }
4737     } catch (Exception ex)
4738     {
4739       ex.printStackTrace();
4740     } catch (OutOfMemoryError oom)
4741     {
4742       try
4743       {
4744         System.gc();
4745       } catch (Exception x)
4746       {
4747       }
4748       new OOMWarning(
4749               "loading data "
4750                       + (sourceType != null
4751                               ? (sourceType == DataSourceType.PASTE
4752                                       ? "from clipboard."
4753                                       : "using " + sourceType + " from "
4754                                               + file)
4755                               : ".")
4756                       + (format != null
4757                               ? "(parsing as '" + format + "' file)"
4758                               : ""),
4759               oom, Desktop.desktop);
4760     }
4761   }
4762
4763   /**
4764    * Method invoked by the ChangeListener on the tabbed pane, in other words
4765    * when a different tabbed pane is selected by the user or programmatically.
4766    */
4767   @Override
4768   public void tabSelectionChanged(int index)
4769   {
4770     if (index > -1)
4771     {
4772       alignPanel = alignPanels.get(index);
4773       viewport = alignPanel.av;
4774       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4775       setMenusFromViewport(viewport);
4776     }
4777
4778     /*
4779      * 'focus' any colour slider that is open to the selected viewport
4780      */
4781     if (viewport.getConservationSelected())
4782     {
4783       SliderPanel.setConservationSlider(alignPanel,
4784               viewport.getResidueShading(), alignPanel.getViewName());
4785     }
4786     else
4787     {
4788       SliderPanel.hideConservationSlider();
4789     }
4790     if (viewport.getAbovePIDThreshold())
4791     {
4792       SliderPanel.setPIDSliderSource(alignPanel,
4793               viewport.getResidueShading(), alignPanel.getViewName());
4794     }
4795     else
4796     {
4797       SliderPanel.hidePIDSlider();
4798     }
4799
4800     /*
4801      * If there is a frame linked to this one in a SplitPane, switch it to the
4802      * same view tab index. No infinite recursion of calls should happen, since
4803      * tabSelectionChanged() should not get invoked on setting the selected
4804      * index to an unchanged value. Guard against setting an invalid index
4805      * before the new view peer tab has been created.
4806      */
4807     final AlignViewportI peer = viewport.getCodingComplement();
4808     if (peer != null)
4809     {
4810       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4811               .getAlignPanel().alignFrame;
4812       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4813       {
4814         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4815       }
4816     }
4817   }
4818
4819   /**
4820    * On right mouse click on view tab, prompt for and set new view name.
4821    */
4822   @Override
4823   public void tabbedPane_mousePressed(MouseEvent e)
4824   {
4825     if (e.isPopupTrigger())
4826     {
4827       String msg = MessageManager.getString("label.enter_view_name");
4828       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4829               JvOptionPane.QUESTION_MESSAGE);
4830
4831       if (reply != null)
4832       {
4833         viewport.viewName = reply;
4834         // TODO warn if reply is in getExistingViewNames()?
4835         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4836       }
4837     }
4838   }
4839
4840   public AlignViewport getCurrentView()
4841   {
4842     return viewport;
4843   }
4844
4845   /**
4846    * Open the dialog for regex description parsing.
4847    */
4848   @Override
4849   protected void extractScores_actionPerformed(ActionEvent e)
4850   {
4851     ParseProperties pp = new jalview.analysis.ParseProperties(
4852             viewport.getAlignment());
4853     // TODO: verify regex and introduce GUI dialog for version 2.5
4854     // if (pp.getScoresFromDescription("col", "score column ",
4855     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4856     // true)>0)
4857     if (pp.getScoresFromDescription("description column",
4858             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4859     {
4860       buildSortByAnnotationScoresMenu();
4861     }
4862   }
4863
4864   /*
4865    * (non-Javadoc)
4866    *
4867    * @see
4868    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4869    * )
4870    */
4871   @Override
4872   protected void showDbRefs_actionPerformed(ActionEvent e)
4873   {
4874     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4875   }
4876
4877   /*
4878    * (non-Javadoc)
4879    *
4880    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4881    * ActionEvent)
4882    */
4883   @Override
4884   protected void showNpFeats_actionPerformed(ActionEvent e)
4885   {
4886     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4887   }
4888
4889   /**
4890    * find the viewport amongst the tabs in this alignment frame and close that
4891    * tab
4892    *
4893    * @param av
4894    */
4895   public boolean closeView(AlignViewportI av)
4896   {
4897     if (viewport == av)
4898     {
4899       this.closeMenuItem_actionPerformed(false);
4900       return true;
4901     }
4902     Component[] comp = tabbedPane.getComponents();
4903     for (int i = 0; comp != null && i < comp.length; i++)
4904     {
4905       if (comp[i] instanceof AlignmentPanel)
4906       {
4907         if (((AlignmentPanel) comp[i]).av == av)
4908         {
4909           // close the view.
4910           closeView((AlignmentPanel) comp[i]);
4911           return true;
4912         }
4913       }
4914     }
4915     return false;
4916   }
4917
4918   protected void build_fetchdbmenu(JMenu webService)
4919   {
4920     // Temporary hack - DBRef Fetcher always top level ws entry.
4921     // TODO We probably want to store a sequence database checklist in
4922     // preferences and have checkboxes.. rather than individual sources selected
4923     // here
4924     final JMenu rfetch = new JMenu(
4925             MessageManager.getString("action.fetch_db_references"));
4926     rfetch.setToolTipText(MessageManager.getString(
4927             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4928     webService.add(rfetch);
4929
4930     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4931             MessageManager.getString("option.trim_retrieved_seqs"));
4932     trimrs.setToolTipText(
4933             MessageManager.getString("label.trim_retrieved_sequences"));
4934     trimrs.setSelected(
4935             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4936     trimrs.addActionListener(new ActionListener()
4937     {
4938       @Override
4939       public void actionPerformed(ActionEvent e)
4940       {
4941         trimrs.setSelected(trimrs.isSelected());
4942         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4943                 Boolean.valueOf(trimrs.isSelected()).toString());
4944       };
4945     });
4946     rfetch.add(trimrs);
4947     JMenuItem fetchr = new JMenuItem(
4948             MessageManager.getString("label.standard_databases"));
4949     fetchr.setToolTipText(
4950             MessageManager.getString("label.fetch_embl_uniprot"));
4951     fetchr.addActionListener(new ActionListener()
4952     {
4953
4954       @Override
4955       public void actionPerformed(ActionEvent e)
4956       {
4957         new Thread(new Runnable()
4958         {
4959           @Override
4960           public void run()
4961           {
4962             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4963                     .getAlignment().isNucleotide();
4964             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4965                     alignPanel.av.getSequenceSelection(),
4966                     alignPanel.alignFrame, null,
4967                     alignPanel.alignFrame.featureSettings, isNucleotide);
4968             dbRefFetcher.addListener(new FetchFinishedListenerI()
4969             {
4970               @Override
4971               public void finished()
4972               {
4973                 AlignFrame.this.setMenusForViewport();
4974               }
4975             });
4976             dbRefFetcher.fetchDBRefs(false);
4977           }
4978         }).start();
4979
4980       }
4981
4982     });
4983     rfetch.add(fetchr);
4984     final AlignFrame me = this;
4985     new Thread(new Runnable()
4986     {
4987       @Override
4988       public void run()
4989       {
4990         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4991                 .getSequenceFetcherSingleton(me);
4992         javax.swing.SwingUtilities.invokeLater(new Runnable()
4993         {
4994           @Override
4995           public void run()
4996           {
4997             String[] dbclasses = sf.getOrderedSupportedSources();
4998             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4999             // jalview.util.QuickSort.sort(otherdb, otherdb);
5000             List<DbSourceProxy> otherdb;
5001             JMenu dfetch = new JMenu();
5002             JMenu ifetch = new JMenu();
5003             JMenuItem fetchr = null;
5004             int comp = 0, icomp = 0, mcomp = 15;
5005             String mname = null;
5006             int dbi = 0;
5007             for (String dbclass : dbclasses)
5008             {
5009               otherdb = sf.getSourceProxy(dbclass);
5010               // add a single entry for this class, or submenu allowing 'fetch
5011               // all' or pick one
5012               if (otherdb == null || otherdb.size() < 1)
5013               {
5014                 continue;
5015               }
5016               // List<DbSourceProxy> dbs=otherdb;
5017               // otherdb=new ArrayList<DbSourceProxy>();
5018               // for (DbSourceProxy db:dbs)
5019               // {
5020               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5021               // }
5022               if (mname == null)
5023               {
5024                 mname = "From " + dbclass;
5025               }
5026               if (otherdb.size() == 1)
5027               {
5028                 final DbSourceProxy[] dassource = otherdb
5029                         .toArray(new DbSourceProxy[0]);
5030                 DbSourceProxy src = otherdb.get(0);
5031                 fetchr = new JMenuItem(src.getDbSource());
5032                 fetchr.addActionListener(new ActionListener()
5033                 {
5034
5035                   @Override
5036                   public void actionPerformed(ActionEvent e)
5037                   {
5038                     new Thread(new Runnable()
5039                     {
5040
5041                       @Override
5042                       public void run()
5043                       {
5044                         boolean isNucleotide = alignPanel.alignFrame
5045                                 .getViewport().getAlignment()
5046                                 .isNucleotide();
5047                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5048                                 alignPanel.av.getSequenceSelection(),
5049                                 alignPanel.alignFrame, dassource,
5050                                 alignPanel.alignFrame.featureSettings,
5051                                 isNucleotide);
5052                         dbRefFetcher
5053                                 .addListener(new FetchFinishedListenerI()
5054                                 {
5055                                   @Override
5056                                   public void finished()
5057                                   {
5058                                     AlignFrame.this.setMenusForViewport();
5059                                   }
5060                                 });
5061                         dbRefFetcher.fetchDBRefs(false);
5062                       }
5063                     }).start();
5064                   }
5065
5066                 });
5067                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5068                         MessageManager.formatMessage(
5069                                 "label.fetch_retrieve_from", new Object[]
5070                                 { src.getDbName() })));
5071                 dfetch.add(fetchr);
5072                 comp++;
5073               }
5074               else
5075               {
5076                 final DbSourceProxy[] dassource = otherdb
5077                         .toArray(new DbSourceProxy[0]);
5078                 // fetch all entry
5079                 DbSourceProxy src = otherdb.get(0);
5080                 fetchr = new JMenuItem(MessageManager
5081                         .formatMessage("label.fetch_all_param", new Object[]
5082                         { src.getDbSource() }));
5083                 fetchr.addActionListener(new ActionListener()
5084                 {
5085                   @Override
5086                   public void actionPerformed(ActionEvent e)
5087                   {
5088                     new Thread(new Runnable()
5089                     {
5090
5091                       @Override
5092                       public void run()
5093                       {
5094                         boolean isNucleotide = alignPanel.alignFrame
5095                                 .getViewport().getAlignment()
5096                                 .isNucleotide();
5097                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5098                                 alignPanel.av.getSequenceSelection(),
5099                                 alignPanel.alignFrame, dassource,
5100                                 alignPanel.alignFrame.featureSettings,
5101                                 isNucleotide);
5102                         dbRefFetcher
5103                                 .addListener(new FetchFinishedListenerI()
5104                                 {
5105                                   @Override
5106                                   public void finished()
5107                                   {
5108                                     AlignFrame.this.setMenusForViewport();
5109                                   }
5110                                 });
5111                         dbRefFetcher.fetchDBRefs(false);
5112                       }
5113                     }).start();
5114                   }
5115                 });
5116
5117                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5118                         MessageManager.formatMessage(
5119                                 "label.fetch_retrieve_from_all_sources",
5120                                 new Object[]
5121                                 { Integer.valueOf(otherdb.size())
5122                                         .toString(),
5123                                     src.getDbSource(), src.getDbName() })));
5124                 dfetch.add(fetchr);
5125                 comp++;
5126                 // and then build the rest of the individual menus
5127                 ifetch = new JMenu(MessageManager.formatMessage(
5128                         "label.source_from_db_source", new Object[]
5129                         { src.getDbSource() }));
5130                 icomp = 0;
5131                 String imname = null;
5132                 int i = 0;
5133                 for (DbSourceProxy sproxy : otherdb)
5134                 {
5135                   String dbname = sproxy.getDbName();
5136                   String sname = dbname.length() > 5
5137                           ? dbname.substring(0, 5) + "..."
5138                           : dbname;
5139                   String msname = dbname.length() > 10
5140                           ? dbname.substring(0, 10) + "..."
5141                           : dbname;
5142                   if (imname == null)
5143                   {
5144                     imname = MessageManager
5145                             .formatMessage("label.from_msname", new Object[]
5146                             { sname });
5147                   }
5148                   fetchr = new JMenuItem(msname);
5149                   final DbSourceProxy[] dassrc = { sproxy };
5150                   fetchr.addActionListener(new ActionListener()
5151                   {
5152
5153                     @Override
5154                     public void actionPerformed(ActionEvent e)
5155                     {
5156                       new Thread(new Runnable()
5157                       {
5158
5159                         @Override
5160                         public void run()
5161                         {
5162                           boolean isNucleotide = alignPanel.alignFrame
5163                                   .getViewport().getAlignment()
5164                                   .isNucleotide();
5165                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5166                                   alignPanel.av.getSequenceSelection(),
5167                                   alignPanel.alignFrame, dassrc,
5168                                   alignPanel.alignFrame.featureSettings,
5169                                   isNucleotide);
5170                           dbRefFetcher
5171                                   .addListener(new FetchFinishedListenerI()
5172                                   {
5173                                     @Override
5174                                     public void finished()
5175                                     {
5176                                       AlignFrame.this.setMenusForViewport();
5177                                     }
5178                                   });
5179                           dbRefFetcher.fetchDBRefs(false);
5180                         }
5181                       }).start();
5182                     }
5183
5184                   });
5185                   fetchr.setToolTipText(
5186                           "<html>" + MessageManager.formatMessage(
5187                                   "label.fetch_retrieve_from", new Object[]
5188                                   { dbname }));
5189                   ifetch.add(fetchr);
5190                   ++i;
5191                   if (++icomp >= mcomp || i == (otherdb.size()))
5192                   {
5193                     ifetch.setText(MessageManager.formatMessage(
5194                             "label.source_to_target", imname, sname));
5195                     dfetch.add(ifetch);
5196                     ifetch = new JMenu();
5197                     imname = null;
5198                     icomp = 0;
5199                     comp++;
5200                   }
5201                 }
5202               }
5203               ++dbi;
5204               if (comp >= mcomp || dbi >= (dbclasses.length))
5205               {
5206                 dfetch.setText(MessageManager.formatMessage(
5207                         "label.source_to_target", mname, dbclass));
5208                 rfetch.add(dfetch);
5209                 dfetch = new JMenu();
5210                 mname = null;
5211                 comp = 0;
5212               }
5213             }
5214           }
5215         });
5216       }
5217     }).start();
5218
5219   }
5220
5221   /**
5222    * Left justify the whole alignment.
5223    */
5224   @Override
5225   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5226   {
5227     AlignmentI al = viewport.getAlignment();
5228     al.justify(false);
5229     viewport.firePropertyChange("alignment", null, al);
5230   }
5231
5232   /**
5233    * Right justify the whole alignment.
5234    */
5235   @Override
5236   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5237   {
5238     AlignmentI al = viewport.getAlignment();
5239     al.justify(true);
5240     viewport.firePropertyChange("alignment", null, al);
5241   }
5242
5243   @Override
5244   public void setShowSeqFeatures(boolean b)
5245   {
5246     showSeqFeatures.setSelected(b);
5247     viewport.setShowSequenceFeatures(b);
5248   }
5249
5250   /*
5251    * (non-Javadoc)
5252    *
5253    * @see
5254    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5255    * awt.event.ActionEvent)
5256    */
5257   @Override
5258   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5259   {
5260     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5261     alignPanel.paintAlignment(false, false);
5262   }
5263
5264   /*
5265    * (non-Javadoc)
5266    *
5267    * @see
5268    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5269    * .ActionEvent)
5270    */
5271   @Override
5272   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5273   {
5274     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5275     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5276
5277   }
5278
5279   /*
5280    * (non-Javadoc)
5281    *
5282    * @see
5283    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5284    * .event.ActionEvent)
5285    */
5286   @Override
5287   protected void showGroupConservation_actionPerformed(ActionEvent e)
5288   {
5289     viewport.setShowGroupConservation(showGroupConservation.getState());
5290     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5291   }
5292
5293   /*
5294    * (non-Javadoc)
5295    *
5296    * @see
5297    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5298    * .event.ActionEvent)
5299    */
5300   @Override
5301   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5302   {
5303     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5304     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5305   }
5306
5307   /*
5308    * (non-Javadoc)
5309    *
5310    * @see
5311    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5312    * .event.ActionEvent)
5313    */
5314   @Override
5315   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5316   {
5317     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5318     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5319   }
5320
5321   @Override
5322   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5323   {
5324     showSequenceLogo.setState(true);
5325     viewport.setShowSequenceLogo(true);
5326     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5327     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5328   }
5329
5330   @Override
5331   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5332   {
5333     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5334   }
5335
5336   /*
5337    * (non-Javadoc)
5338    *
5339    * @see
5340    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5341    * .event.ActionEvent)
5342    */
5343   @Override
5344   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5345   {
5346     if (avc.makeGroupsFromSelection())
5347     {
5348       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5349       alignPanel.updateAnnotation();
5350       alignPanel.paintAlignment(true, true);
5351     }
5352   }
5353
5354   public void clearAlignmentSeqRep()
5355   {
5356     // TODO refactor alignmentseqrep to controller
5357     if (viewport.getAlignment().hasSeqrep())
5358     {
5359       viewport.getAlignment().setSeqrep(null);
5360       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5361       alignPanel.updateAnnotation();
5362       alignPanel.paintAlignment(true, true);
5363     }
5364   }
5365
5366   @Override
5367   protected void createGroup_actionPerformed(ActionEvent e)
5368   {
5369     if (avc.createGroup())
5370     {
5371       alignPanel.alignmentChanged();
5372     }
5373   }
5374
5375   @Override
5376   protected void unGroup_actionPerformed(ActionEvent e)
5377   {
5378     if (avc.unGroup())
5379     {
5380       alignPanel.alignmentChanged();
5381     }
5382   }
5383
5384   /**
5385    * make the given alignmentPanel the currently selected tab
5386    *
5387    * @param alignmentPanel
5388    */
5389   public void setDisplayedView(AlignmentPanel alignmentPanel)
5390   {
5391     if (!viewport.getSequenceSetId()
5392             .equals(alignmentPanel.av.getSequenceSetId()))
5393     {
5394       throw new Error(MessageManager.getString(
5395               "error.implementation_error_cannot_show_view_alignment_frame"));
5396     }
5397     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5398             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5399     {
5400       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5401     }
5402   }
5403
5404   /**
5405    * Action on selection of menu options to Show or Hide annotations.
5406    *
5407    * @param visible
5408    * @param forSequences
5409    *          update sequence-related annotations
5410    * @param forAlignment
5411    *          update non-sequence-related annotations
5412    */
5413   @Override
5414   protected void setAnnotationsVisibility(boolean visible,
5415           boolean forSequences, boolean forAlignment)
5416   {
5417     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5418             .getAlignmentAnnotation();
5419     if (anns == null)
5420     {
5421       return;
5422     }
5423     for (AlignmentAnnotation aa : anns)
5424     {
5425       /*
5426        * don't display non-positional annotations on an alignment
5427        */
5428       if (aa.annotations == null)
5429       {
5430         continue;
5431       }
5432       boolean apply = (aa.sequenceRef == null && forAlignment)
5433               || (aa.sequenceRef != null && forSequences);
5434       if (apply)
5435       {
5436         aa.visible = visible;
5437       }
5438     }
5439     alignPanel.validateAnnotationDimensions(true);
5440     alignPanel.alignmentChanged();
5441   }
5442
5443   /**
5444    * Store selected annotation sort order for the view and repaint.
5445    */
5446   @Override
5447   protected void sortAnnotations_actionPerformed()
5448   {
5449     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5450     this.alignPanel.av
5451             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5452     alignPanel.paintAlignment(false, false);
5453   }
5454
5455   /**
5456    *
5457    * @return alignment panels in this alignment frame
5458    */
5459   public List<? extends AlignmentViewPanel> getAlignPanels()
5460   {
5461     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5462   }
5463
5464   /**
5465    * Open a new alignment window, with the cDNA associated with this (protein)
5466    * alignment, aligned as is the protein.
5467    */
5468   protected void viewAsCdna_actionPerformed()
5469   {
5470     // TODO no longer a menu action - refactor as required
5471     final AlignmentI alignment = getViewport().getAlignment();
5472     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5473     if (mappings == null)
5474     {
5475       return;
5476     }
5477     List<SequenceI> cdnaSeqs = new ArrayList<>();
5478     for (SequenceI aaSeq : alignment.getSequences())
5479     {
5480       for (AlignedCodonFrame acf : mappings)
5481       {
5482         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5483         if (dnaSeq != null)
5484         {
5485           /*
5486            * There is a cDNA mapping for this protein sequence - add to new
5487            * alignment. It will share the same dataset sequence as other mapped
5488            * cDNA (no new mappings need to be created).
5489            */
5490           final Sequence newSeq = new Sequence(dnaSeq);
5491           newSeq.setDatasetSequence(dnaSeq);
5492           cdnaSeqs.add(newSeq);
5493         }
5494       }
5495     }
5496     if (cdnaSeqs.size() == 0)
5497     {
5498       // show a warning dialog no mapped cDNA
5499       return;
5500     }
5501     AlignmentI cdna = new Alignment(
5502             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5503     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5504             AlignFrame.DEFAULT_HEIGHT);
5505     cdna.alignAs(alignment);
5506     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5507             + this.title;
5508     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5509             AlignFrame.DEFAULT_HEIGHT);
5510   }
5511
5512   /**
5513    * Set visibility of dna/protein complement view (available when shown in a
5514    * split frame).
5515    *
5516    * @param show
5517    */
5518   @Override
5519   protected void showComplement_actionPerformed(boolean show)
5520   {
5521     SplitContainerI sf = getSplitViewContainer();
5522     if (sf != null)
5523     {
5524       sf.setComplementVisible(this, show);
5525     }
5526   }
5527
5528   /**
5529    * Generate the reverse (optionally complemented) of the selected sequences,
5530    * and add them to the alignment
5531    */
5532   @Override
5533   protected void showReverse_actionPerformed(boolean complement)
5534   {
5535     AlignmentI al = null;
5536     try
5537     {
5538       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5539       al = dna.reverseCdna(complement);
5540       viewport.addAlignment(al, "");
5541       addHistoryItem(new EditCommand(
5542               MessageManager.getString("label.add_sequences"), Action.PASTE,
5543               al.getSequencesArray(), 0, al.getWidth(),
5544               viewport.getAlignment()));
5545     } catch (Exception ex)
5546     {
5547       System.err.println(ex.getMessage());
5548       return;
5549     }
5550   }
5551
5552   /**
5553    * Try to run a script in the Groovy console, having first ensured that this
5554    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5555    * be targeted at this alignment.
5556    */
5557   @Override
5558   protected void runGroovy_actionPerformed()
5559   {
5560     Jalview.setCurrentAlignFrame(this);
5561     groovy.ui.Console console = Desktop.getGroovyConsole();
5562     if (console != null)
5563     {
5564       try
5565       {
5566         console.runScript();
5567       } catch (Exception ex)
5568       {
5569         System.err.println((ex.toString()));
5570         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5571                 MessageManager.getString("label.couldnt_run_groovy_script"),
5572                 MessageManager.getString("label.groovy_support_failed"),
5573                 JvOptionPane.ERROR_MESSAGE);
5574       }
5575     }
5576     else
5577     {
5578       System.err.println("Can't run Groovy script as console not found");
5579     }
5580   }
5581
5582   /**
5583    * Hides columns containing (or not containing) a specified feature, provided
5584    * that would not leave all columns hidden
5585    *
5586    * @param featureType
5587    * @param columnsContaining
5588    * @return
5589    */
5590   public boolean hideFeatureColumns(String featureType,
5591           boolean columnsContaining)
5592   {
5593     boolean notForHiding = avc.markColumnsContainingFeatures(
5594             columnsContaining, false, false, featureType);
5595     if (notForHiding)
5596     {
5597       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5598               false, featureType))
5599       {
5600         getViewport().hideSelectedColumns();
5601         return true;
5602       }
5603     }
5604     return false;
5605   }
5606
5607   @Override
5608   protected void selectHighlightedColumns_actionPerformed(
5609           ActionEvent actionEvent)
5610   {
5611     // include key modifier check in case user selects from menu
5612     avc.markHighlightedColumns(
5613             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5614             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5615                     | ActionEvent.CTRL_MASK)) != 0);
5616   }
5617
5618   /**
5619    * Rebuilds the Colour menu, including any user-defined colours which have
5620    * been loaded either on startup or during the session
5621    */
5622   public void buildColourMenu()
5623   {
5624     colourMenu.removeAll();
5625
5626     colourMenu.add(applyToAllGroups);
5627     colourMenu.add(textColour);
5628     colourMenu.addSeparator();
5629
5630     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5631             false);
5632
5633     colourMenu.addSeparator();
5634     colourMenu.add(conservationMenuItem);
5635     colourMenu.add(modifyConservation);
5636     colourMenu.add(abovePIDThreshold);
5637     colourMenu.add(modifyPID);
5638     colourMenu.add(annotationColour);
5639
5640     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5641     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5642   }
5643
5644   /**
5645    * Open a dialog (if not already open) that allows the user to select and
5646    * calculate PCA or Tree analysis
5647    */
5648   protected void openTreePcaDialog()
5649   {
5650     if (alignPanel.getCalculationDialog() == null)
5651     {
5652       new CalculationChooser(AlignFrame.this);
5653     }
5654   }
5655
5656   @Override
5657   protected void loadVcf_actionPerformed()
5658   {
5659     // TODO: JAL-3048 - No VCF support in JsJalview
5660     JalviewFileChooser chooser = new JalviewFileChooser(
5661             Cache.getProperty("LAST_DIRECTORY"));
5662     chooser.setFileView(new JalviewFileView());
5663     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5664     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5665
5666     int value = chooser.showOpenDialog(null);
5667
5668     if (value == JalviewFileChooser.APPROVE_OPTION)
5669     {
5670       String choice = chooser.getSelectedFile().getPath();
5671       Cache.setProperty("LAST_DIRECTORY", choice);
5672       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5673       new VCFLoader(choice).loadVCF(seqs, this);
5674     }
5675
5676   }
5677
5678 }
5679
5680 class PrintThread extends Thread
5681 {
5682   AlignmentPanel ap;
5683
5684   public PrintThread(AlignmentPanel ap)
5685   {
5686     this.ap = ap;
5687   }
5688
5689   static PageFormat pf;
5690
5691   @Override
5692   public void run()
5693   {
5694     PrinterJob printJob = PrinterJob.getPrinterJob();
5695
5696     if (pf != null)
5697     {
5698       printJob.setPrintable(ap, pf);
5699     }
5700     else
5701     {
5702       printJob.setPrintable(ap);
5703     }
5704
5705     if (printJob.printDialog())
5706     {
5707       try
5708       {
5709         printJob.print();
5710       } catch (Exception PrintException)
5711       {
5712         PrintException.printStackTrace();
5713       }
5714     }
5715   }
5716 }